Starting phenix.real_space_refine on Fri Mar 6 07:36:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wbh_32398/03_2026/7wbh_32398.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wbh_32398/03_2026/7wbh_32398.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wbh_32398/03_2026/7wbh_32398.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wbh_32398/03_2026/7wbh_32398.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wbh_32398/03_2026/7wbh_32398.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wbh_32398/03_2026/7wbh_32398.map" } resolution = 3.7 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= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 129 5.16 5 C 18573 2.51 5 N 4761 2.21 5 O 5724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 117 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29187 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 7761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7761 Classifications: {'peptide': 1006} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 23} Link IDs: {'PTRANS': 54, 'TRANS': 951} Chain breaks: 8 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 3, 'ASN:plan1': 2, 'GLN:plan1': 2, 'HIS:plan': 2, 'GLU:plan': 2, 'TYR:plan': 1, 'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "B" Number of atoms: 7732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1000, 7732 Classifications: {'peptide': 1000} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 54, 'TRANS': 945} Chain breaks: 8 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 3, 'ARG:plan': 1, 'GLN:plan1': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "C" Number of atoms: 7677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1000, 7677 Classifications: {'peptide': 1000} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 54, 'TRANS': 945} Chain breaks: 8 Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASN:plan1': 3, 'ARG:plan': 5, 'GLN:plan1': 3, 'PHE:plan': 3, 'TYR:plan': 1, 'ASP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 82 Chain: "U" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "V" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "O" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "Q" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "P" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "S" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "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 dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "S" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.84, per 1000 atoms: 0.23 Number of scatterers: 29187 At special positions: 0 Unit cell: (144.72, 166.32, 192.24, 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 5724 8.00 N 4761 7.00 C 18573 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.06 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 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 U 22 " - pdb=" SG CYS U 96 " distance=2.03 Simple disulfide: pdb=" SG CYS V 23 " - pdb=" SG CYS V 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.04 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 23 " - pdb=" SG CYS S 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG R 1 " - " NAG R 2 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A1201 " - " ASN A 282 " " NAG A1202 " - " ASN A 603 " " NAG A1204 " - " ASN A 657 " " NAG A1205 " - " ASN A 709 " " NAG B1303 " - " ASN B 282 " " NAG B1306 " - " ASN B 616 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B 717 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C1098 " " NAG C1308 " - " ASN C1134 " " NAG D 1 " - " ASN A 343 " " NAG E 1 " - " ASN B 343 " " NAG F 1 " - " ASN C 343 " " NAG H 1 " - " ASN A 717 " " NAG I 1 " - " ASN A 801 " " NAG J 1 " - " ASN A1074 " " NAG L 1 " - " ASN B 801 " " NAG M 1 " - " ASN B1074 " " NAG N 1 " - " ASN C 717 " " NAG R 1 " - " ASN C 801 " " NAG T 1 " - " ASN C1074 " Time building additional restraints: 2.47 Conformation dependent library (CDL) restraints added in 1.4 seconds 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6846 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 69 sheets defined 19.4% alpha, 25.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 4.503A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.849A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.655A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 907 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.756A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.823A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.984A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.773A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.534A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 388' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.857A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.893A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.606A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.586A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.285A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 983 removed outlier: 3.847A pdb=" N ARG B 983 " --> pdb=" O ASP B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.693A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 4.829A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.760A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.307A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.647A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.190A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 983 removed outlier: 3.808A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.877A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.090A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.521A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.226A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.569A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.281A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.316A pdb=" N ASN A 122 " --> pdb=" O ASN A 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.676A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 325 removed outlier: 7.238A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.544A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.077A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 400 through 403 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.555A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.195A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.757A pdb=" N VAL A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 714 through 715 Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.233A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.011A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 789 removed outlier: 6.044A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.975A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.248A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.422A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.578A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.512A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.529A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.529A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TRP B 436 " --> pdb=" O ARG B 509 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.572A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 539 through 543 removed outlier: 4.952A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.115A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 701 through 703 Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.637A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.088A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.504A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD8, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.327A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.327A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.876A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.114A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.681A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.405A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.729A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE C 434 " --> pdb=" O VAL C 511 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR C 380 " --> pdb=" O GLY C 431 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.886A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE8, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.167A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AF2, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.230A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.025A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.630A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF6, first strand: chain 'U' and resid 5 through 6 removed outlier: 3.587A pdb=" N VAL U 5 " --> pdb=" O LYS U 23 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'U' and resid 11 through 12 removed outlier: 3.890A pdb=" N LYS U 12 " --> pdb=" O THR U 116 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'U' and resid 17 through 20 Processing sheet with id=AF9, first strand: chain 'U' and resid 58 through 60 removed outlier: 3.575A pdb=" N THR U 59 " --> pdb=" O TRP U 50 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N TRP U 36 " --> pdb=" O MET U 48 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'V' and resid 5 through 7 removed outlier: 3.624A pdb=" N THR V 22 " --> pdb=" O SER V 7 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL V 19 " --> pdb=" O ILE V 75 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE V 21 " --> pdb=" O LEU V 73 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU V 73 " --> pdb=" O ILE V 21 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'V' and resid 10 through 13 removed outlier: 3.929A pdb=" N LEU V 11 " --> pdb=" O LYS V 103 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU V 105 " --> pdb=" O LEU V 11 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE V 48 " --> pdb=" O TRP V 35 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLN V 37 " --> pdb=" O LEU V 46 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU V 46 " --> pdb=" O GLN V 37 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'O' and resid 3 through 6 removed outlier: 3.713A pdb=" N GLN O 3 " --> pdb=" O SER O 25 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER O 25 " --> pdb=" O GLN O 3 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'O' and resid 11 through 12 removed outlier: 3.942A pdb=" N LYS O 12 " --> pdb=" O THR O 116 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'O' and resid 17 through 20 removed outlier: 3.722A pdb=" N THR O 78 " --> pdb=" O ASP O 73 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'O' and resid 36 through 39 removed outlier: 7.003A pdb=" N TRP O 36 " --> pdb=" O MET O 48 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'O' and resid 93 through 94 removed outlier: 3.898A pdb=" N TYR O 94 " --> pdb=" O THR O 113 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N THR O 113 " --> pdb=" O TYR O 94 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'Q' and resid 5 through 7 removed outlier: 3.642A pdb=" N THR Q 22 " --> pdb=" O SER Q 7 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL Q 19 " --> pdb=" O ILE Q 75 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE Q 21 " --> pdb=" O LEU Q 73 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE Q 71 " --> pdb=" O CYS Q 23 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP Q 70 " --> pdb=" O SER Q 67 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER Q 67 " --> pdb=" O ASP Q 70 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Q' and resid 10 through 13 removed outlier: 3.721A pdb=" N LEU Q 11 " --> pdb=" O LYS Q 103 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU Q 105 " --> pdb=" O LEU Q 11 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Q' and resid 48 through 49 Processing sheet with id=AH2, first strand: chain 'P' and resid 3 through 6 removed outlier: 3.761A pdb=" N GLN P 3 " --> pdb=" O SER P 25 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER P 25 " --> pdb=" O GLN P 3 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'P' and resid 11 through 12 removed outlier: 3.943A pdb=" N LYS P 12 " --> pdb=" O THR P 116 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL P 115 " --> pdb=" O ALA P 92 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA P 92 " --> pdb=" O VAL P 115 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N MET P 34 " --> pdb=" O TRP P 50 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N TRP P 50 " --> pdb=" O MET P 34 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N TRP P 36 " --> pdb=" O MET P 48 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'P' and resid 18 through 20 removed outlier: 4.024A pdb=" N THR P 78 " --> pdb=" O ASP P 73 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ASP P 73 " --> pdb=" O THR P 78 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'S' and resid 4 through 5 removed outlier: 3.575A pdb=" N VAL S 19 " --> pdb=" O ILE S 75 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE S 21 " --> pdb=" O LEU S 73 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU S 73 " --> pdb=" O ILE S 21 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE S 71 " --> pdb=" O CYS S 23 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP S 70 " --> pdb=" O SER S 67 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'S' and resid 10 through 12 removed outlier: 7.006A pdb=" N LEU S 11 " --> pdb=" O GLU S 105 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLN S 37 " --> pdb=" O LEU S 46 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU S 46 " --> pdb=" O GLN S 37 " (cutoff:3.500A) 1017 hydrogen bonds defined for protein. 2820 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.79 Time building geometry restraints manager: 3.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 9175 1.35 - 1.47: 7913 1.47 - 1.60: 12602 1.60 - 1.73: 0 1.73 - 1.86: 162 Bond restraints: 29852 Sorted by residual: bond pdb=" C1 NAG A1201 " pdb=" O5 NAG A1201 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" C LEU B 560 " pdb=" N PRO B 561 " ideal model delta sigma weight residual 1.337 1.370 -0.034 9.80e-03 1.04e+04 1.17e+01 bond pdb=" C VAL C 83 " pdb=" N LEU C 84 " ideal model delta sigma weight residual 1.331 1.385 -0.054 1.59e-02 3.96e+03 1.14e+01 bond pdb=" C LEU A 560 " pdb=" N PRO A 561 " ideal model delta sigma weight residual 1.337 1.374 -0.037 1.11e-02 8.12e+03 1.12e+01 bond pdb=" C LYS B 462 " pdb=" N PRO B 463 " ideal model delta sigma weight residual 1.332 1.376 -0.044 1.34e-02 5.57e+03 1.10e+01 ... (remaining 29847 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.83: 40034 3.83 - 7.66: 539 7.66 - 11.48: 73 11.48 - 15.31: 6 15.31 - 19.14: 1 Bond angle restraints: 40653 Sorted by residual: angle pdb=" CA LYS C 378 " pdb=" CB LYS C 378 " pdb=" CG LYS C 378 " ideal model delta sigma weight residual 114.10 127.48 -13.38 2.00e+00 2.50e-01 4.48e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 118.48 -7.78 1.22e+00 6.72e-01 4.07e+01 angle pdb=" C PHE A 515 " pdb=" N GLU A 516 " pdb=" CA GLU A 516 " ideal model delta sigma weight residual 120.79 129.48 -8.69 1.39e+00 5.18e-01 3.91e+01 angle pdb=" C SER B 172 " pdb=" N GLN B 173 " pdb=" CA GLN B 173 " ideal model delta sigma weight residual 120.49 129.29 -8.80 1.42e+00 4.96e-01 3.84e+01 angle pdb=" N CYS B 525 " pdb=" CA CYS B 525 " pdb=" C CYS B 525 " ideal model delta sigma weight residual 107.73 115.71 -7.98 1.34e+00 5.57e-01 3.55e+01 ... (remaining 40648 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.25: 17018 21.25 - 42.51: 1088 42.51 - 63.76: 186 63.76 - 85.02: 62 85.02 - 106.27: 42 Dihedral angle restraints: 18396 sinusoidal: 7734 harmonic: 10662 Sorted by residual: dihedral pdb=" CB CYS A 743 " pdb=" SG CYS A 743 " pdb=" SG CYS A 749 " pdb=" CB CYS A 749 " ideal model delta sinusoidal sigma weight residual 93.00 177.74 -84.74 1 1.00e+01 1.00e-02 8.72e+01 dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual 93.00 19.04 73.96 1 1.00e+01 1.00e-02 6.95e+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 -156.50 70.50 1 1.00e+01 1.00e-02 6.40e+01 ... (remaining 18393 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 4385 0.114 - 0.228: 318 0.228 - 0.342: 30 0.342 - 0.456: 11 0.456 - 0.570: 4 Chirality restraints: 4748 Sorted by residual: chirality pdb=" C1 NAG C1301 " pdb=" ND2 ASN C 282 " pdb=" C2 NAG C1301 " pdb=" O5 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-01 2.50e+01 8.13e+00 chirality pdb=" C2 NAG K 1 " pdb=" C1 NAG K 1 " pdb=" C3 NAG K 1 " pdb=" N2 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.02 -0.47 2.00e-01 2.50e+01 5.50e+00 chirality pdb=" C1 NAG B1308 " pdb=" ND2 ASN B 709 " pdb=" C2 NAG B1308 " pdb=" O5 NAG B1308 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.50e+00 ... (remaining 4745 not shown) Planarity restraints: 5206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 282 " 0.007 2.00e-02 2.50e+03 4.32e-02 2.34e+01 pdb=" CG ASN A 282 " -0.048 2.00e-02 2.50e+03 pdb=" OD1 ASN A 282 " 0.049 2.00e-02 2.50e+03 pdb=" ND2 ASN A 282 " -0.052 2.00e-02 2.50e+03 pdb=" C1 NAG A1201 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 38 " 0.073 5.00e-02 4.00e+02 1.12e-01 1.99e+01 pdb=" N PRO A 39 " -0.193 5.00e-02 4.00e+02 pdb=" CA PRO A 39 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO A 39 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 38 " -0.064 5.00e-02 4.00e+02 9.72e-02 1.51e+01 pdb=" N PRO C 39 " 0.168 5.00e-02 4.00e+02 pdb=" CA PRO C 39 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO C 39 " -0.053 5.00e-02 4.00e+02 ... (remaining 5203 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 8571 2.83 - 3.35: 23155 3.35 - 3.86: 48407 3.86 - 4.38: 51575 4.38 - 4.90: 92464 Nonbonded interactions: 224172 Sorted by model distance: nonbonded pdb=" O GLY C 880 " pdb=" OG SER C 884 " model vdw 2.310 3.040 nonbonded pdb=" OG1 THR B1116 " pdb=" OD1 ASP B1118 " model vdw 2.317 3.040 nonbonded pdb=" OH TYR B 741 " pdb=" O LEU B 962 " model vdw 2.325 3.040 nonbonded pdb=" OG SER B 349 " pdb=" O LEU B 452 " model vdw 2.329 3.040 nonbonded pdb=" OG1 THR A 108 " pdb=" O ASN A 234 " model vdw 2.329 3.040 ... (remaining 224167 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 66 or resid 81 through 101 or (resid 102 and (n \ ame N or name CA or name C or name O or name CB )) or resid 103 through 128 or ( \ resid 129 and (name N or name CA or name C or name O or name CB )) or resid 130 \ through 140 or (resid 157 through 160 and (name N or name CA or name C or name O \ or name CB )) or resid 161 through 187 or (resid 188 and (name N or name CA or \ name C or name O or name CB )) or resid 189 or (resid 190 and (name N or name CA \ or name C or name O or name CB )) or resid 191 through 194 or (resid 195 throug \ h 198 and (name N or name CA or name C or name O or name CB )) or resid 199 thro \ ugh 209 or resid 217 through 236 or (resid 237 and (name N or name CA or name C \ or name O or name CB )) or resid 238 or (resid 239 and (name N or name CA or nam \ e C or name O or name CB )) or resid 240 through 241 or resid 263 through 331 or \ (resid 332 through 333 and (name N or name CA or name C or name O or name CB )) \ or resid 334 through 620 or resid 641 through 1206)) selection = (chain 'B' and (resid 27 through 95 or resid 99 through 128 or (resid 129 and (n \ ame N or name CA or name C or name O or name CB )) or resid 130 through 140 or ( \ resid 157 through 160 and (name N or name CA or name C or name O or name CB )) o \ r resid 161 through 175 or (resid 176 through 188 and (name N or name CA or name \ C or name O or name CB )) or resid 189 or (resid 190 and (name N or name CA or \ name C or name O or name CB )) or resid 191 through 195 or (resid 196 through 19 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 199 through \ 236 or (resid 237 and (name N or name CA or name C or name O or name CB )) or re \ sid 238 or (resid 239 and (name N or name CA or name C or name O or name CB )) o \ r resid 240 through 289 or (resid 290 and (name N or name CA or name C or name O \ or name CB )) or resid 291 through 527 or (resid 528 through 529 and (name N or \ name CA or name C or name O or name CB )) or resid 530 through 620 or resid 641 \ through 1306)) selection = (chain 'C' and (resid 27 through 59 or (resid 60 and (name N or name CA or name \ C or name O or name CB )) or resid 61 through 187 or (resid 188 and (name N or n \ ame CA or name C or name O or name CB )) or resid 189 through 209 or resid 217 t \ hrough 241 or resid 263 through 280 or (resid 281 and (name N or name CA or name \ C or name O or name CB )) or resid 282 through 1306)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'R' selection = chain 'T' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'U' } ncs_group { reference = chain 'Q' selection = (chain 'S' and resid 1 through 107) selection = chain 'V' } 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: 4.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 29.010 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 29939 Z= 0.312 Angle : 1.167 19.142 40870 Z= 0.630 Chirality : 0.067 0.570 4748 Planarity : 0.009 0.112 5179 Dihedral : 15.479 106.274 11418 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.34 % Favored : 94.63 % Rotamer: Outliers : 0.06 % Allowed : 0.61 % Favored : 99.33 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.71 (0.12), residues: 3615 helix: -2.12 (0.15), residues: 652 sheet: -1.00 (0.17), residues: 833 loop : -2.08 (0.12), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 567 TYR 0.037 0.002 TYR C 495 PHE 0.056 0.003 PHE C 456 TRP 0.044 0.003 TRP P 102 HIS 0.006 0.001 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00609 (29852) covalent geometry : angle 1.12951 (40653) SS BOND : bond 0.00550 ( 44) SS BOND : angle 2.09287 ( 88) hydrogen bonds : bond 0.20413 ( 987) hydrogen bonds : angle 8.99156 ( 2820) link_BETA1-4 : bond 0.01376 ( 16) link_BETA1-4 : angle 4.56844 ( 48) link_NAG-ASN : bond 0.00810 ( 27) link_NAG-ASN : angle 5.50471 ( 81) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 317 time to evaluate : 1.267 Fit side-chains revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7016 (mttt) cc_final: 0.6335 (mmmt) REVERT: A 574 ASP cc_start: 0.7889 (t0) cc_final: 0.7599 (t0) REVERT: A 904 TYR cc_start: 0.7293 (m-10) cc_final: 0.6899 (m-10) REVERT: B 117 LEU cc_start: 0.7329 (tt) cc_final: 0.6228 (mp) REVERT: B 453 TYR cc_start: 0.7108 (p90) cc_final: 0.6404 (p90) REVERT: B 960 ASN cc_start: 0.7723 (m-40) cc_final: 0.7356 (m-40) REVERT: C 455 LEU cc_start: 0.8513 (pt) cc_final: 0.8224 (pt) REVERT: Q 4 MET cc_start: 0.4559 (mtp) cc_final: 0.3724 (tmm) REVERT: S 87 TYR cc_start: 0.3316 (m-80) cc_final: 0.3007 (m-80) outliers start: 2 outliers final: 0 residues processed: 318 average time/residue: 0.1714 time to fit residues: 92.5142 Evaluate side-chains 235 residues out of total 3206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.0010 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 1.9990 overall best weight: 1.0990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 580 GLN A 926 GLN B 448 ASN B 655 HIS B 755 GLN B 901 GLN B 914 ASN B 955 ASN B 965 GLN B 969 ASN C 417 ASN O 82 GLN Q 92 ASN P 6 GLN P 82 GLN ** S 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.155786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.118912 restraints weight = 53883.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.116010 restraints weight = 91280.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.112751 restraints weight = 77884.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.111399 restraints weight = 76491.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.111318 restraints weight = 68902.062| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29939 Z= 0.153 Angle : 0.678 15.300 40870 Z= 0.334 Chirality : 0.047 0.496 4748 Planarity : 0.005 0.068 5179 Dihedral : 10.003 82.157 5077 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.98 % Favored : 95.99 % Rotamer: Outliers : 0.89 % Allowed : 7.47 % Favored : 91.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.72 (0.13), residues: 3615 helix: 0.01 (0.20), residues: 647 sheet: -0.76 (0.17), residues: 878 loop : -1.74 (0.12), residues: 2090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1039 TYR 0.031 0.002 TYR C 380 PHE 0.022 0.001 PHE A 643 TRP 0.025 0.002 TRP S 35 HIS 0.006 0.001 HIS A1101 Details of bonding type rmsd covalent geometry : bond 0.00345 (29852) covalent geometry : angle 0.64825 (40653) SS BOND : bond 0.00386 ( 44) SS BOND : angle 1.47196 ( 88) hydrogen bonds : bond 0.03950 ( 987) hydrogen bonds : angle 6.40741 ( 2820) link_BETA1-4 : bond 0.01043 ( 16) link_BETA1-4 : angle 2.88606 ( 48) link_NAG-ASN : bond 0.00470 ( 27) link_NAG-ASN : angle 3.75271 ( 81) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 251 time to evaluate : 1.050 Fit side-chains REVERT: A 120 VAL cc_start: 0.8020 (t) cc_final: 0.7557 (m) REVERT: A 129 LYS cc_start: 0.7124 (mttt) cc_final: 0.6601 (mmmt) REVERT: A 569 ILE cc_start: 0.8182 (mm) cc_final: 0.7777 (mm) REVERT: A 904 TYR cc_start: 0.7322 (m-10) cc_final: 0.6787 (m-10) REVERT: A 1029 MET cc_start: 0.8969 (tpp) cc_final: 0.8152 (ttm) REVERT: B 307 THR cc_start: 0.8204 (OUTLIER) cc_final: 0.7935 (t) REVERT: B 453 TYR cc_start: 0.6757 (p90) cc_final: 0.6493 (p90) REVERT: B 701 VAL cc_start: 0.8954 (p) cc_final: 0.8686 (m) REVERT: B 754 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8530 (mt) REVERT: C 52 GLN cc_start: 0.7810 (tp40) cc_final: 0.7164 (tm-30) REVERT: C 188 ASN cc_start: 0.5846 (p0) cc_final: 0.5636 (p0) REVERT: C 347 PHE cc_start: 0.6822 (m-80) cc_final: 0.6614 (m-80) REVERT: C 402 ILE cc_start: 0.7785 (OUTLIER) cc_final: 0.6923 (tp) REVERT: U 48 MET cc_start: 0.1488 (ptt) cc_final: 0.0472 (ttp) REVERT: U 103 ASP cc_start: 0.6534 (p0) cc_final: 0.6329 (p0) REVERT: Q 4 MET cc_start: 0.4750 (mtp) cc_final: 0.4088 (tmm) REVERT: S 45 LYS cc_start: 0.4569 (OUTLIER) cc_final: 0.3789 (ttpt) outliers start: 28 outliers final: 14 residues processed: 269 average time/residue: 0.1778 time to fit residues: 80.6891 Evaluate side-chains 231 residues out of total 3206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 213 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 109 TRP Chi-restraints excluded: chain S residue 45 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 242 optimal weight: 6.9990 chunk 351 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 249 optimal weight: 0.1980 chunk 321 optimal weight: 3.9990 chunk 53 optimal weight: 0.0980 chunk 51 optimal weight: 0.7980 chunk 269 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 298 optimal weight: 0.5980 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS B 448 ASN B 919 ASN B 969 ASN C 417 ASN ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 92 ASN S 37 GLN ** S 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.156079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.119253 restraints weight = 53926.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.116028 restraints weight = 91885.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.114186 restraints weight = 75218.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.112255 restraints weight = 77112.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.112030 restraints weight = 71754.295| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 29939 Z= 0.110 Angle : 0.629 14.409 40870 Z= 0.303 Chirality : 0.046 0.444 4748 Planarity : 0.004 0.058 5179 Dihedral : 8.675 78.753 5077 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.07 % Favored : 95.91 % Rotamer: Outliers : 1.05 % Allowed : 9.87 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % 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: -1.31 (0.13), residues: 3615 helix: 0.70 (0.21), residues: 649 sheet: -0.61 (0.17), residues: 902 loop : -1.54 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 357 TYR 0.027 0.001 TYR C 380 PHE 0.026 0.001 PHE C 429 TRP 0.021 0.001 TRP C 436 HIS 0.002 0.000 HIS Q 34 Details of bonding type rmsd covalent geometry : bond 0.00237 (29852) covalent geometry : angle 0.59930 (40653) SS BOND : bond 0.00285 ( 44) SS BOND : angle 1.35863 ( 88) hydrogen bonds : bond 0.03570 ( 987) hydrogen bonds : angle 5.89334 ( 2820) link_BETA1-4 : bond 0.00938 ( 16) link_BETA1-4 : angle 2.78521 ( 48) link_NAG-ASN : bond 0.00537 ( 27) link_NAG-ASN : angle 3.55788 ( 81) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 3206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 237 time to evaluate : 1.086 Fit side-chains REVERT: A 120 VAL cc_start: 0.8214 (t) cc_final: 0.7808 (m) REVERT: A 129 LYS cc_start: 0.7109 (mttt) cc_final: 0.6600 (mmmt) REVERT: A 904 TYR cc_start: 0.7473 (m-10) cc_final: 0.7030 (m-10) REVERT: A 1029 MET cc_start: 0.8974 (tpp) cc_final: 0.8445 (ttm) REVERT: B 421 TYR cc_start: 0.5531 (m-10) cc_final: 0.5304 (m-80) REVERT: B 453 TYR cc_start: 0.6742 (p90) cc_final: 0.6488 (p90) REVERT: B 701 VAL cc_start: 0.8961 (OUTLIER) cc_final: 0.8668 (m) REVERT: B 754 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8601 (mt) REVERT: B 902 MET cc_start: 0.8940 (mmm) cc_final: 0.8717 (mmm) REVERT: C 52 GLN cc_start: 0.7839 (tp40) cc_final: 0.7181 (tm-30) REVERT: C 188 ASN cc_start: 0.5954 (p0) cc_final: 0.5663 (p0) REVERT: C 402 ILE cc_start: 0.7694 (mm) cc_final: 0.7145 (tp) REVERT: C 1081 ILE cc_start: 0.9042 (mm) cc_final: 0.8689 (mm) REVERT: U 48 MET cc_start: 0.1825 (ptt) cc_final: 0.0458 (ttp) REVERT: U 103 ASP cc_start: 0.6544 (p0) cc_final: 0.6250 (p0) REVERT: O 94 TYR cc_start: 0.3325 (m-10) cc_final: 0.3068 (m-10) REVERT: O 105 TYR cc_start: 0.6699 (p90) cc_final: 0.6396 (p90) REVERT: Q 4 MET cc_start: 0.4815 (mtp) cc_final: 0.4259 (tmm) REVERT: P 48 MET cc_start: 0.6790 (mpp) cc_final: 0.6533 (mpp) REVERT: S 45 LYS cc_start: 0.4440 (OUTLIER) cc_final: 0.3738 (ttpt) outliers start: 33 outliers final: 16 residues processed: 259 average time/residue: 0.1751 time to fit residues: 76.8160 Evaluate side-chains 228 residues out of total 3206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 209 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain S residue 45 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 314 optimal weight: 10.0000 chunk 126 optimal weight: 2.9990 chunk 36 optimal weight: 20.0000 chunk 62 optimal weight: 0.7980 chunk 300 optimal weight: 0.0070 chunk 306 optimal weight: 10.0000 chunk 133 optimal weight: 20.0000 chunk 333 optimal weight: 10.0000 chunk 338 optimal weight: 9.9990 chunk 149 optimal weight: 3.9990 chunk 96 optimal weight: 0.1980 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 907 ASN B 394 ASN B 448 ASN B 957 GLN B1002 GLN C 417 ASN C 450 ASN ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 901 GLN U 82 GLN ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 92 ASN ** S 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.152247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.114932 restraints weight = 53578.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.111206 restraints weight = 95821.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.109021 restraints weight = 107769.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.108883 restraints weight = 93214.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.108776 restraints weight = 83287.696| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 29939 Z= 0.192 Angle : 0.664 14.379 40870 Z= 0.322 Chirality : 0.047 0.460 4748 Planarity : 0.004 0.061 5179 Dihedral : 7.591 81.513 5077 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.98 % Favored : 95.99 % Rotamer: Outliers : 1.82 % Allowed : 11.05 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.14 (0.13), residues: 3615 helix: 0.98 (0.21), residues: 649 sheet: -0.57 (0.17), residues: 930 loop : -1.46 (0.13), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG P 38 TYR 0.023 0.002 TYR C 170 PHE 0.024 0.002 PHE A 168 TRP 0.016 0.001 TRP C 436 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00449 (29852) covalent geometry : angle 0.63494 (40653) SS BOND : bond 0.00590 ( 44) SS BOND : angle 1.54878 ( 88) hydrogen bonds : bond 0.03745 ( 987) hydrogen bonds : angle 5.70601 ( 2820) link_BETA1-4 : bond 0.00806 ( 16) link_BETA1-4 : angle 2.84846 ( 48) link_NAG-ASN : bond 0.00559 ( 27) link_NAG-ASN : angle 3.52279 ( 81) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 3206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 230 time to evaluate : 1.085 Fit side-chains revert: symmetry clash REVERT: A 120 VAL cc_start: 0.8477 (t) cc_final: 0.8132 (m) REVERT: A 129 LYS cc_start: 0.7262 (mttt) cc_final: 0.6880 (mmmt) REVERT: A 900 MET cc_start: 0.8439 (mtm) cc_final: 0.8169 (mtp) REVERT: A 904 TYR cc_start: 0.7845 (m-10) cc_final: 0.6780 (m-10) REVERT: A 1144 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7056 (mp0) REVERT: B 868 GLU cc_start: 0.7374 (pp20) cc_final: 0.6919 (pp20) REVERT: C 52 GLN cc_start: 0.7924 (tp40) cc_final: 0.7223 (tm-30) REVERT: C 188 ASN cc_start: 0.5993 (p0) cc_final: 0.5703 (p0) REVERT: C 327 VAL cc_start: 0.7639 (m) cc_final: 0.7435 (m) REVERT: C 402 ILE cc_start: 0.7467 (mm) cc_final: 0.7056 (tp) REVERT: C 437 ASN cc_start: 0.6072 (t0) cc_final: 0.5855 (t0) REVERT: C 498 GLN cc_start: 0.6509 (mp10) cc_final: 0.5971 (mp10) REVERT: O 94 TYR cc_start: 0.3501 (m-80) cc_final: 0.3272 (m-10) REVERT: Q 4 MET cc_start: 0.4504 (mtp) cc_final: 0.4105 (tmm) REVERT: S 45 LYS cc_start: 0.4458 (OUTLIER) cc_final: 0.3712 (ttpt) outliers start: 57 outliers final: 31 residues processed: 272 average time/residue: 0.1685 time to fit residues: 78.0702 Evaluate side-chains 238 residues out of total 3206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 206 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain V residue 14 SER Chi-restraints excluded: chain O residue 115 VAL Chi-restraints excluded: chain P residue 35 ASN Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain S residue 45 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 260 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 141 optimal weight: 10.0000 chunk 201 optimal weight: 0.6980 chunk 354 optimal weight: 8.9990 chunk 77 optimal weight: 0.9990 chunk 173 optimal weight: 0.5980 chunk 184 optimal weight: 0.9990 chunk 28 optimal weight: 9.9990 chunk 262 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1135 ASN B 437 ASN B 448 ASN ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN C 804 GLN ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 92 ASN ** S 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.153186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.116916 restraints weight = 53545.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.115322 restraints weight = 89090.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.113535 restraints weight = 83033.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.111834 restraints weight = 82423.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.110463 restraints weight = 80621.303| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29939 Z= 0.124 Angle : 0.612 13.627 40870 Z= 0.297 Chirality : 0.046 0.437 4748 Planarity : 0.004 0.052 5179 Dihedral : 6.949 83.363 5077 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.23 % Favored : 95.74 % Rotamer: Outliers : 1.60 % Allowed : 12.29 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.14), residues: 3615 helix: 1.30 (0.21), residues: 641 sheet: -0.54 (0.17), residues: 915 loop : -1.38 (0.13), residues: 2059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 237 TYR 0.033 0.001 TYR C 380 PHE 0.025 0.001 PHE C 429 TRP 0.013 0.001 TRP C 436 HIS 0.003 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00285 (29852) covalent geometry : angle 0.58358 (40653) SS BOND : bond 0.00269 ( 44) SS BOND : angle 1.60241 ( 88) hydrogen bonds : bond 0.03360 ( 987) hydrogen bonds : angle 5.48965 ( 2820) link_BETA1-4 : bond 0.00879 ( 16) link_BETA1-4 : angle 2.80092 ( 48) link_NAG-ASN : bond 0.00453 ( 27) link_NAG-ASN : angle 3.28642 ( 81) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 223 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.9132 (OUTLIER) cc_final: 0.8763 (p) REVERT: A 129 LYS cc_start: 0.7222 (mttt) cc_final: 0.6922 (mmmt) REVERT: A 904 TYR cc_start: 0.7736 (m-10) cc_final: 0.7052 (m-10) REVERT: A 1029 MET cc_start: 0.9066 (tpp) cc_final: 0.8281 (ttm) REVERT: A 1144 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7071 (mp0) REVERT: B 868 GLU cc_start: 0.7258 (pp20) cc_final: 0.6821 (pp20) REVERT: C 52 GLN cc_start: 0.7955 (tp40) cc_final: 0.7251 (tm-30) REVERT: C 188 ASN cc_start: 0.5952 (p0) cc_final: 0.5560 (p0) REVERT: C 327 VAL cc_start: 0.7762 (m) cc_final: 0.7562 (m) REVERT: C 402 ILE cc_start: 0.7478 (mm) cc_final: 0.7205 (tp) REVERT: U 48 MET cc_start: 0.0306 (ppp) cc_final: -0.0439 (ttp) REVERT: O 94 TYR cc_start: 0.3525 (m-80) cc_final: 0.3300 (m-10) REVERT: Q 4 MET cc_start: 0.4504 (mtp) cc_final: 0.4188 (tmm) REVERT: S 45 LYS cc_start: 0.4489 (OUTLIER) cc_final: 0.3750 (ttpt) outliers start: 50 outliers final: 32 residues processed: 261 average time/residue: 0.1685 time to fit residues: 75.0123 Evaluate side-chains 243 residues out of total 3206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 209 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain V residue 14 SER Chi-restraints excluded: chain O residue 113 THR Chi-restraints excluded: chain O residue 115 VAL Chi-restraints excluded: chain P residue 35 ASN Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain S residue 45 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 73 optimal weight: 1.9990 chunk 328 optimal weight: 10.0000 chunk 88 optimal weight: 0.6980 chunk 151 optimal weight: 4.9990 chunk 307 optimal weight: 9.9990 chunk 159 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 104 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 204 optimal weight: 7.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 ASN B 448 ASN B1005 GLN ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN C1119 ASN ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 92 ASN ** S 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.151570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.116416 restraints weight = 53440.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.112996 restraints weight = 92734.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.111090 restraints weight = 81704.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.109571 restraints weight = 79050.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.108023 restraints weight = 75817.746| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 29939 Z= 0.176 Angle : 0.636 13.530 40870 Z= 0.311 Chirality : 0.046 0.435 4748 Planarity : 0.004 0.053 5179 Dihedral : 6.612 84.271 5077 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.37 % Favored : 95.60 % Rotamer: Outliers : 2.01 % Allowed : 12.93 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.14), residues: 3615 helix: 1.31 (0.21), residues: 649 sheet: -0.55 (0.17), residues: 930 loop : -1.39 (0.13), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG P 38 TYR 0.029 0.001 TYR O 105 PHE 0.015 0.001 PHE C 392 TRP 0.017 0.002 TRP B 436 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00415 (29852) covalent geometry : angle 0.60896 (40653) SS BOND : bond 0.00279 ( 44) SS BOND : angle 1.48781 ( 88) hydrogen bonds : bond 0.03525 ( 987) hydrogen bonds : angle 5.46306 ( 2820) link_BETA1-4 : bond 0.00871 ( 16) link_BETA1-4 : angle 2.90201 ( 48) link_NAG-ASN : bond 0.00424 ( 27) link_NAG-ASN : angle 3.26654 ( 81) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 218 time to evaluate : 1.061 Fit side-chains revert: symmetry clash REVERT: A 33 THR cc_start: 0.9159 (OUTLIER) cc_final: 0.8794 (p) REVERT: A 129 LYS cc_start: 0.7292 (mttt) cc_final: 0.7014 (mmmt) REVERT: A 231 ILE cc_start: 0.7906 (OUTLIER) cc_final: 0.7590 (mm) REVERT: A 740 MET cc_start: 0.7177 (ttt) cc_final: 0.6948 (tpt) REVERT: A 1002 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.8168 (tm-30) REVERT: A 1029 MET cc_start: 0.8940 (tpp) cc_final: 0.8047 (ttm) REVERT: A 1117 THR cc_start: 0.9249 (OUTLIER) cc_final: 0.8974 (p) REVERT: B 868 GLU cc_start: 0.7429 (pp20) cc_final: 0.7011 (pp20) REVERT: C 52 GLN cc_start: 0.8129 (tp40) cc_final: 0.7426 (tm-30) REVERT: C 188 ASN cc_start: 0.6038 (p0) cc_final: 0.5540 (p0) REVERT: C 327 VAL cc_start: 0.8028 (m) cc_final: 0.7824 (m) REVERT: C 402 ILE cc_start: 0.7474 (OUTLIER) cc_final: 0.7197 (tp) REVERT: V 81 GLU cc_start: 0.1947 (OUTLIER) cc_final: 0.0920 (pt0) REVERT: O 94 TYR cc_start: 0.3594 (m-80) cc_final: 0.3339 (m-10) REVERT: Q 4 MET cc_start: 0.4620 (mtp) cc_final: 0.4192 (tmm) REVERT: S 45 LYS cc_start: 0.4557 (OUTLIER) cc_final: 0.3806 (ttpt) outliers start: 63 outliers final: 37 residues processed: 265 average time/residue: 0.1684 time to fit residues: 76.0905 Evaluate side-chains 244 residues out of total 3206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 200 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain V residue 14 SER Chi-restraints excluded: chain V residue 81 GLU Chi-restraints excluded: chain O residue 113 THR Chi-restraints excluded: chain O residue 115 VAL Chi-restraints excluded: chain P residue 35 ASN Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain S residue 45 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 48 optimal weight: 6.9990 chunk 214 optimal weight: 0.0020 chunk 159 optimal weight: 0.9980 chunk 348 optimal weight: 10.0000 chunk 256 optimal weight: 6.9990 chunk 101 optimal weight: 0.9980 chunk 153 optimal weight: 1.9990 chunk 322 optimal weight: 0.6980 chunk 312 optimal weight: 8.9990 chunk 72 optimal weight: 0.0570 chunk 280 optimal weight: 0.6980 overall best weight: 0.4906 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A1135 ASN B 448 ASN C 125 ASN C 207 HIS ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Q 92 ASN ** S 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.153342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.116128 restraints weight = 53429.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.114995 restraints weight = 92296.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.113389 restraints weight = 94086.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.112186 restraints weight = 87075.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.112038 restraints weight = 76221.593| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 29939 Z= 0.106 Angle : 0.595 12.731 40870 Z= 0.290 Chirality : 0.045 0.408 4748 Planarity : 0.004 0.068 5179 Dihedral : 6.181 80.405 5077 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.07 % Favored : 95.91 % Rotamer: Outliers : 1.88 % Allowed : 13.47 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % 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: -0.83 (0.14), residues: 3615 helix: 1.55 (0.21), residues: 642 sheet: -0.49 (0.17), residues: 911 loop : -1.29 (0.13), residues: 2062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG O 38 TYR 0.022 0.001 TYR C 453 PHE 0.038 0.001 PHE O 64 TRP 0.019 0.001 TRP B 886 HIS 0.002 0.000 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00235 (29852) covalent geometry : angle 0.56926 (40653) SS BOND : bond 0.00297 ( 44) SS BOND : angle 1.31271 ( 88) hydrogen bonds : bond 0.03172 ( 987) hydrogen bonds : angle 5.27991 ( 2820) link_BETA1-4 : bond 0.00984 ( 16) link_BETA1-4 : angle 2.86502 ( 48) link_NAG-ASN : bond 0.00451 ( 27) link_NAG-ASN : angle 3.06950 ( 81) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 213 time to evaluate : 1.072 Fit side-chains revert: symmetry clash REVERT: A 33 THR cc_start: 0.9128 (OUTLIER) cc_final: 0.8744 (p) REVERT: A 1002 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.8131 (tm-30) REVERT: A 1029 MET cc_start: 0.8802 (tpp) cc_final: 0.8075 (ttm) REVERT: A 1117 THR cc_start: 0.9158 (OUTLIER) cc_final: 0.8874 (p) REVERT: A 1144 GLU cc_start: 0.7513 (mm-30) cc_final: 0.6905 (mp0) REVERT: B 868 GLU cc_start: 0.7261 (pp20) cc_final: 0.6831 (pp20) REVERT: C 52 GLN cc_start: 0.8117 (tp40) cc_final: 0.7370 (tm-30) REVERT: C 188 ASN cc_start: 0.6317 (p0) cc_final: 0.6077 (p0) REVERT: C 498 GLN cc_start: 0.6093 (mp10) cc_final: 0.5795 (mp10) REVERT: U 48 MET cc_start: 0.0138 (ppp) cc_final: -0.0271 (ttp) REVERT: V 81 GLU cc_start: 0.1953 (OUTLIER) cc_final: 0.1041 (pt0) REVERT: O 94 TYR cc_start: 0.3609 (m-80) cc_final: 0.3347 (m-10) REVERT: Q 4 MET cc_start: 0.4545 (mtp) cc_final: 0.4156 (tmm) REVERT: S 45 LYS cc_start: 0.4551 (OUTLIER) cc_final: 0.3847 (ttpt) outliers start: 59 outliers final: 38 residues processed: 258 average time/residue: 0.1696 time to fit residues: 74.8731 Evaluate side-chains 240 residues out of total 3206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 197 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain V residue 81 GLU Chi-restraints excluded: chain O residue 113 THR Chi-restraints excluded: chain P residue 35 ASN Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain S residue 45 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 70 optimal weight: 1.9990 chunk 262 optimal weight: 0.0010 chunk 209 optimal weight: 4.9990 chunk 255 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 360 optimal weight: 0.0570 chunk 86 optimal weight: 2.9990 chunk 182 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 80 optimal weight: 0.6980 chunk 358 optimal weight: 5.9990 overall best weight: 0.9508 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN B 448 ASN B 563 GLN C 125 ASN ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN V 34 HIS V 89 GLN Q 92 ASN ** S 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.152452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.113354 restraints weight = 53380.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.112059 restraints weight = 87280.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.110018 restraints weight = 83560.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.108053 restraints weight = 86746.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.106793 restraints weight = 88806.684| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29939 Z= 0.131 Angle : 0.603 12.639 40870 Z= 0.294 Chirality : 0.045 0.404 4748 Planarity : 0.004 0.085 5179 Dihedral : 6.034 78.092 5077 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.23 % Favored : 95.74 % Rotamer: Outliers : 1.47 % Allowed : 13.98 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.14), residues: 3615 helix: 1.55 (0.21), residues: 647 sheet: -0.46 (0.17), residues: 916 loop : -1.27 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG O 38 TYR 0.025 0.001 TYR C 453 PHE 0.036 0.001 PHE O 64 TRP 0.029 0.001 TRP P 102 HIS 0.002 0.000 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00303 (29852) covalent geometry : angle 0.57564 (40653) SS BOND : bond 0.00252 ( 44) SS BOND : angle 1.63283 ( 88) hydrogen bonds : bond 0.03220 ( 987) hydrogen bonds : angle 5.25436 ( 2820) link_BETA1-4 : bond 0.00911 ( 16) link_BETA1-4 : angle 2.91739 ( 48) link_NAG-ASN : bond 0.00397 ( 27) link_NAG-ASN : angle 3.02713 ( 81) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 211 time to evaluate : 1.106 Fit side-chains revert: symmetry clash REVERT: A 1002 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.8148 (tm-30) REVERT: A 1029 MET cc_start: 0.9015 (tpp) cc_final: 0.8176 (ttm) REVERT: A 1117 THR cc_start: 0.9215 (OUTLIER) cc_final: 0.8955 (p) REVERT: A 1144 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7091 (mp0) REVERT: B 563 GLN cc_start: 0.5069 (OUTLIER) cc_final: 0.4819 (mt0) REVERT: B 868 GLU cc_start: 0.7376 (pp20) cc_final: 0.6969 (pp20) REVERT: C 52 GLN cc_start: 0.8170 (tp40) cc_final: 0.7448 (tm-30) REVERT: C 402 ILE cc_start: 0.7446 (OUTLIER) cc_final: 0.7171 (tp) REVERT: C 498 GLN cc_start: 0.6258 (mp10) cc_final: 0.5865 (mp10) REVERT: U 48 MET cc_start: 0.0411 (ppp) cc_final: -0.0271 (ttp) REVERT: V 81 GLU cc_start: 0.2059 (OUTLIER) cc_final: 0.1081 (pt0) REVERT: O 94 TYR cc_start: 0.3572 (m-80) cc_final: 0.3307 (m-10) REVERT: Q 4 MET cc_start: 0.4681 (mtp) cc_final: 0.4148 (tmm) outliers start: 46 outliers final: 37 residues processed: 245 average time/residue: 0.1733 time to fit residues: 71.9913 Evaluate side-chains 241 residues out of total 3206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 199 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain V residue 14 SER Chi-restraints excluded: chain V residue 81 GLU Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain O residue 113 THR Chi-restraints excluded: chain P residue 35 ASN Chi-restraints excluded: chain P residue 51 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 334 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 339 optimal weight: 4.9990 chunk 53 optimal weight: 0.1980 chunk 257 optimal weight: 3.9990 chunk 161 optimal weight: 5.9990 chunk 345 optimal weight: 0.7980 chunk 185 optimal weight: 0.5980 chunk 331 optimal weight: 7.9990 chunk 77 optimal weight: 0.5980 chunk 266 optimal weight: 2.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 448 ASN B 563 GLN C 493 GLN Q 92 ASN ** S 90 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 = 0.4068 r_free = 0.4068 target = 0.152945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.113364 restraints weight = 53467.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.111566 restraints weight = 93403.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.111840 restraints weight = 88170.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.110522 restraints weight = 69364.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.110822 restraints weight = 65602.910| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29939 Z= 0.112 Angle : 0.596 12.377 40870 Z= 0.290 Chirality : 0.045 0.395 4748 Planarity : 0.004 0.099 5179 Dihedral : 5.887 73.752 5077 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.09 % Favored : 95.88 % Rotamer: Outliers : 1.66 % Allowed : 14.30 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.14), residues: 3615 helix: 1.58 (0.21), residues: 650 sheet: -0.45 (0.17), residues: 905 loop : -1.24 (0.13), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG O 38 TYR 0.028 0.001 TYR C 453 PHE 0.036 0.001 PHE O 64 TRP 0.024 0.001 TRP P 102 HIS 0.002 0.000 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00254 (29852) covalent geometry : angle 0.56947 (40653) SS BOND : bond 0.00240 ( 44) SS BOND : angle 1.50482 ( 88) hydrogen bonds : bond 0.03123 ( 987) hydrogen bonds : angle 5.18608 ( 2820) link_BETA1-4 : bond 0.00918 ( 16) link_BETA1-4 : angle 2.91361 ( 48) link_NAG-ASN : bond 0.00412 ( 27) link_NAG-ASN : angle 2.96995 ( 81) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 3206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 206 time to evaluate : 1.042 Fit side-chains revert: symmetry clash REVERT: A 33 THR cc_start: 0.9109 (OUTLIER) cc_final: 0.8744 (p) REVERT: A 231 ILE cc_start: 0.7931 (OUTLIER) cc_final: 0.7653 (mm) REVERT: A 1002 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.8146 (tm-30) REVERT: A 1029 MET cc_start: 0.8906 (tpp) cc_final: 0.8091 (ttm) REVERT: A 1117 THR cc_start: 0.9196 (OUTLIER) cc_final: 0.8938 (p) REVERT: A 1144 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7042 (mp0) REVERT: B 868 GLU cc_start: 0.7254 (pp20) cc_final: 0.6848 (pp20) REVERT: C 52 GLN cc_start: 0.8163 (tp40) cc_final: 0.7433 (tm-30) REVERT: C 498 GLN cc_start: 0.6196 (mp10) cc_final: 0.5845 (mp10) REVERT: U 48 MET cc_start: 0.0317 (ppp) cc_final: -0.0291 (ttp) REVERT: V 81 GLU cc_start: 0.1995 (OUTLIER) cc_final: 0.1375 (pt0) REVERT: Q 4 MET cc_start: 0.4646 (mtp) cc_final: 0.4165 (tmm) outliers start: 52 outliers final: 39 residues processed: 244 average time/residue: 0.1710 time to fit residues: 71.4464 Evaluate side-chains 242 residues out of total 3206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 198 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain V residue 14 SER Chi-restraints excluded: chain V residue 81 GLU Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain O residue 113 THR Chi-restraints excluded: chain P residue 35 ASN Chi-restraints excluded: chain P residue 51 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 90 optimal weight: 0.9990 chunk 243 optimal weight: 6.9990 chunk 239 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 257 optimal weight: 5.9990 chunk 337 optimal weight: 8.9990 chunk 110 optimal weight: 20.0000 chunk 52 optimal weight: 1.9990 chunk 313 optimal weight: 2.9990 chunk 169 optimal weight: 0.5980 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 448 ASN B 563 GLN B 580 GLN C1119 ASN Q 92 ASN ** S 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.151813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.113619 restraints weight = 53217.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.109347 restraints weight = 88483.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.105755 restraints weight = 85917.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.106116 restraints weight = 77529.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.105878 restraints weight = 61171.519| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29939 Z= 0.143 Angle : 0.614 12.350 40870 Z= 0.300 Chirality : 0.045 0.393 4748 Planarity : 0.004 0.058 5179 Dihedral : 5.842 68.465 5077 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.34 % Favored : 95.63 % Rotamer: Outliers : 1.56 % Allowed : 14.59 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.14), residues: 3615 helix: 1.58 (0.21), residues: 647 sheet: -0.52 (0.17), residues: 918 loop : -1.23 (0.13), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG O 38 TYR 0.035 0.001 TYR C 380 PHE 0.036 0.001 PHE O 64 TRP 0.019 0.001 TRP P 102 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00332 (29852) covalent geometry : angle 0.58724 (40653) SS BOND : bond 0.00307 ( 44) SS BOND : angle 1.53952 ( 88) hydrogen bonds : bond 0.03249 ( 987) hydrogen bonds : angle 5.21147 ( 2820) link_BETA1-4 : bond 0.01024 ( 16) link_BETA1-4 : angle 2.99495 ( 48) link_NAG-ASN : bond 0.00369 ( 27) link_NAG-ASN : angle 3.00628 ( 81) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 204 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.9136 (OUTLIER) cc_final: 0.8771 (p) REVERT: A 1002 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.8156 (tm-30) REVERT: A 1029 MET cc_start: 0.8895 (tpp) cc_final: 0.8055 (ttm) REVERT: A 1117 THR cc_start: 0.9217 (OUTLIER) cc_final: 0.8970 (p) REVERT: B 697 MET cc_start: 0.8485 (ttm) cc_final: 0.8183 (ttp) REVERT: B 868 GLU cc_start: 0.7248 (pp20) cc_final: 0.6881 (pp20) REVERT: C 52 GLN cc_start: 0.8180 (tp40) cc_final: 0.7475 (tm-30) REVERT: C 402 ILE cc_start: 0.7296 (OUTLIER) cc_final: 0.7080 (tp) REVERT: U 48 MET cc_start: 0.0693 (ppp) cc_final: -0.0329 (ttp) REVERT: V 81 GLU cc_start: 0.1840 (OUTLIER) cc_final: 0.1180 (pt0) REVERT: Q 4 MET cc_start: 0.4710 (mtp) cc_final: 0.4159 (tmm) REVERT: P 67 ARG cc_start: 0.4988 (ptt-90) cc_final: 0.4419 (mpp-170) outliers start: 49 outliers final: 37 residues processed: 241 average time/residue: 0.1835 time to fit residues: 74.3819 Evaluate side-chains 238 residues out of total 3206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 196 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain V residue 14 SER Chi-restraints excluded: chain V residue 81 GLU Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain O residue 113 THR Chi-restraints excluded: chain P residue 35 ASN Chi-restraints excluded: chain P residue 51 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 84 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 232 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 320 optimal weight: 4.9990 chunk 244 optimal weight: 4.9990 chunk 292 optimal weight: 0.6980 chunk 327 optimal weight: 8.9990 chunk 329 optimal weight: 8.9990 chunk 210 optimal weight: 7.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN A1071 GLN B 448 ASN C 901 GLN Q 92 ASN ** S 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.151175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.112033 restraints weight = 53575.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 75)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.106461 restraints weight = 86563.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.101888 restraints weight = 72895.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.101810 restraints weight = 75268.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.101914 restraints weight = 62043.255| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 29939 Z= 0.155 Angle : 0.627 12.602 40870 Z= 0.305 Chirality : 0.046 0.390 4748 Planarity : 0.004 0.056 5179 Dihedral : 5.818 60.157 5077 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.51 % Favored : 95.46 % Rotamer: Outliers : 1.37 % Allowed : 15.04 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % 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: -0.80 (0.14), residues: 3615 helix: 1.51 (0.21), residues: 653 sheet: -0.53 (0.17), residues: 911 loop : -1.24 (0.13), residues: 2051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 403 TYR 0.028 0.001 TYR C 380 PHE 0.020 0.001 PHE O 64 TRP 0.019 0.001 TRP S 35 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00364 (29852) covalent geometry : angle 0.59977 (40653) SS BOND : bond 0.00304 ( 44) SS BOND : angle 1.60224 ( 88) hydrogen bonds : bond 0.03317 ( 987) hydrogen bonds : angle 5.25023 ( 2820) link_BETA1-4 : bond 0.00936 ( 16) link_BETA1-4 : angle 3.02786 ( 48) link_NAG-ASN : bond 0.00358 ( 27) link_NAG-ASN : angle 3.07610 ( 81) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4665.85 seconds wall clock time: 81 minutes 52.96 seconds (4912.96 seconds total)