Starting phenix.real_space_refine on Wed Jun 25 06:22:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wbh_32398/06_2025/7wbh_32398.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wbh_32398/06_2025/7wbh_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7wbh_32398/06_2025/7wbh_32398.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wbh_32398/06_2025/7wbh_32398.map" model { file = "/net/cci-nas-00/data/ceres_data/7wbh_32398/06_2025/7wbh_32398.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wbh_32398/06_2025/7wbh_32398.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 1.48s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 2, 'ARG:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 2, 'ASP:plan': 2} 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: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG: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: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 3, 'ARG:plan': 5} 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: 18.50, per 1000 atoms: 0.63 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: 6.99 Conformation dependent library (CDL) restraints added in 3.6 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: 4.43 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: 15.29 Time building geometry restraints manager: 8.33 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 1146 or resid 1201 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 1146 or resid 1301 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 1146 or resid 1301 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: 4.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 1.260 Check model and map are aligned: 0.220 Set scattering table: 0.300 Process input model: 69.890 Find NCS groups from input model: 1.990 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.100 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.044 0.003 TRP P 102 HIS 0.006 0.001 HIS B 655 PHE 0.056 0.003 PHE C 456 TYR 0.037 0.002 TYR C 495 ARG 0.015 0.001 ARG C 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00810 ( 27) link_NAG-ASN : angle 5.50471 ( 81) link_BETA1-4 : bond 0.01376 ( 16) link_BETA1-4 : angle 4.56844 ( 48) hydrogen bonds : bond 0.20413 ( 987) hydrogen bonds : angle 8.99156 ( 2820) SS BOND : bond 0.00550 ( 44) SS BOND : angle 2.09287 ( 88) covalent geometry : bond 0.00609 (29852) covalent geometry : angle 1.12951 (40653) *********************** 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 : 2.895 Fit side-chains 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 402 ILE cc_start: 0.7925 (pt) cc_final: 0.7283 (pt) REVERT: C 455 LEU cc_start: 0.8513 (pt) cc_final: 0.8216 (pt) REVERT: Q 4 MET cc_start: 0.4559 (mtp) cc_final: 0.3723 (tmm) REVERT: S 87 TYR cc_start: 0.3316 (m-80) cc_final: 0.3005 (m-80) outliers start: 2 outliers final: 0 residues processed: 318 average time/residue: 0.3662 time to fit residues: 195.7456 Evaluate side-chains 237 residues out of total 3206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 2.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 306 optimal weight: 9.9990 chunk 275 optimal weight: 1.9990 chunk 152 optimal weight: 0.0980 chunk 93 optimal weight: 0.8980 chunk 185 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 284 optimal weight: 0.9980 chunk 110 optimal weight: 6.9990 chunk 173 optimal weight: 2.9990 chunk 211 optimal weight: 0.0270 chunk 329 optimal weight: 20.0000 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN A 926 GLN B 448 ASN B 755 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.156983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.121063 restraints weight = 53953.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.117413 restraints weight = 91408.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.115001 restraints weight = 86675.655| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29939 Z= 0.135 Angle : 0.670 15.346 40870 Z= 0.331 Chirality : 0.047 0.490 4748 Planarity : 0.006 0.069 5179 Dihedral : 10.371 84.374 5077 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.01 % Favored : 95.96 % Rotamer: Outliers : 0.67 % Allowed : 7.15 % Favored : 92.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.13), residues: 3615 helix: -0.12 (0.20), residues: 657 sheet: -0.75 (0.17), residues: 870 loop : -1.79 (0.12), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP S 35 HIS 0.007 0.001 HIS A1101 PHE 0.025 0.001 PHE O 68 TYR 0.031 0.001 TYR C 380 ARG 0.008 0.001 ARG C 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00556 ( 27) link_NAG-ASN : angle 3.83191 ( 81) link_BETA1-4 : bond 0.01015 ( 16) link_BETA1-4 : angle 2.91031 ( 48) hydrogen bonds : bond 0.04150 ( 987) hydrogen bonds : angle 6.54780 ( 2820) SS BOND : bond 0.00510 ( 44) SS BOND : angle 1.41032 ( 88) covalent geometry : bond 0.00296 (29852) covalent geometry : angle 0.63842 (40653) *********************** 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 269 residues out of total 3206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 248 time to evaluate : 3.128 Fit side-chains REVERT: A 120 VAL cc_start: 0.7915 (t) cc_final: 0.7478 (m) REVERT: A 129 LYS cc_start: 0.7152 (mttt) cc_final: 0.6759 (mmmt) REVERT: A 569 ILE cc_start: 0.8087 (mm) cc_final: 0.7707 (mm) REVERT: A 574 ASP cc_start: 0.7943 (t0) cc_final: 0.7727 (t0) REVERT: A 904 TYR cc_start: 0.7155 (m-10) cc_final: 0.6686 (m-10) REVERT: B 307 THR cc_start: 0.8160 (OUTLIER) cc_final: 0.7883 (t) REVERT: B 701 VAL cc_start: 0.8852 (p) cc_final: 0.8603 (m) REVERT: B 754 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8534 (mt) REVERT: C 52 GLN cc_start: 0.7806 (tp40) cc_final: 0.7188 (tm-30) REVERT: C 402 ILE cc_start: 0.8330 (pt) cc_final: 0.8107 (tt) REVERT: U 48 MET cc_start: 0.0840 (ptt) cc_final: 0.0130 (ttp) REVERT: Q 4 MET cc_start: 0.4535 (mtp) cc_final: 0.4122 (tmm) outliers start: 21 outliers final: 16 residues processed: 262 average time/residue: 0.3813 time to fit residues: 168.8515 Evaluate side-chains 236 residues out of total 3206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 218 time to evaluate : 3.115 ------------------------------------------------------------------------------- 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 307 THR Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 511 VAL 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 698 SER Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain O residue 18 VAL 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 225 optimal weight: 8.9990 chunk 338 optimal weight: 6.9990 chunk 222 optimal weight: 0.6980 chunk 333 optimal weight: 9.9990 chunk 174 optimal weight: 0.1980 chunk 313 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 204 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 329 optimal weight: 9.9990 chunk 258 optimal weight: 3.9990 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 134 GLN A 616 ASN A 907 ASN A1071 GLN ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN B 394 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN B 804 GLN B 901 GLN B 919 ASN B 957 GLN ** B1134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 901 GLN U 82 GLN ** V 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 37 GLN ** V 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 82 GLN Q 92 ASN P 82 GLN S 37 GLN ** S 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.148879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.110598 restraints weight = 53735.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.110165 restraints weight = 94123.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.106854 restraints weight = 90421.565| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.100 29939 Z= 0.375 Angle : 0.855 17.224 40870 Z= 0.421 Chirality : 0.055 0.547 4748 Planarity : 0.006 0.061 5179 Dihedral : 9.362 82.757 5077 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.28 % Favored : 94.69 % Rotamer: Outliers : 2.01 % Allowed : 11.08 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.13), residues: 3615 helix: 0.18 (0.20), residues: 657 sheet: -0.85 (0.17), residues: 938 loop : -1.83 (0.12), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 886 HIS 0.008 0.002 HIS B1048 PHE 0.033 0.003 PHE A 906 TYR 0.034 0.003 TYR C 380 ARG 0.012 0.001 ARG P 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00821 ( 27) link_NAG-ASN : angle 4.31136 ( 81) link_BETA1-4 : bond 0.00882 ( 16) link_BETA1-4 : angle 3.11425 ( 48) hydrogen bonds : bond 0.04988 ( 987) hydrogen bonds : angle 6.34213 ( 2820) SS BOND : bond 0.00423 ( 44) SS BOND : angle 1.73228 ( 88) covalent geometry : bond 0.00891 (29852) covalent geometry : angle 0.82426 (40653) *********************** 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 294 residues out of total 3206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 231 time to evaluate : 2.995 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7361 (mttt) cc_final: 0.6900 (mmmt) REVERT: A 231 ILE cc_start: 0.7956 (mp) cc_final: 0.7577 (mm) REVERT: B 421 TYR cc_start: 0.5445 (m-10) cc_final: 0.5052 (m-10) REVERT: C 410 ILE cc_start: 0.8528 (pt) cc_final: 0.8264 (pt) REVERT: C 498 GLN cc_start: 0.6675 (mp10) cc_final: 0.5996 (mp10) REVERT: O 48 MET cc_start: 0.5879 (mtt) cc_final: 0.5343 (ptp) REVERT: Q 4 MET cc_start: 0.4476 (mtp) cc_final: 0.4039 (tmm) outliers start: 63 outliers final: 31 residues processed: 279 average time/residue: 0.3787 time to fit residues: 177.7319 Evaluate side-chains 229 residues out of total 3206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 198 time to evaluate : 4.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 651 ILE 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 858 LEU 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 267 VAL 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 754 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1142 GLN Chi-restraints excluded: chain C residue 118 LEU 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 418 ILE Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 1077 THR 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 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 14 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 272 optimal weight: 0.8980 chunk 145 optimal weight: 3.9990 chunk 174 optimal weight: 0.5980 chunk 335 optimal weight: 9.9990 chunk 221 optimal weight: 0.0980 chunk 157 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 194 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 804 GLN B 448 ASN C 414 GLN C 751 ASN C 804 GLN V 37 GLN ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 90 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.152053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.114941 restraints weight = 53754.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.112625 restraints weight = 92922.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.111320 restraints weight = 95650.130| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 29939 Z= 0.123 Angle : 0.652 14.719 40870 Z= 0.319 Chirality : 0.047 0.479 4748 Planarity : 0.005 0.104 5179 Dihedral : 7.952 72.254 5077 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.12 % Favored : 95.85 % Rotamer: Outliers : 1.40 % Allowed : 13.19 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.13), residues: 3615 helix: 0.68 (0.20), residues: 658 sheet: -0.74 (0.17), residues: 928 loop : -1.61 (0.13), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 436 HIS 0.004 0.001 HIS A 66 PHE 0.022 0.001 PHE C 429 TYR 0.029 0.001 TYR O 105 ARG 0.006 0.000 ARG C 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00475 ( 27) link_NAG-ASN : angle 3.61047 ( 81) link_BETA1-4 : bond 0.00888 ( 16) link_BETA1-4 : angle 2.87595 ( 48) hydrogen bonds : bond 0.03812 ( 987) hydrogen bonds : angle 5.88967 ( 2820) SS BOND : bond 0.00286 ( 44) SS BOND : angle 1.72144 ( 88) covalent geometry : bond 0.00283 (29852) covalent geometry : angle 0.62066 (40653) *********************** 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 261 residues out of total 3206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 217 time to evaluate : 3.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7266 (mttt) cc_final: 0.6949 (mmmt) REVERT: A 1002 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.8178 (tm-30) REVERT: A 1029 MET cc_start: 0.8847 (tpp) cc_final: 0.7927 (ttm) REVERT: B 868 GLU cc_start: 0.7499 (pp20) cc_final: 0.7077 (pp20) REVERT: C 347 PHE cc_start: 0.6945 (m-80) cc_final: 0.6622 (m-80) REVERT: C 410 ILE cc_start: 0.8346 (pt) cc_final: 0.8116 (pt) REVERT: Q 4 MET cc_start: 0.4418 (mtp) cc_final: 0.4053 (tmm) REVERT: P 81 LEU cc_start: 0.1407 (tt) cc_final: 0.1153 (tt) outliers start: 44 outliers final: 25 residues processed: 251 average time/residue: 0.3655 time to fit residues: 155.7022 Evaluate side-chains 221 residues out of total 3206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 195 time to evaluate : 2.891 ------------------------------------------------------------------------------- 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 511 VAL Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1002 GLN 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 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 754 LEU Chi-restraints excluded: chain B residue 943 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 382 VAL Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 1077 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 340 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 349 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 131 optimal weight: 9.9990 chunk 250 optimal weight: 0.9980 chunk 352 optimal weight: 0.1980 chunk 15 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 437 ASN B 448 ASN B 641 ASN B1005 GLN C 901 GLN ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 90 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 = 0.4060 r_free = 0.4060 target = 0.152309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.113614 restraints weight = 53197.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 103)---------------| | r_work = 0.3443 r_free = 0.3443 target = 0.108965 restraints weight = 86362.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.106097 restraints weight = 73282.510| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 29939 Z= 0.123 Angle : 0.624 13.835 40870 Z= 0.306 Chirality : 0.046 0.446 4748 Planarity : 0.004 0.057 5179 Dihedral : 7.068 59.972 5077 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.29 % Favored : 95.68 % Rotamer: Outliers : 1.85 % Allowed : 13.89 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.13), residues: 3615 helix: 0.96 (0.20), residues: 663 sheet: -0.67 (0.17), residues: 915 loop : -1.50 (0.13), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 436 HIS 0.010 0.001 HIS A 66 PHE 0.015 0.001 PHE C 497 TYR 0.018 0.001 TYR C 170 ARG 0.007 0.000 ARG P 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00484 ( 27) link_NAG-ASN : angle 3.35876 ( 81) link_BETA1-4 : bond 0.00862 ( 16) link_BETA1-4 : angle 2.86913 ( 48) hydrogen bonds : bond 0.03497 ( 987) hydrogen bonds : angle 5.62753 ( 2820) SS BOND : bond 0.00311 ( 44) SS BOND : angle 1.55196 ( 88) covalent geometry : bond 0.00284 (29852) covalent geometry : angle 0.59476 (40653) *********************** 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: 58 poor density : 215 time to evaluate : 3.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.9149 (OUTLIER) cc_final: 0.8826 (p) REVERT: A 129 LYS cc_start: 0.7304 (mttt) cc_final: 0.6773 (mmmt) REVERT: A 1002 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.8096 (tm-30) REVERT: A 1029 MET cc_start: 0.8876 (tpp) cc_final: 0.7922 (ttm) REVERT: B 868 GLU cc_start: 0.7687 (pp20) cc_final: 0.7322 (pp20) REVERT: C 335 LEU cc_start: 0.7903 (tp) cc_final: 0.7689 (tt) REVERT: U 48 MET cc_start: 0.0991 (ppp) cc_final: -0.0134 (ttp) REVERT: V 81 GLU cc_start: 0.2436 (OUTLIER) cc_final: 0.1286 (pt0) REVERT: Q 4 MET cc_start: 0.4604 (mtp) cc_final: 0.4003 (tmm) REVERT: P 48 MET cc_start: 0.6820 (mpp) cc_final: 0.6548 (mpp) outliers start: 58 outliers final: 32 residues processed: 259 average time/residue: 0.3740 time to fit residues: 164.4501 Evaluate side-chains 230 residues out of total 3206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 195 time to evaluate : 3.245 ------------------------------------------------------------------------------- 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 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 743 CYS Chi-restraints excluded: chain A residue 878 LEU 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 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 525 CYS Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 990 GLU 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 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 1077 THR Chi-restraints excluded: chain V residue 14 SER Chi-restraints excluded: chain V residue 81 GLU Chi-restraints excluded: chain V residue 87 TYR Chi-restraints excluded: chain O residue 115 VAL Chi-restraints excluded: chain P residue 35 ASN Chi-restraints excluded: chain P residue 51 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 76 optimal weight: 0.7980 chunk 313 optimal weight: 10.0000 chunk 241 optimal weight: 7.9990 chunk 113 optimal weight: 8.9990 chunk 157 optimal weight: 0.6980 chunk 23 optimal weight: 0.1980 chunk 182 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 154 optimal weight: 0.8980 chunk 291 optimal weight: 3.9990 chunk 220 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 437 ASN B 448 ASN C 751 ASN C1119 ASN ** Q 90 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.152254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.113376 restraints weight = 53432.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.109740 restraints weight = 88053.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.106009 restraints weight = 75233.609| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 29939 Z= 0.117 Angle : 0.613 13.247 40870 Z= 0.298 Chirality : 0.045 0.426 4748 Planarity : 0.004 0.055 5179 Dihedral : 6.946 102.837 5077 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.18 % Favored : 95.80 % Rotamer: Outliers : 2.04 % Allowed : 14.37 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.14), residues: 3615 helix: 1.16 (0.21), residues: 663 sheet: -0.64 (0.17), residues: 922 loop : -1.41 (0.13), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 436 HIS 0.003 0.000 HIS B 655 PHE 0.025 0.001 PHE A 168 TYR 0.032 0.001 TYR O 105 ARG 0.005 0.000 ARG P 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00437 ( 27) link_NAG-ASN : angle 3.28175 ( 81) link_BETA1-4 : bond 0.00832 ( 16) link_BETA1-4 : angle 2.82859 ( 48) hydrogen bonds : bond 0.03343 ( 987) hydrogen bonds : angle 5.47684 ( 2820) SS BOND : bond 0.00307 ( 44) SS BOND : angle 1.42896 ( 88) covalent geometry : bond 0.00269 (29852) covalent geometry : angle 0.58566 (40653) *********************** 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 279 residues out of total 3206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 215 time to evaluate : 3.288 Fit side-chains revert: symmetry clash REVERT: A 33 THR cc_start: 0.9087 (OUTLIER) cc_final: 0.8764 (p) REVERT: A 129 LYS cc_start: 0.7296 (mttt) cc_final: 0.6840 (mmmt) REVERT: A 1002 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.8088 (tm-30) REVERT: A 1029 MET cc_start: 0.8847 (tpp) cc_final: 0.7862 (ttm) REVERT: A 1117 THR cc_start: 0.9212 (OUTLIER) cc_final: 0.8985 (p) REVERT: B 380 TYR cc_start: 0.8032 (m-80) cc_final: 0.7678 (m-80) REVERT: B 868 GLU cc_start: 0.7656 (pp20) cc_final: 0.7331 (pp20) REVERT: C 498 GLN cc_start: 0.6303 (mp10) cc_final: 0.5916 (mp10) REVERT: U 48 MET cc_start: 0.1084 (ppp) cc_final: -0.0079 (ttp) REVERT: V 81 GLU cc_start: 0.2067 (OUTLIER) cc_final: 0.1018 (pt0) REVERT: Q 4 MET cc_start: 0.4633 (mtp) cc_final: 0.4024 (tmm) REVERT: P 48 MET cc_start: 0.6870 (mpp) cc_final: 0.6596 (mpp) outliers start: 64 outliers final: 37 residues processed: 266 average time/residue: 0.3591 time to fit residues: 160.9600 Evaluate side-chains 243 residues out of total 3206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 202 time to evaluate : 2.863 ------------------------------------------------------------------------------- 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 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 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 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 990 GLU 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 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 698 SER Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 705 VAL 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 192 optimal weight: 2.9990 chunk 242 optimal weight: 10.0000 chunk 341 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 239 optimal weight: 2.9990 chunk 206 optimal weight: 9.9990 chunk 182 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 228 optimal weight: 0.0270 chunk 91 optimal weight: 1.9990 chunk 348 optimal weight: 10.0000 overall best weight: 2.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN B 448 ASN B 580 GLN C 655 HIS C 901 GLN V 37 GLN Q 92 ASN S 31 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 = 0.4006 r_free = 0.4006 target = 0.148342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.110518 restraints weight = 53382.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.107102 restraints weight = 95653.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.105216 restraints weight = 104817.346| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 29939 Z= 0.276 Angle : 0.726 13.982 40870 Z= 0.356 Chirality : 0.049 0.449 4748 Planarity : 0.005 0.056 5179 Dihedral : 7.215 110.927 5077 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.95 % Favored : 94.99 % Rotamer: Outliers : 2.23 % Allowed : 14.81 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.14), residues: 3615 helix: 1.01 (0.21), residues: 662 sheet: -0.74 (0.17), residues: 925 loop : -1.52 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP S 35 HIS 0.006 0.001 HIS B 655 PHE 0.022 0.002 PHE A 168 TYR 0.030 0.002 TYR C 380 ARG 0.009 0.001 ARG B1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00625 ( 27) link_NAG-ASN : angle 3.54990 ( 81) link_BETA1-4 : bond 0.00863 ( 16) link_BETA1-4 : angle 3.06496 ( 48) hydrogen bonds : bond 0.04119 ( 987) hydrogen bonds : angle 5.70311 ( 2820) SS BOND : bond 0.00415 ( 44) SS BOND : angle 1.82076 ( 88) covalent geometry : bond 0.00658 (29852) covalent geometry : angle 0.69768 (40653) *********************** 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 277 residues out of total 3206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 207 time to evaluate : 3.939 Fit side-chains revert: symmetry clash REVERT: A 33 THR cc_start: 0.9145 (OUTLIER) cc_final: 0.8801 (p) REVERT: A 129 LYS cc_start: 0.7372 (mttt) cc_final: 0.7086 (mmmt) REVERT: A 231 ILE cc_start: 0.7697 (OUTLIER) cc_final: 0.7317 (mm) REVERT: A 1002 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.8204 (tm-30) REVERT: A 1117 THR cc_start: 0.9293 (OUTLIER) cc_final: 0.9079 (p) REVERT: B 380 TYR cc_start: 0.8099 (m-80) cc_final: 0.7756 (m-80) REVERT: B 563 GLN cc_start: 0.5866 (OUTLIER) cc_final: 0.5364 (mm-40) REVERT: B 868 GLU cc_start: 0.7663 (pp20) cc_final: 0.7359 (pp20) REVERT: Q 4 MET cc_start: 0.4651 (mtp) cc_final: 0.4116 (tmm) REVERT: P 67 ARG cc_start: 0.4691 (ptt-90) cc_final: 0.4263 (mtm180) outliers start: 70 outliers final: 42 residues processed: 265 average time/residue: 0.4370 time to fit residues: 194.6940 Evaluate side-chains 236 residues out of total 3206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 189 time to evaluate : 3.319 ------------------------------------------------------------------------------- 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 118 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 338 PHE 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 651 ILE Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 878 LEU 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 563 GLN Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 990 GLU 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 325 SER 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 698 SER 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 87 TYR 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 186 optimal weight: 0.6980 chunk 139 optimal weight: 4.9990 chunk 222 optimal weight: 2.9990 chunk 200 optimal weight: 8.9990 chunk 337 optimal weight: 0.6980 chunk 319 optimal weight: 7.9990 chunk 153 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 328 optimal weight: 7.9990 chunk 35 optimal weight: 0.7980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN B 448 ASN Q 92 ASN ** S 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.149579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.110013 restraints weight = 53467.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.108775 restraints weight = 89125.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.108163 restraints weight = 85320.549| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 29939 Z= 0.181 Angle : 0.650 13.637 40870 Z= 0.317 Chirality : 0.047 0.433 4748 Planarity : 0.004 0.055 5179 Dihedral : 6.976 112.440 5077 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.15 % Favored : 95.82 % Rotamer: Outliers : 1.79 % Allowed : 16.00 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.14), residues: 3615 helix: 1.16 (0.21), residues: 659 sheet: -0.78 (0.17), residues: 920 loop : -1.47 (0.13), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 436 HIS 0.004 0.001 HIS B 655 PHE 0.024 0.001 PHE A 168 TYR 0.023 0.001 TYR P 80 ARG 0.004 0.000 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00425 ( 27) link_NAG-ASN : angle 3.37918 ( 81) link_BETA1-4 : bond 0.00925 ( 16) link_BETA1-4 : angle 2.98389 ( 48) hydrogen bonds : bond 0.03637 ( 987) hydrogen bonds : angle 5.57172 ( 2820) SS BOND : bond 0.00343 ( 44) SS BOND : angle 1.59564 ( 88) covalent geometry : bond 0.00428 (29852) covalent geometry : angle 0.62075 (40653) *********************** 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 258 residues out of total 3206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 202 time to evaluate : 3.542 Fit side-chains revert: symmetry clash REVERT: A 33 THR cc_start: 0.9086 (OUTLIER) cc_final: 0.8751 (p) REVERT: A 129 LYS cc_start: 0.7357 (mttt) cc_final: 0.7022 (mmmt) REVERT: A 1002 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.8125 (tm-30) REVERT: B 380 TYR cc_start: 0.8118 (m-80) cc_final: 0.7821 (m-80) REVERT: C 498 GLN cc_start: 0.6244 (mp10) cc_final: 0.5837 (mp10) REVERT: U 48 MET cc_start: 0.0720 (ppp) cc_final: -0.0404 (ttp) REVERT: P 48 MET cc_start: 0.6980 (mpp) cc_final: 0.6729 (mpp) REVERT: P 67 ARG cc_start: 0.4779 (ptt-90) cc_final: 0.4090 (mpp-170) outliers start: 56 outliers final: 40 residues processed: 249 average time/residue: 0.6002 time to fit residues: 252.6425 Evaluate side-chains 232 residues out of total 3206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 190 time to evaluate : 3.640 ------------------------------------------------------------------------------- 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 118 LEU 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 743 CYS Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 878 LEU 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 1135 ASN 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 377 PHE 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 615 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 990 GLU 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 320 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain V residue 14 SER Chi-restraints excluded: chain V residue 87 TYR 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 178 optimal weight: 0.7980 chunk 231 optimal weight: 6.9990 chunk 160 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 244 optimal weight: 7.9990 chunk 321 optimal weight: 0.9980 chunk 350 optimal weight: 9.9990 chunk 285 optimal weight: 0.5980 chunk 12 optimal weight: 8.9990 chunk 89 optimal weight: 0.6980 chunk 211 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 ASN A1135 ASN B 448 ASN B 563 GLN C 450 ASN V 37 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 = 0.4034 r_free = 0.4034 target = 0.150536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.110716 restraints weight = 53212.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.109607 restraints weight = 88044.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.108451 restraints weight = 85917.694| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 29939 Z= 0.125 Angle : 0.623 12.827 40870 Z= 0.304 Chirality : 0.046 0.413 4748 Planarity : 0.004 0.055 5179 Dihedral : 6.695 110.361 5077 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.43 % Favored : 95.55 % Rotamer: Outliers : 1.72 % Allowed : 16.03 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.14), residues: 3615 helix: 1.29 (0.21), residues: 659 sheet: -0.74 (0.17), residues: 924 loop : -1.39 (0.13), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP P 102 HIS 0.003 0.001 HIS B 655 PHE 0.025 0.001 PHE A 168 TYR 0.037 0.001 TYR C 380 ARG 0.005 0.000 ARG B 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00415 ( 27) link_NAG-ASN : angle 3.16984 ( 81) link_BETA1-4 : bond 0.00905 ( 16) link_BETA1-4 : angle 2.95495 ( 48) hydrogen bonds : bond 0.03406 ( 987) hydrogen bonds : angle 5.43210 ( 2820) SS BOND : bond 0.00291 ( 44) SS BOND : angle 1.47552 ( 88) covalent geometry : bond 0.00288 (29852) covalent geometry : angle 0.59555 (40653) *********************** 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 254 residues out of total 3206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 200 time to evaluate : 4.023 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.9065 (OUTLIER) cc_final: 0.8731 (p) REVERT: A 129 LYS cc_start: 0.7222 (mttt) cc_final: 0.6996 (mmmt) REVERT: A 1002 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.8138 (tm-30) REVERT: B 380 TYR cc_start: 0.8130 (m-80) cc_final: 0.7918 (m-80) REVERT: C 498 GLN cc_start: 0.6263 (mp10) cc_final: 0.5896 (mp10) REVERT: U 48 MET cc_start: 0.0997 (ppp) cc_final: 0.0007 (ttp) REVERT: P 48 MET cc_start: 0.6933 (mpp) cc_final: 0.6676 (mpp) REVERT: P 67 ARG cc_start: 0.4937 (ptt-90) cc_final: 0.4256 (mpp-170) outliers start: 54 outliers final: 39 residues processed: 244 average time/residue: 0.5497 time to fit residues: 228.8188 Evaluate side-chains 233 residues out of total 3206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 192 time to evaluate : 3.510 ------------------------------------------------------------------------------- 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 118 LEU Chi-restraints excluded: chain A residue 338 PHE 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 743 CYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1135 ASN 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 430 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1081 ILE 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 320 VAL Chi-restraints excluded: chain C residue 325 SER 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 698 SER Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain V residue 87 TYR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 296 optimal weight: 0.6980 chunk 214 optimal weight: 0.0000 chunk 94 optimal weight: 5.9990 chunk 314 optimal weight: 9.9990 chunk 182 optimal weight: 5.9990 chunk 356 optimal weight: 9.9990 chunk 263 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 119 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1135 ASN B 448 ASN B 563 GLN C 901 GLN C 957 GLN 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 = 0.4041 r_free = 0.4041 target = 0.151024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.112884 restraints weight = 53230.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.112272 restraints weight = 92798.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.111446 restraints weight = 83426.902| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 29939 Z= 0.115 Angle : 0.614 12.431 40870 Z= 0.299 Chirality : 0.045 0.398 4748 Planarity : 0.004 0.055 5179 Dihedral : 6.502 109.898 5077 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.12 % Favored : 95.85 % Rotamer: Outliers : 1.60 % Allowed : 16.19 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.14), residues: 3615 helix: 1.40 (0.21), residues: 647 sheet: -0.69 (0.17), residues: 926 loop : -1.33 (0.13), residues: 2042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP P 102 HIS 0.003 0.001 HIS B 655 PHE 0.033 0.001 PHE C 497 TYR 0.028 0.001 TYR C 380 ARG 0.003 0.000 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00414 ( 27) link_NAG-ASN : angle 3.01671 ( 81) link_BETA1-4 : bond 0.00910 ( 16) link_BETA1-4 : angle 2.95868 ( 48) hydrogen bonds : bond 0.03292 ( 987) hydrogen bonds : angle 5.32668 ( 2820) SS BOND : bond 0.00286 ( 44) SS BOND : angle 1.38586 ( 88) covalent geometry : bond 0.00265 (29852) covalent geometry : angle 0.58812 (40653) ********************** 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 245 residues out of total 3206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 195 time to evaluate : 2.927 Fit side-chains revert: symmetry clash REVERT: A 33 THR cc_start: 0.9017 (OUTLIER) cc_final: 0.8692 (p) REVERT: A 1002 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.8125 (tm-30) REVERT: A 1029 MET cc_start: 0.8937 (tpp) cc_final: 0.7832 (ttm) REVERT: C 498 GLN cc_start: 0.6157 (mp10) cc_final: 0.5780 (mp10) REVERT: U 48 MET cc_start: 0.1054 (ppp) cc_final: 0.0285 (ttp) REVERT: Q 4 MET cc_start: 0.4229 (mtm) cc_final: 0.3940 (tmm) REVERT: P 48 MET cc_start: 0.6855 (mpp) cc_final: 0.6629 (mpp) REVERT: P 67 ARG cc_start: 0.5025 (ptt-90) cc_final: 0.4401 (mpp-170) REVERT: P 102 TRP cc_start: 0.6396 (t60) cc_final: 0.6182 (t60) outliers start: 50 outliers final: 40 residues processed: 238 average time/residue: 0.4495 time to fit residues: 179.1961 Evaluate side-chains 228 residues out of total 3206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 186 time to evaluate : 3.442 ------------------------------------------------------------------------------- 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 338 PHE 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 743 CYS Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 878 LEU 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 1135 ASN 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 430 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1081 ILE 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 320 VAL Chi-restraints excluded: chain C residue 325 SER 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 705 VAL Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain V residue 87 TYR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 210 optimal weight: 8.9990 chunk 295 optimal weight: 0.0670 chunk 307 optimal weight: 30.0000 chunk 163 optimal weight: 0.6980 chunk 215 optimal weight: 0.9990 chunk 318 optimal weight: 9.9990 chunk 198 optimal weight: 1.9990 chunk 286 optimal weight: 0.9980 chunk 106 optimal weight: 10.0000 chunk 152 optimal weight: 3.9990 chunk 135 optimal weight: 9.9990 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1135 ASN B 448 ASN C 417 ASN Q 92 ASN ** S 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4036 r_free = 0.4036 target = 0.150656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.110949 restraints weight = 53364.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.109501 restraints weight = 87521.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.107182 restraints weight = 85764.203| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 29939 Z= 0.133 Angle : 0.622 12.237 40870 Z= 0.303 Chirality : 0.045 0.394 4748 Planarity : 0.004 0.056 5179 Dihedral : 6.433 109.783 5077 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.43 % Favored : 95.55 % Rotamer: Outliers : 1.47 % Allowed : 16.38 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.14), residues: 3615 helix: 1.39 (0.21), residues: 651 sheet: -0.66 (0.17), residues: 922 loop : -1.30 (0.13), residues: 2042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP P 102 HIS 0.003 0.001 HIS B 655 PHE 0.031 0.001 PHE C 497 TYR 0.044 0.001 TYR B 508 ARG 0.006 0.000 ARG B 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00390 ( 27) link_NAG-ASN : angle 2.96779 ( 81) link_BETA1-4 : bond 0.00895 ( 16) link_BETA1-4 : angle 2.98719 ( 48) hydrogen bonds : bond 0.03325 ( 987) hydrogen bonds : angle 5.29820 ( 2820) SS BOND : bond 0.00286 ( 44) SS BOND : angle 1.40570 ( 88) covalent geometry : bond 0.00311 (29852) covalent geometry : angle 0.59708 (40653) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9337.36 seconds wall clock time: 168 minutes 13.37 seconds (10093.37 seconds total)