Starting phenix.real_space_refine on Mon Jul 6 04:05:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7vne_32040/07_2026/7vne_32040.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vne_32040/07_2026/7vne_32040.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vne_32040/07_2026/7vne_32040.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vne_32040/07_2026/7vne_32040.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7vne_32040/07_2026/7vne_32040.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7vne_32040/07_2026/7vne_32040.cif" model { file = "/net/cci-nas-00/data/ceres_data/7vne_32040/07_2026/7vne_32040.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vne_32040/07_2026/7vne_32040.cif" } resolution = 3.5 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 4947 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 129 5.16 5 C 18224 2.51 5 N 4711 2.21 5 O 5651 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28715 Number of models: 1 Model: "" Number of chains: 31 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: 5 Chain: "W" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 887 Classifications: {'peptide': 116} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 110} Chain: "A" 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: 5 Chain: "U" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 887 Classifications: {'peptide': 116} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 110} Chain: "B" 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: 5 Chain: "V" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 887 Classifications: {'peptide': 116} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 110} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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: "X" 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: "Y" 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: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 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: 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: "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 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: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 5.87, per 1000 atoms: 0.20 Number of scatterers: 28715 At special positions: 0 Unit cell: (194.688, 176.436, 162.24, 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 129 16.00 O 5651 8.00 N 4711 7.00 C 18224 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " 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 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 C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS W 22 " - pdb=" SG CYS W 95 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS U 95 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.02 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS V 22 " - pdb=" SG CYS V 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=1, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " 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 J 2 " - " NAG J 3 " " 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 R 2 " - " NAG R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " NAG-ASN " NAG A1301 " - " ASN A 343 " " NAG A1302 " - " ASN A 61 " " NAG A1303 " - " ASN A 149 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 801 " " NAG B1301 " - " ASN B 343 " " NAG B1302 " - " ASN B 61 " " NAG B1303 " - " ASN B 149 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B 801 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 616 " " NAG C1301 " - " ASN C 343 " " NAG C1302 " - " ASN C 17 " " NAG C1303 " - " ASN C 61 " " NAG C1304 " - " ASN C 149 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C1074 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C 616 " " NAG D 1 " - " ASN C 282 " " NAG E 1 " - " ASN C1134 " " NAG F 1 " - " ASN C 717 " " NAG G 1 " - " ASN C 801 " " NAG H 1 " - " ASN C1098 " " NAG I 1 " - " ASN C 331 " " NAG J 1 " - " ASN A 165 " " NAG K 1 " - " ASN A 282 " " NAG L 1 " - " ASN A1074 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN A 709 " " NAG O 1 " - " ASN A 717 " " NAG P 1 " - " ASN A1098 " " NAG Q 1 " - " ASN A 331 " " NAG R 1 " - " ASN B 165 " " NAG S 1 " - " ASN B 234 " " NAG T 1 " - " ASN B 282 " " NAG X 1 " - " ASN B1074 " " NAG Y 1 " - " ASN B1134 " " NAG Z 1 " - " ASN B 709 " " NAG a 1 " - " ASN B 717 " " NAG b 1 " - " ASN B1098 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.56 Conformation dependent library (CDL) restraints added in 1.3 seconds 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6630 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 52 sheets defined 20.7% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.547A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 369 Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 751 Processing helix chain 'C' and resid 753 through 757 removed outlier: 3.513A pdb=" N GLY C 757 " --> pdb=" O LEU C 754 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.560A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 removed outlier: 3.959A 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) removed outlier: 3.647A pdb=" N TYR C 873 " --> pdb=" O MET C 869 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER C 875 " --> pdb=" O ALA C 871 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.835A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.731A pdb=" N MET C 902 " --> pdb=" O PHE C 898 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN C 907 " --> pdb=" O ALA C 903 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY C 908 " --> pdb=" O TYR C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.756A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.757A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 964 removed outlier: 3.771A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLN C 957 " --> pdb=" O ASN C 953 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN C 960 " --> pdb=" O ALA C 956 " (cutoff:3.500A) Processing helix chain 'C' and resid 965 through 968 removed outlier: 4.062A 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 976 through 984 removed outlier: 4.019A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.972A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA C1026 " --> pdb=" O ALA C1022 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.101A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'W' and resid 26 through 31 Processing helix chain 'W' and resid 101 through 105 removed outlier: 3.978A pdb=" N THR W 104 " --> pdb=" O SER W 101 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLY W 105 " --> pdb=" O GLY W 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 101 through 105' Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.536A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 removed outlier: 4.243A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 372 removed outlier: 3.826A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.090A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.572A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.621A 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 758 through 783 removed outlier: 3.592A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL A 772 " --> pdb=" O THR A 768 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.919A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 882 removed outlier: 3.562A pdb=" N SER A 875 " --> pdb=" O ALA A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.621A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.524A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.511A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.620A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 968 removed outlier: 3.708A pdb=" N SER A 968 " --> pdb=" O GLN A 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 965 through 968' Processing helix chain 'A' and resid 976 through 983 removed outlier: 3.851A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.511A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR A1006 " --> pdb=" O GLN A1002 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A1024 " --> pdb=" O ALA A1020 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA A1026 " --> pdb=" O ALA A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.071A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'U' and resid 60 through 64 removed outlier: 3.594A pdb=" N LYS U 64 " --> pdb=" O PRO U 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 125 removed outlier: 4.416A pdb=" N THR B 124 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN B 125 " --> pdb=" O ASN B 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 121 through 125' Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.525A pdb=" N THR B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 removed outlier: 4.332A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN B 343 " --> pdb=" O GLY B 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 338 through 343' Processing helix chain 'B' and resid 366 through 370 Processing helix chain 'B' and resid 405 through 410 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.573A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.816A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 768 removed outlier: 3.591A pdb=" N ARG B 765 " --> pdb=" O THR B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 783 removed outlier: 3.738A pdb=" N VAL B 772 " --> pdb=" O THR B 768 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLN B 774 " --> pdb=" O ILE B 770 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 822 Processing helix chain 'B' and resid 866 through 882 removed outlier: 3.603A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA B 879 " --> pdb=" O SER B 875 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.575A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.579A pdb=" N MET B 902 " --> pdb=" O PHE B 898 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.563A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.084A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR B 961 " --> pdb=" O GLN B 957 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN B 965 " --> pdb=" O THR B 961 " (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 985 through 1001 removed outlier: 4.180A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1004 through 1022 removed outlier: 3.554A pdb=" N ILE B1018 " --> pdb=" O ARG B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1024 through 1032 Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'V' and resid 27 through 31 removed outlier: 3.567A pdb=" N TYR V 30 " --> pdb=" O SER V 27 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP V 31 " --> pdb=" O SER V 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 27 through 31' Processing helix chain 'V' and resid 60 through 64 removed outlier: 4.024A pdb=" N LYS V 64 " --> pdb=" O PRO V 61 " (cutoff:3.500A) Processing helix chain 'V' and resid 86 through 90 removed outlier: 3.907A pdb=" N ASP V 89 " --> pdb=" O ARG V 86 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR V 90 " --> pdb=" O ALA V 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 86 through 90' Processing helix chain 'V' and resid 98 through 102 removed outlier: 3.533A pdb=" N SER V 101 " --> pdb=" O ASN V 98 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.514A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.051A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.149A pdb=" N PHE C 43 " --> pdb=" O ARG B 567 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 48 through 55 Processing sheet with id=AA5, first strand: chain 'C' and resid 115 through 116 removed outlier: 4.098A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 119 through 120 removed outlier: 3.675A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 195 through 197 removed outlier: 6.119A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 311 through 317 removed outlier: 6.931A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 358 through 359 removed outlier: 3.898A pdb=" N ARG C 509 " --> pdb=" O TRP C 436 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU C 513 " --> pdb=" O CYS C 432 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 538 through 543 removed outlier: 5.343A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N PHE C 565 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.563A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 701 through 704 removed outlier: 6.395A pdb=" N ALA C 701 " --> pdb=" O ILE A 788 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LYS A 790 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ASN C 703 " --> pdb=" O LYS A 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.952A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.952A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AB7, first strand: chain 'C' and resid 787 through 789 removed outlier: 6.093A pdb=" N ILE C 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'W' and resid 6 through 8 Processing sheet with id=AC1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.786A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 36 through 37 removed outlier: 6.474A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.908A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AC5, first strand: chain 'A' and resid 116 through 120 removed outlier: 3.720A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 9.521A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.846A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 378 through 380 removed outlier: 4.340A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TRP A 436 " --> pdb=" O ARG A 509 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ARG A 509 " --> pdb=" O TRP A 436 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 538 through 543 removed outlier: 3.650A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 653 through 655 removed outlier: 6.752A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.333A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'A' and resid 712 through 728 removed outlier: 6.995A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 712 through 728 removed outlier: 6.995A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.578A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'U' and resid 46 through 51 removed outlier: 6.682A pdb=" N TRP U 36 " --> pdb=" O ILE U 48 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N SER U 50 " --> pdb=" O MET U 34 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N MET U 34 " --> pdb=" O SER U 50 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'U' and resid 67 through 68 removed outlier: 3.573A pdb=" N THR U 68 " --> pdb=" O GLN U 81 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.013A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 36 through 37 removed outlier: 6.313A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.544A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AE3, first strand: chain 'B' and resid 225 through 229 removed outlier: 5.249A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 115 through 116 removed outlier: 3.540A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL B 127 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 115 through 116 removed outlier: 3.540A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AE7, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.965A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 378 through 380 removed outlier: 3.625A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.526A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 715 through 728 removed outlier: 6.135A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 715 through 728 removed outlier: 6.135A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.477A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 1076 through 1078 removed outlier: 3.535A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AF6, first strand: chain 'V' and resid 5 through 8 removed outlier: 3.508A pdb=" N VAL V 5 " --> pdb=" O ALA V 23 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N CYS V 22 " --> pdb=" O LEU V 78 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU V 78 " --> pdb=" O CYS V 22 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'V' and resid 91 through 92 removed outlier: 4.207A pdb=" N ALA V 91 " --> pdb=" O VAL V 114 " (cutoff:3.500A) 765 hydrogen bonds defined for protein. 2073 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.64 Time building geometry restraints manager: 3.26 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: 4642 1.31 - 1.44: 8083 1.44 - 1.57: 16464 1.57 - 1.70: 0 1.70 - 1.83: 168 Bond restraints: 29357 Sorted by residual: bond pdb=" C7 NAG D 1 " pdb=" N2 NAG D 1 " ideal model delta sigma weight residual 1.346 1.487 -0.141 2.00e-02 2.50e+03 4.95e+01 bond pdb=" C7 NAG L 2 " pdb=" N2 NAG L 2 " ideal model delta sigma weight residual 1.346 1.484 -0.138 2.00e-02 2.50e+03 4.73e+01 bond pdb=" C7 NAG X 2 " pdb=" N2 NAG X 2 " ideal model delta sigma weight residual 1.346 1.481 -0.135 2.00e-02 2.50e+03 4.54e+01 bond pdb=" C7 NAG T 1 " pdb=" N2 NAG T 1 " ideal model delta sigma weight residual 1.346 1.480 -0.134 2.00e-02 2.50e+03 4.50e+01 bond pdb=" C7 NAG C1307 " pdb=" N2 NAG C1307 " ideal model delta sigma weight residual 1.346 1.480 -0.134 2.00e-02 2.50e+03 4.49e+01 ... (remaining 29352 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 38498 2.25 - 4.50: 1179 4.50 - 6.74: 243 6.74 - 8.99: 16 8.99 - 11.24: 7 Bond angle restraints: 39943 Sorted by residual: angle pdb=" N GLN B 580 " pdb=" CA GLN B 580 " pdb=" C GLN B 580 " ideal model delta sigma weight residual 113.43 107.82 5.61 1.26e+00 6.30e-01 1.98e+01 angle pdb=" C PRO B 330 " pdb=" N ASN B 331 " pdb=" CA ASN B 331 " ideal model delta sigma weight residual 120.28 126.23 -5.95 1.44e+00 4.82e-01 1.71e+01 angle pdb=" N TYR C1067 " pdb=" CA TYR C1067 " pdb=" C TYR C1067 " ideal model delta sigma weight residual 109.59 115.74 -6.15 1.61e+00 3.86e-01 1.46e+01 angle pdb=" C8 NAG D 1 " pdb=" C7 NAG D 1 " pdb=" N2 NAG D 1 " ideal model delta sigma weight residual 115.06 126.30 -11.24 3.00e+00 1.11e-01 1.40e+01 angle pdb=" N TYR B1067 " pdb=" CA TYR B1067 " pdb=" C TYR B1067 " ideal model delta sigma weight residual 109.59 114.95 -5.36 1.61e+00 3.86e-01 1.11e+01 ... (remaining 39938 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 15306 17.99 - 35.97: 1276 35.97 - 53.96: 221 53.96 - 71.94: 31 71.94 - 89.93: 23 Dihedral angle restraints: 16857 sinusoidal: 6525 harmonic: 10332 Sorted by residual: dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -157.85 71.85 1 1.00e+01 1.00e-02 6.61e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -18.63 -67.37 1 1.00e+01 1.00e-02 5.91e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -20.72 -65.28 1 1.00e+01 1.00e-02 5.59e+01 ... (remaining 16854 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 4358 0.099 - 0.198: 309 0.198 - 0.298: 18 0.298 - 0.397: 5 0.397 - 0.496: 1 Chirality restraints: 4691 Sorted by residual: chirality pdb=" C1 NAG X 1 " pdb=" ND2 ASN B1074 " pdb=" C2 NAG X 1 " pdb=" O5 NAG X 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.15e+00 chirality pdb=" C2 NAG T 1 " pdb=" C1 NAG T 1 " pdb=" C3 NAG T 1 " pdb=" N2 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.12 -0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.18e+00 ... (remaining 4688 not shown) Planarity restraints: 5126 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C1067 " -0.041 2.00e-02 2.50e+03 3.16e-02 2.00e+01 pdb=" CG TYR C1067 " 0.077 2.00e-02 2.50e+03 pdb=" CD1 TYR C1067 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR C1067 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR C1067 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR C1067 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR C1067 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR C1067 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B1067 " -0.039 2.00e-02 2.50e+03 2.90e-02 1.68e+01 pdb=" CG TYR B1067 " 0.070 2.00e-02 2.50e+03 pdb=" CD1 TYR B1067 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR B1067 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR B1067 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B1067 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B1067 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR B1067 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 741 " 0.028 2.00e-02 2.50e+03 2.26e-02 1.02e+01 pdb=" CG TYR B 741 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TYR B 741 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR B 741 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 741 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 741 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR B 741 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 741 " 0.001 2.00e-02 2.50e+03 ... (remaining 5123 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 403 2.65 - 3.21: 26017 3.21 - 3.77: 40464 3.77 - 4.34: 57377 4.34 - 4.90: 93697 Nonbonded interactions: 217958 Sorted by model distance: nonbonded pdb=" OG SER B 673 " pdb=" OH TYR B 695 " model vdw 2.083 3.040 nonbonded pdb=" OE1 GLN B 134 " pdb=" OG SER B 161 " model vdw 2.118 3.040 nonbonded pdb=" O ARG C 214 " pdb=" OH TYR C 266 " model vdw 2.129 3.040 nonbonded pdb=" OG1 THR B 109 " pdb=" OD1 ASP B 111 " model vdw 2.178 3.040 nonbonded pdb=" O THR C 393 " pdb=" OG1 THR C 523 " model vdw 2.185 3.040 ... (remaining 217953 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' and resid 14 through 1306) selection = (chain 'C' and resid 14 through 1306) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' } ncs_group { reference = chain 'J' selection = chain 'R' } ncs_group { reference = chain 'U' selection = chain 'V' selection = chain 'W' } 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: 1.030 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: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 27.000 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.120 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 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 : 0.011 0.141 29449 Z= 0.538 Angle : 0.919 11.525 40192 Z= 0.422 Chirality : 0.055 0.496 4691 Planarity : 0.005 0.066 5083 Dihedral : 13.813 89.926 10155 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.01 % Favored : 89.99 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.70 (0.13), residues: 3516 helix: -2.21 (0.18), residues: 604 sheet: -0.52 (0.22), residues: 593 loop : -2.14 (0.12), residues: 2319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 454 TYR 0.077 0.002 TYR C1067 PHE 0.039 0.002 PHE A 906 TRP 0.048 0.003 TRP C 886 HIS 0.011 0.001 HIS B1058 Details of bonding type rmsd/Z covalent geometry : bond 0.01123 / 0.54 (29357) covalent geometry : angle 0.90081 / 0.42 (39943) SS BOND : bond 0.00366 / 0.23 ( 24) SS BOND : angle 1.81979 / 1.34 ( 48) hydrogen bonds : bond 0.29177 / 19.10 ( 742) hydrogen bonds : angle 10.76400 / 7.38 ( 2073) Misc. bond : bond 0.00004 / 0.00 ( 1) link_BETA1-4 : bond 0.00523 / 0.32 ( 24) link_BETA1-4 : angle 2.35426 / 1.50 ( 72) link_NAG-ASN : bond 0.00701 / 0.48 ( 43) link_NAG-ASN : angle 2.77819 / 2.05 ( 129) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 106 PHE cc_start: 0.6849 (m-80) cc_final: 0.6562 (m-80) REVERT: B 902 MET cc_start: 0.8478 (mmm) cc_final: 0.8218 (mmt) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.1686 time to fit residues: 57.2236 Evaluate side-chains 175 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 30.0000 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 9.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 856 ASN C 955 ASN C 965 GLN C1005 GLN A 81 ASN B 474 GLN B 655 HIS B1048 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.199298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.149440 restraints weight = 43223.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.137355 restraints weight = 54495.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.133571 restraints weight = 41558.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.133067 restraints weight = 39858.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.133992 restraints weight = 30589.398| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 29449 Z= 0.171 Angle : 0.729 14.356 40192 Z= 0.349 Chirality : 0.052 0.450 4691 Planarity : 0.004 0.050 5083 Dihedral : 5.406 35.981 3825 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 0.42 % Allowed : 5.14 % Favored : 94.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.35 (0.14), residues: 3516 helix: -1.18 (0.19), residues: 639 sheet: -0.42 (0.21), residues: 667 loop : -2.15 (0.13), residues: 2210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1019 TYR 0.034 0.002 TYR C1067 PHE 0.027 0.002 PHE A 238 TRP 0.019 0.001 TRP W 47 HIS 0.006 0.001 HIS A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 (29357) covalent geometry : angle 0.70760 / 0.34 (39943) SS BOND : bond 0.00263 / 0.18 ( 24) SS BOND : angle 1.09223 / 0.80 ( 48) hydrogen bonds : bond 0.05921 / 3.85 ( 742) hydrogen bonds : angle 6.85362 / 4.63 ( 2073) Misc. bond : bond 0.00039 / 0.02 ( 1) link_BETA1-4 : bond 0.00914 / 0.58 ( 24) link_BETA1-4 : angle 2.63935 / 1.72 ( 72) link_NAG-ASN : bond 0.00742 / 0.47 ( 43) link_NAG-ASN : angle 2.52843 / 1.88 ( 129) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 195 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: W 47 TRP cc_start: 0.5327 (p-90) cc_final: 0.4508 (p-90) REVERT: A 957 GLN cc_start: 0.8651 (tm-30) cc_final: 0.8259 (tt0) REVERT: B 106 PHE cc_start: 0.7491 (m-80) cc_final: 0.7016 (m-80) REVERT: B 544 ASN cc_start: 0.7901 (m110) cc_final: 0.6346 (p0) REVERT: B 990 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7872 (tp30) outliers start: 13 outliers final: 6 residues processed: 202 average time/residue: 0.1598 time to fit residues: 53.7052 Evaluate side-chains 180 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 173 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain U residue 47 TRP Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 990 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 132 optimal weight: 20.0000 chunk 300 optimal weight: 0.6980 chunk 43 optimal weight: 40.0000 chunk 189 optimal weight: 2.9990 chunk 262 optimal weight: 4.9990 chunk 309 optimal weight: 2.9990 chunk 35 optimal weight: 40.0000 chunk 326 optimal weight: 0.9990 chunk 217 optimal weight: 5.9990 chunk 180 optimal weight: 1.9990 chunk 292 optimal weight: 7.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 69 HIS C 762 GLN C 965 GLN A 81 ASN B 134 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.200003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.153328 restraints weight = 43058.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.139517 restraints weight = 58833.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.136929 restraints weight = 50094.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.136350 restraints weight = 39968.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.136814 restraints weight = 35280.676| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 29449 Z= 0.149 Angle : 0.678 14.304 40192 Z= 0.320 Chirality : 0.051 0.453 4691 Planarity : 0.004 0.047 5083 Dihedral : 5.175 34.677 3825 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 0.81 % Allowed : 8.85 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.13 (0.14), residues: 3516 helix: -0.58 (0.20), residues: 631 sheet: -0.45 (0.21), residues: 651 loop : -2.08 (0.13), residues: 2234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1019 TYR 0.026 0.001 TYR C1067 PHE 0.022 0.001 PHE A 238 TRP 0.013 0.001 TRP A 258 HIS 0.006 0.001 HIS A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (29357) covalent geometry : angle 0.65577 / 0.32 (39943) SS BOND : bond 0.00232 / 0.16 ( 24) SS BOND : angle 0.87887 / 0.63 ( 48) hydrogen bonds : bond 0.04615 / 2.98 ( 742) hydrogen bonds : angle 6.09828 / 4.10 ( 2073) Misc. bond : bond 0.00016 / 0.01 ( 1) link_BETA1-4 : bond 0.00796 / 0.49 ( 24) link_BETA1-4 : angle 2.48139 / 1.60 ( 72) link_NAG-ASN : bond 0.00727 / 0.44 ( 43) link_NAG-ASN : angle 2.48939 / 1.82 ( 129) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 192 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 191 GLU cc_start: 0.5372 (tt0) cc_final: 0.4797 (tt0) REVERT: C 226 LEU cc_start: 0.8021 (mp) cc_final: 0.7797 (mt) REVERT: C 878 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8879 (tt) REVERT: C 1067 TYR cc_start: 0.5943 (OUTLIER) cc_final: 0.5734 (m-10) REVERT: A 957 GLN cc_start: 0.8596 (tm-30) cc_final: 0.8317 (tt0) REVERT: B 106 PHE cc_start: 0.7493 (m-80) cc_final: 0.6938 (m-80) REVERT: B 544 ASN cc_start: 0.7863 (m110) cc_final: 0.6407 (p0) REVERT: B 990 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7877 (tp30) outliers start: 25 outliers final: 11 residues processed: 211 average time/residue: 0.1582 time to fit residues: 55.8476 Evaluate side-chains 193 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 179 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1067 TYR Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 990 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 148 optimal weight: 3.9990 chunk 182 optimal weight: 4.9990 chunk 192 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 339 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 311 optimal weight: 0.0970 chunk 229 optimal weight: 7.9990 chunk 151 optimal weight: 0.0010 chunk 68 optimal weight: 8.9990 chunk 176 optimal weight: 0.0980 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN A 196 ASN B 134 GLN B 658 ASN B 895 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.201111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.155218 restraints weight = 43274.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.138575 restraints weight = 61801.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.136621 restraints weight = 47382.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.135996 restraints weight = 39294.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.136553 restraints weight = 32659.093| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29449 Z= 0.108 Angle : 0.634 13.556 40192 Z= 0.298 Chirality : 0.050 0.443 4691 Planarity : 0.004 0.049 5083 Dihedral : 4.934 33.737 3825 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 0.87 % Allowed : 10.82 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: -1.95 (0.14), residues: 3516 helix: -0.23 (0.21), residues: 638 sheet: -0.42 (0.21), residues: 643 loop : -2.00 (0.13), residues: 2235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1019 TYR 0.018 0.001 TYR C1067 PHE 0.026 0.001 PHE A 238 TRP 0.016 0.001 TRP W 47 HIS 0.004 0.000 HIS A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (29357) covalent geometry : angle 0.61233 / 0.29 (39943) SS BOND : bond 0.00196 / 0.14 ( 24) SS BOND : angle 0.67052 / 0.47 ( 48) hydrogen bonds : bond 0.03773 / 2.42 ( 742) hydrogen bonds : angle 5.73399 / 3.85 ( 2073) Misc. bond : bond 0.00008 / 0.00 ( 1) link_BETA1-4 : bond 0.00761 / 0.48 ( 24) link_BETA1-4 : angle 2.43281 / 1.56 ( 72) link_NAG-ASN : bond 0.00603 / 0.39 ( 43) link_NAG-ASN : angle 2.39934 / 1.85 ( 129) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 203 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 191 GLU cc_start: 0.5082 (tt0) cc_final: 0.4827 (tt0) REVERT: C 226 LEU cc_start: 0.7839 (mp) cc_final: 0.7625 (mt) REVERT: C 878 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8822 (tt) REVERT: C 1067 TYR cc_start: 0.5986 (OUTLIER) cc_final: 0.5683 (m-10) REVERT: W 47 TRP cc_start: 0.5330 (p-90) cc_final: 0.4400 (p-90) REVERT: A 237 ARG cc_start: 0.7442 (mtm180) cc_final: 0.7126 (ptt-90) REVERT: A 957 GLN cc_start: 0.8549 (tm-30) cc_final: 0.8246 (tt0) REVERT: A 1002 GLN cc_start: 0.8697 (tm-30) cc_final: 0.8172 (tm-30) REVERT: B 106 PHE cc_start: 0.7500 (m-80) cc_final: 0.6942 (m-80) REVERT: B 544 ASN cc_start: 0.7993 (m110) cc_final: 0.6460 (p0) REVERT: B 741 TYR cc_start: 0.6259 (OUTLIER) cc_final: 0.5780 (m-80) REVERT: B 990 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7858 (tp30) outliers start: 27 outliers final: 10 residues processed: 220 average time/residue: 0.1594 time to fit residues: 59.1686 Evaluate side-chains 199 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 185 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1067 TYR Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 741 TYR Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 990 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 248 optimal weight: 0.7980 chunk 183 optimal weight: 6.9990 chunk 180 optimal weight: 0.5980 chunk 320 optimal weight: 2.9990 chunk 168 optimal weight: 8.9990 chunk 67 optimal weight: 0.5980 chunk 88 optimal weight: 0.0170 chunk 118 optimal weight: 50.0000 chunk 178 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 148 optimal weight: 5.9990 overall best weight: 1.0020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN A 81 ASN A 115 GLN B 134 GLN B 207 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.200845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.154906 restraints weight = 43294.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.139604 restraints weight = 61647.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.137189 restraints weight = 48545.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.136505 restraints weight = 39443.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.136869 restraints weight = 35066.158| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29449 Z= 0.113 Angle : 0.629 12.817 40192 Z= 0.295 Chirality : 0.050 0.468 4691 Planarity : 0.004 0.050 5083 Dihedral : 4.818 32.968 3825 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 1.16 % Allowed : 11.56 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: -1.82 (0.14), residues: 3516 helix: -0.01 (0.21), residues: 637 sheet: -0.22 (0.21), residues: 617 loop : -1.97 (0.13), residues: 2262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 995 TYR 0.025 0.001 TYR C 695 PHE 0.033 0.001 PHE A 238 TRP 0.011 0.001 TRP W 47 HIS 0.005 0.001 HIS A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.11 (29357) covalent geometry : angle 0.60880 / 0.29 (39943) SS BOND : bond 0.00192 / 0.14 ( 24) SS BOND : angle 0.65483 / 0.46 ( 48) hydrogen bonds : bond 0.03657 / 2.34 ( 742) hydrogen bonds : angle 5.52510 / 3.71 ( 2073) Misc. bond : bond 0.00012 / 0.01 ( 1) link_BETA1-4 : bond 0.00692 / 0.43 ( 24) link_BETA1-4 : angle 2.37218 / 1.53 ( 72) link_NAG-ASN : bond 0.00622 / 0.39 ( 43) link_NAG-ASN : angle 2.31818 / 1.77 ( 129) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 197 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 226 LEU cc_start: 0.7859 (mp) cc_final: 0.7646 (mt) REVERT: C 878 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8797 (tt) REVERT: C 1067 TYR cc_start: 0.6250 (OUTLIER) cc_final: 0.5907 (m-80) REVERT: A 81 ASN cc_start: 0.7968 (OUTLIER) cc_final: 0.7730 (p0) REVERT: A 957 GLN cc_start: 0.8535 (tm-30) cc_final: 0.8216 (tt0) REVERT: A 1002 GLN cc_start: 0.8680 (tm-30) cc_final: 0.8150 (tm-30) REVERT: B 106 PHE cc_start: 0.7533 (m-80) cc_final: 0.6991 (m-80) REVERT: B 544 ASN cc_start: 0.7960 (m110) cc_final: 0.6494 (p0) REVERT: B 741 TYR cc_start: 0.6192 (OUTLIER) cc_final: 0.5628 (m-80) REVERT: B 990 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7811 (tp30) outliers start: 36 outliers final: 17 residues processed: 220 average time/residue: 0.1525 time to fit residues: 56.7548 Evaluate side-chains 213 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 191 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1067 TYR Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 741 TYR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1050 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 10 optimal weight: 30.0000 chunk 109 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 350 optimal weight: 8.9990 chunk 91 optimal weight: 4.9990 chunk 295 optimal weight: 7.9990 chunk 211 optimal weight: 0.8980 chunk 289 optimal weight: 5.9990 chunk 231 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 349 optimal weight: 8.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 762 GLN A 196 ASN A 955 ASN A1054 GLN B 134 GLN B 207 HIS B 474 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.198234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.151114 restraints weight = 42873.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.137679 restraints weight = 65159.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.135395 restraints weight = 48280.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.134057 restraints weight = 39354.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.134397 restraints weight = 35061.659| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 29449 Z= 0.172 Angle : 0.667 13.052 40192 Z= 0.314 Chirality : 0.051 0.480 4691 Planarity : 0.004 0.050 5083 Dihedral : 4.944 34.143 3825 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 1.42 % Allowed : 12.27 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.89 (0.14), residues: 3516 helix: -0.09 (0.21), residues: 630 sheet: -0.31 (0.21), residues: 624 loop : -1.99 (0.13), residues: 2262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG W 38 TYR 0.029 0.001 TYR B 741 PHE 0.030 0.001 PHE A 238 TRP 0.029 0.001 TRP W 47 HIS 0.006 0.001 HIS B1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.17 (29357) covalent geometry : angle 0.64561 / 0.31 (39943) SS BOND : bond 0.00308 / 0.21 ( 24) SS BOND : angle 1.27364 / 1.00 ( 48) hydrogen bonds : bond 0.04187 / 2.67 ( 742) hydrogen bonds : angle 5.56953 / 3.75 ( 2073) Misc. bond : bond 0.00015 / 0.01 ( 1) link_BETA1-4 : bond 0.00665 / 0.41 ( 24) link_BETA1-4 : angle 2.40814 / 1.56 ( 72) link_NAG-ASN : bond 0.00600 / 0.37 ( 43) link_NAG-ASN : angle 2.38759 / 1.81 ( 129) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 178 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 878 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8869 (tt) REVERT: W 47 TRP cc_start: 0.5445 (p-90) cc_final: 0.4345 (p-90) REVERT: A 81 ASN cc_start: 0.8127 (p0) cc_final: 0.7618 (p0) REVERT: A 237 ARG cc_start: 0.7394 (mtm180) cc_final: 0.7108 (ptt-90) REVERT: A 957 GLN cc_start: 0.8547 (tm-30) cc_final: 0.8236 (tt0) REVERT: B 106 PHE cc_start: 0.7500 (m-80) cc_final: 0.6919 (m-80) REVERT: B 544 ASN cc_start: 0.7979 (m110) cc_final: 0.6529 (p0) REVERT: B 741 TYR cc_start: 0.6720 (OUTLIER) cc_final: 0.5900 (m-80) REVERT: B 858 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8169 (mt) REVERT: B 990 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7676 (tp30) outliers start: 44 outliers final: 27 residues processed: 211 average time/residue: 0.1438 time to fit residues: 51.4697 Evaluate side-chains 206 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 175 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1067 TYR Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 37 TYR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 741 TYR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1050 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 149 optimal weight: 6.9990 chunk 214 optimal weight: 0.9990 chunk 166 optimal weight: 50.0000 chunk 258 optimal weight: 8.9990 chunk 136 optimal weight: 0.0370 chunk 29 optimal weight: 6.9990 chunk 284 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 122 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 overall best weight: 4.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 907 ASN A 354 ASN B 134 GLN B 207 HIS ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.197469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.150200 restraints weight = 42613.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.135186 restraints weight = 64950.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.132213 restraints weight = 48027.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.131316 restraints weight = 36312.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.131594 restraints weight = 32937.293| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 29449 Z= 0.232 Angle : 0.735 13.380 40192 Z= 0.349 Chirality : 0.053 0.487 4691 Planarity : 0.004 0.054 5083 Dihedral : 5.276 35.437 3825 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 1.81 % Allowed : 12.98 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 3516 helix: -0.44 (0.21), residues: 628 sheet: -0.39 (0.21), residues: 651 loop : -2.06 (0.13), residues: 2237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG W 38 TYR 0.043 0.002 TYR B1067 PHE 0.024 0.002 PHE A 238 TRP 0.028 0.002 TRP W 47 HIS 0.014 0.002 HIS C 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00564 / 0.23 (29357) covalent geometry : angle 0.71303 / 0.34 (39943) SS BOND : bond 0.00311 / 0.21 ( 24) SS BOND : angle 1.23010 / 0.92 ( 48) hydrogen bonds : bond 0.04838 / 3.10 ( 742) hydrogen bonds : angle 5.80086 / 3.92 ( 2073) Misc. bond : bond 0.00017 / 0.01 ( 1) link_BETA1-4 : bond 0.00676 / 0.41 ( 24) link_BETA1-4 : angle 2.57084 / 1.66 ( 72) link_NAG-ASN : bond 0.00622 / 0.38 ( 43) link_NAG-ASN : angle 2.55771 / 1.91 ( 129) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 179 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 191 GLU cc_start: 0.5746 (tt0) cc_final: 0.5462 (tt0) REVERT: C 392 PHE cc_start: 0.5096 (m-80) cc_final: 0.4872 (m-80) REVERT: C 878 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8916 (tt) REVERT: A 453 TYR cc_start: 0.1282 (OUTLIER) cc_final: 0.0368 (m-80) REVERT: A 957 GLN cc_start: 0.8586 (tm-30) cc_final: 0.8268 (tt0) REVERT: A 1036 GLN cc_start: 0.9276 (OUTLIER) cc_final: 0.8423 (tt0) REVERT: B 544 ASN cc_start: 0.7804 (m110) cc_final: 0.6265 (p0) REVERT: B 858 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8338 (mt) REVERT: B 990 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7725 (tp30) REVERT: B 1002 GLN cc_start: 0.8297 (tm-30) cc_final: 0.8060 (tm-30) outliers start: 56 outliers final: 35 residues processed: 222 average time/residue: 0.1481 time to fit residues: 56.0159 Evaluate side-chains 210 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 170 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 280 ASN Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1067 TYR Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1036 GLN Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 37 TYR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 741 TYR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1067 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 252 optimal weight: 4.9990 chunk 4 optimal weight: 0.0670 chunk 83 optimal weight: 1.9990 chunk 298 optimal weight: 0.0570 chunk 312 optimal weight: 1.9990 chunk 166 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 318 optimal weight: 0.8980 chunk 35 optimal weight: 40.0000 chunk 117 optimal weight: 50.0000 chunk 227 optimal weight: 7.9990 overall best weight: 1.0040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 66 HIS C 955 ASN A 493 GLN B 134 GLN ** B 414 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 = 0.4310 r_free = 0.4310 target = 0.200781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.151481 restraints weight = 42847.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.138387 restraints weight = 57916.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.135747 restraints weight = 43200.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.134571 restraints weight = 37981.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.135051 restraints weight = 32166.679| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 29449 Z= 0.119 Angle : 0.648 12.910 40192 Z= 0.306 Chirality : 0.050 0.462 4691 Planarity : 0.004 0.054 5083 Dihedral : 4.955 32.994 3825 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 1.45 % Allowed : 13.70 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.85 (0.14), residues: 3516 helix: -0.01 (0.21), residues: 622 sheet: -0.38 (0.21), residues: 656 loop : -1.96 (0.13), residues: 2238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG W 38 TYR 0.025 0.001 TYR C 695 PHE 0.034 0.001 PHE A 238 TRP 0.034 0.001 TRP W 47 HIS 0.004 0.000 HIS A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (29357) covalent geometry : angle 0.62656 / 0.30 (39943) SS BOND : bond 0.00208 / 0.15 ( 24) SS BOND : angle 0.76424 / 0.55 ( 48) hydrogen bonds : bond 0.03707 / 2.35 ( 742) hydrogen bonds : angle 5.41401 / 3.64 ( 2073) Misc. bond : bond 0.00008 / 0.00 ( 1) link_BETA1-4 : bond 0.00683 / 0.42 ( 24) link_BETA1-4 : angle 2.41514 / 1.56 ( 72) link_NAG-ASN : bond 0.00615 / 0.38 ( 43) link_NAG-ASN : angle 2.37661 / 1.79 ( 129) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 184 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 191 GLU cc_start: 0.5677 (tt0) cc_final: 0.5424 (tt0) REVERT: C 226 LEU cc_start: 0.8138 (mt) cc_final: 0.7870 (mt) REVERT: C 878 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8911 (tt) REVERT: A 118 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7745 (tp) REVERT: A 453 TYR cc_start: 0.1123 (OUTLIER) cc_final: 0.0154 (m-80) REVERT: A 957 GLN cc_start: 0.8565 (tm-30) cc_final: 0.8253 (tt0) REVERT: A 1002 GLN cc_start: 0.8644 (tm-30) cc_final: 0.8055 (tm-30) REVERT: A 1036 GLN cc_start: 0.9087 (OUTLIER) cc_final: 0.8078 (tt0) REVERT: B 544 ASN cc_start: 0.7684 (m110) cc_final: 0.6258 (p0) REVERT: B 741 TYR cc_start: 0.7188 (OUTLIER) cc_final: 0.5838 (m-80) REVERT: B 858 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8182 (mt) REVERT: B 990 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7663 (tp30) outliers start: 45 outliers final: 30 residues processed: 218 average time/residue: 0.1543 time to fit residues: 56.5959 Evaluate side-chains 210 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 173 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1067 TYR Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1036 GLN Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 37 TYR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 741 TYR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1067 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 94 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 323 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 159 optimal weight: 8.9990 chunk 319 optimal weight: 4.9990 chunk 138 optimal weight: 0.0370 chunk 283 optimal weight: 7.9990 chunk 238 optimal weight: 0.7980 chunk 145 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 overall best weight: 1.1062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 955 ASN B 134 GLN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.199112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.152875 restraints weight = 43163.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.136146 restraints weight = 61569.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.133112 restraints weight = 48562.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.133681 restraints weight = 40154.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.133970 restraints weight = 30534.451| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29449 Z= 0.116 Angle : 0.639 12.801 40192 Z= 0.300 Chirality : 0.050 0.456 4691 Planarity : 0.004 0.054 5083 Dihedral : 4.816 32.834 3825 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 1.42 % Allowed : 13.92 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.75 (0.14), residues: 3516 helix: 0.26 (0.21), residues: 616 sheet: -0.37 (0.21), residues: 658 loop : -1.94 (0.13), residues: 2242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 237 TYR 0.027 0.001 TYR C 695 PHE 0.041 0.001 PHE A 238 TRP 0.037 0.001 TRP W 47 HIS 0.004 0.001 HIS A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (29357) covalent geometry : angle 0.61829 / 0.30 (39943) SS BOND : bond 0.00215 / 0.15 ( 24) SS BOND : angle 0.76218 / 0.56 ( 48) hydrogen bonds : bond 0.03552 / 2.25 ( 742) hydrogen bonds : angle 5.26577 / 3.54 ( 2073) Misc. bond : bond 0.00011 / 0.01 ( 1) link_BETA1-4 : bond 0.00674 / 0.42 ( 24) link_BETA1-4 : angle 2.38288 / 1.53 ( 72) link_NAG-ASN : bond 0.00595 / 0.36 ( 43) link_NAG-ASN : angle 2.29926 / 1.74 ( 129) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 180 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 191 GLU cc_start: 0.5405 (tt0) cc_final: 0.5166 (tt0) REVERT: C 226 LEU cc_start: 0.8179 (mt) cc_final: 0.7918 (mt) REVERT: C 878 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8812 (tt) REVERT: A 118 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7489 (tp) REVERT: A 453 TYR cc_start: 0.1107 (OUTLIER) cc_final: 0.0122 (m-80) REVERT: A 957 GLN cc_start: 0.8536 (tm-30) cc_final: 0.8219 (tt0) REVERT: A 1002 GLN cc_start: 0.8641 (tm-30) cc_final: 0.8044 (tm-30) REVERT: A 1036 GLN cc_start: 0.9064 (OUTLIER) cc_final: 0.8096 (tt0) REVERT: B 544 ASN cc_start: 0.7886 (m110) cc_final: 0.6472 (p0) REVERT: B 741 TYR cc_start: 0.6914 (OUTLIER) cc_final: 0.5801 (m-80) REVERT: B 954 GLN cc_start: 0.7251 (mt0) cc_final: 0.6956 (mt0) REVERT: B 990 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7656 (tp30) outliers start: 44 outliers final: 31 residues processed: 212 average time/residue: 0.1484 time to fit residues: 53.7716 Evaluate side-chains 210 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 173 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1067 TYR Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1036 GLN Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 37 TYR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 741 TYR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1067 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 3 optimal weight: 0.7980 chunk 143 optimal weight: 6.9990 chunk 248 optimal weight: 8.9990 chunk 208 optimal weight: 9.9990 chunk 303 optimal weight: 5.9990 chunk 262 optimal weight: 4.9990 chunk 204 optimal weight: 1.9990 chunk 352 optimal weight: 7.9990 chunk 33 optimal weight: 30.0000 chunk 299 optimal weight: 4.9990 chunk 174 optimal weight: 4.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 134 GLN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.196941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.148270 restraints weight = 42595.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.134842 restraints weight = 51048.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.129970 restraints weight = 42241.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.129367 restraints weight = 38377.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.129382 restraints weight = 34366.275| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 29449 Z= 0.209 Angle : 0.711 13.081 40192 Z= 0.338 Chirality : 0.052 0.480 4691 Planarity : 0.004 0.055 5083 Dihedral : 5.112 34.230 3825 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 1.42 % Allowed : 14.28 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.93 (0.14), residues: 3516 helix: -0.10 (0.21), residues: 618 sheet: -0.28 (0.21), residues: 622 loop : -2.04 (0.13), residues: 2276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 237 TYR 0.040 0.002 TYR B 741 PHE 0.045 0.002 PHE A 238 TRP 0.043 0.002 TRP W 47 HIS 0.015 0.001 HIS B 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.21 (29357) covalent geometry : angle 0.69049 / 0.33 (39943) SS BOND : bond 0.00273 / 0.19 ( 24) SS BOND : angle 0.99110 / 0.72 ( 48) hydrogen bonds : bond 0.04497 / 2.87 ( 742) hydrogen bonds : angle 5.55738 / 3.74 ( 2073) Misc. bond : bond 0.00016 / 0.01 ( 1) link_BETA1-4 : bond 0.00635 / 0.39 ( 24) link_BETA1-4 : angle 2.50741 / 1.62 ( 72) link_NAG-ASN : bond 0.00581 / 0.35 ( 43) link_NAG-ASN : angle 2.46741 / 1.86 ( 129) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 170 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 191 GLU cc_start: 0.5511 (tt0) cc_final: 0.5245 (tt0) REVERT: C 226 LEU cc_start: 0.8209 (mt) cc_final: 0.7988 (mt) REVERT: C 878 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8915 (tt) REVERT: A 453 TYR cc_start: 0.1088 (OUTLIER) cc_final: 0.0106 (m-80) REVERT: A 957 GLN cc_start: 0.8557 (tm-30) cc_final: 0.8274 (tt0) REVERT: A 1036 GLN cc_start: 0.9252 (OUTLIER) cc_final: 0.8395 (tt0) REVERT: B 544 ASN cc_start: 0.7811 (m110) cc_final: 0.6274 (p0) REVERT: B 858 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8274 (mt) REVERT: B 954 GLN cc_start: 0.7391 (mt0) cc_final: 0.7099 (mt0) REVERT: B 990 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7692 (tp30) REVERT: B 1002 GLN cc_start: 0.8314 (tm-30) cc_final: 0.8062 (tm-30) outliers start: 44 outliers final: 33 residues processed: 202 average time/residue: 0.1461 time to fit residues: 50.8994 Evaluate side-chains 204 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 166 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1067 TYR Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1036 GLN Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 37 TYR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 741 TYR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain V residue 37 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 163 optimal weight: 40.0000 chunk 322 optimal weight: 3.9990 chunk 143 optimal weight: 0.7980 chunk 348 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 24 optimal weight: 8.9990 chunk 242 optimal weight: 40.0000 chunk 298 optimal weight: 2.9990 chunk 202 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 506 GLN B 134 GLN B 414 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.199445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.151680 restraints weight = 42883.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.135463 restraints weight = 53035.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.134093 restraints weight = 48844.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.133827 restraints weight = 33892.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.133933 restraints weight = 31271.052| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29449 Z= 0.117 Angle : 0.640 12.740 40192 Z= 0.302 Chirality : 0.050 0.455 4691 Planarity : 0.004 0.054 5083 Dihedral : 4.906 34.655 3825 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 1.42 % Allowed : 14.15 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.78 (0.14), residues: 3516 helix: 0.22 (0.21), residues: 617 sheet: -0.30 (0.21), residues: 637 loop : -1.97 (0.13), residues: 2262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 237 TYR 0.029 0.001 TYR C 695 PHE 0.039 0.001 PHE A 238 TRP 0.038 0.001 TRP W 47 HIS 0.004 0.001 HIS A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (29357) covalent geometry : angle 0.61932 / 0.30 (39943) SS BOND : bond 0.00202 / 0.15 ( 24) SS BOND : angle 0.96912 / 0.65 ( 48) hydrogen bonds : bond 0.03591 / 2.27 ( 742) hydrogen bonds : angle 5.28666 / 3.55 ( 2073) Misc. bond : bond 0.00011 / 0.01 ( 1) link_BETA1-4 : bond 0.00699 / 0.44 ( 24) link_BETA1-4 : angle 2.38784 / 1.53 ( 72) link_NAG-ASN : bond 0.00608 / 0.37 ( 43) link_NAG-ASN : angle 2.31827 / 1.76 ( 129) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4284.70 seconds wall clock time: 75 minutes 6.87 seconds (4506.87 seconds total)