Starting phenix.real_space_refine on Tue May 27 16:31:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8elj_28228/05_2025/8elj_28228.cif Found real_map, /net/cci-nas-00/data/ceres_data/8elj_28228/05_2025/8elj_28228.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8elj_28228/05_2025/8elj_28228.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8elj_28228/05_2025/8elj_28228.map" model { file = "/net/cci-nas-00/data/ceres_data/8elj_28228/05_2025/8elj_28228.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8elj_28228/05_2025/8elj_28228.cif" } resolution = 3.6 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= 0.011 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 132 5.16 5 C 18732 2.51 5 N 4827 2.21 5 O 5772 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 180 residue(s): 2.73s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 29463 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7823 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 Chain: "B" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7823 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 Chain: "C" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7823 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 Chain: "S" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 956 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "T" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 790 Classifications: {'peptide': 108} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "U" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 956 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "V" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 790 Classifications: {'peptide': 108} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "W" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 956 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "X" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 790 Classifications: {'peptide': 108} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 19.64, per 1000 atoms: 0.67 Number of scatterers: 29463 At special positions: 0 Unit cell: (136.8, 139.365, 202.635, 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 132 16.00 O 5772 8.00 N 4827 7.00 C 18732 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.08 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.06 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.07 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.06 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.06 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.05 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.06 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.07 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.08 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.05 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.07 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.07 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.07 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.06 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.05 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.05 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.08 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.08 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.05 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.07 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.07 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.07 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.05 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.05 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.05 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.08 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS T 22 " - pdb=" SG CYS T 90 " distance=2.04 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS U 96 " distance=2.03 Simple disulfide: pdb=" SG CYS V 22 " - pdb=" SG CYS V 90 " distance=2.04 Simple disulfide: pdb=" SG CYS W 22 " - pdb=" SG CYS W 96 " distance=2.03 Simple disulfide: pdb=" SG CYS X 22 " - pdb=" SG CYS X 90 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=7, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C1074 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG J 1 " - " ASN B 717 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN B1098 " " NAG M 1 " - " ASN B1134 " " NAG O 1 " - " ASN C 717 " " NAG P 1 " - " ASN C 801 " " NAG Q 1 " - " ASN C1098 " " NAG R 1 " - " ASN C1134 " Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.04 Conformation dependent library (CDL) restraints added in 3.7 seconds 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6852 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 60 sheets defined 22.1% alpha, 33.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.02 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.812A pdb=" N ASP A 389 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.756A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 759 removed outlier: 7.022A pdb=" N SER A 758 " --> pdb=" O GLN A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 783 removed outlier: 3.529A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 4.006A 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: 3.586A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.059A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1031 removed outlier: 4.792A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.810A pdb=" N ASP B 389 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.754A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) 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 755 through 759 removed outlier: 7.021A pdb=" N SER B 758 " --> pdb=" O GLN B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 783 removed outlier: 3.529A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.548A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.060A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (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 982 Processing helix chain 'B' and resid 985 through 1031 removed outlier: 4.793A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.811A pdb=" N ASP C 389 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.755A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) 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 Processing helix chain 'C' and resid 755 through 759 removed outlier: 7.023A pdb=" N SER C 758 " --> pdb=" O GLN C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 760 through 783 removed outlier: 3.529A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.523A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.059A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (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 982 Processing helix chain 'C' and resid 985 through 1031 removed outlier: 4.792A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.948A pdb=" N TYR S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 65 Processing helix chain 'S' and resid 87 through 91 Processing helix chain 'T' and resid 81 through 85 Processing helix chain 'U' and resid 28 through 32 removed outlier: 3.949A pdb=" N TYR U 32 " --> pdb=" O PHE U 29 " (cutoff:3.500A) Processing helix chain 'U' and resid 62 through 65 Processing helix chain 'U' and resid 87 through 91 Processing helix chain 'V' and resid 81 through 85 Processing helix chain 'W' and resid 28 through 32 removed outlier: 3.948A pdb=" N TYR W 32 " --> pdb=" O PHE W 29 " (cutoff:3.500A) Processing helix chain 'W' and resid 62 through 65 Processing helix chain 'W' and resid 87 through 91 Processing helix chain 'X' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.245A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.657A pdb=" N ARG C 567 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.380A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.715A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.491A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.290A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.375A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.758A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TRP A 436 " --> pdb=" O ARG A 509 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.237A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.491A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.315A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.315A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.541A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.239A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.380A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.716A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.482A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.292A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.373A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.758A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TRP B 436 " --> pdb=" O ARG B 509 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.238A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.477A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.320A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.320A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.538A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.248A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.381A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.715A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.478A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.290A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.757A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE C 402 " --> pdb=" O TYR C 508 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.238A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.320A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.320A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.538A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'S' and resid 3 through 6 Processing sheet with id=AE8, first strand: chain 'S' and resid 10 through 11 removed outlier: 6.656A pdb=" N PHE S 34 " --> pdb=" O TRP S 50 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N TRP S 50 " --> pdb=" O PHE S 34 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TRP S 36 " --> pdb=" O MET S 48 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'S' and resid 10 through 11 Processing sheet with id=AF1, first strand: chain 'T' and resid 9 through 12 removed outlier: 6.568A pdb=" N VAL T 10 " --> pdb=" O THR T 108 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N TRP T 37 " --> pdb=" O MET T 49 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'T' and resid 9 through 12 removed outlier: 6.568A pdb=" N VAL T 10 " --> pdb=" O THR T 108 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'T' and resid 18 through 23 Processing sheet with id=AF4, first strand: chain 'U' and resid 3 through 6 Processing sheet with id=AF5, first strand: chain 'U' and resid 10 through 11 removed outlier: 6.651A pdb=" N PHE U 34 " --> pdb=" O TRP U 50 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N TRP U 50 " --> pdb=" O PHE U 34 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N TRP U 36 " --> pdb=" O MET U 48 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'U' and resid 10 through 11 Processing sheet with id=AF7, first strand: chain 'V' and resid 9 through 12 removed outlier: 6.568A pdb=" N VAL V 10 " --> pdb=" O THR V 108 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N TRP V 37 " --> pdb=" O MET V 49 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'V' and resid 9 through 12 removed outlier: 6.568A pdb=" N VAL V 10 " --> pdb=" O THR V 108 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'V' and resid 18 through 23 Processing sheet with id=AG1, first strand: chain 'W' and resid 3 through 6 Processing sheet with id=AG2, first strand: chain 'W' and resid 10 through 11 removed outlier: 6.651A pdb=" N PHE W 34 " --> pdb=" O TRP W 50 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N TRP W 50 " --> pdb=" O PHE W 34 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N TRP W 36 " --> pdb=" O MET W 48 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'W' and resid 10 through 11 Processing sheet with id=AG4, first strand: chain 'X' and resid 9 through 12 removed outlier: 6.569A pdb=" N VAL X 10 " --> pdb=" O THR X 108 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N TRP X 37 " --> pdb=" O MET X 49 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'X' and resid 9 through 12 removed outlier: 6.569A pdb=" N VAL X 10 " --> pdb=" O THR X 108 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'X' and resid 18 through 23 1216 hydrogen bonds defined for protein. 3204 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: 17.26 Time building geometry restraints manager: 9.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 4829 1.32 - 1.45: 9913 1.45 - 1.59: 15219 1.59 - 1.73: 0 1.73 - 1.86: 168 Bond restraints: 30129 Sorted by residual: bond pdb=" CE1 HIS C1048 " pdb=" NE2 HIS C1048 " ideal model delta sigma weight residual 1.321 1.368 -0.047 1.00e-02 1.00e+04 2.19e+01 bond pdb=" C THR C1027 " pdb=" O THR C1027 " ideal model delta sigma weight residual 1.237 1.181 0.055 1.19e-02 7.06e+03 2.16e+01 bond pdb=" CE1 HIS A1048 " pdb=" NE2 HIS A1048 " ideal model delta sigma weight residual 1.321 1.367 -0.046 1.00e-02 1.00e+04 2.11e+01 bond pdb=" CE1 HIS B1048 " pdb=" NE2 HIS B1048 " ideal model delta sigma weight residual 1.321 1.367 -0.046 1.00e-02 1.00e+04 2.08e+01 bond pdb=" C THR B1027 " pdb=" O THR B1027 " ideal model delta sigma weight residual 1.237 1.183 0.053 1.19e-02 7.06e+03 2.00e+01 ... (remaining 30124 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.19: 37899 3.19 - 6.39: 2859 6.39 - 9.58: 212 9.58 - 12.78: 25 12.78 - 15.97: 3 Bond angle restraints: 40998 Sorted by residual: angle pdb=" CA PHE B 486 " pdb=" CB PHE B 486 " pdb=" CG PHE B 486 " ideal model delta sigma weight residual 113.80 122.25 -8.45 1.00e+00 1.00e+00 7.15e+01 angle pdb=" CA PHE A 486 " pdb=" CB PHE A 486 " pdb=" CG PHE A 486 " ideal model delta sigma weight residual 113.80 122.22 -8.42 1.00e+00 1.00e+00 7.10e+01 angle pdb=" CA PHE C 486 " pdb=" CB PHE C 486 " pdb=" CG PHE C 486 " ideal model delta sigma weight residual 113.80 122.22 -8.42 1.00e+00 1.00e+00 7.09e+01 angle pdb=" N ILE B 909 " pdb=" CA ILE B 909 " pdb=" C ILE B 909 " ideal model delta sigma weight residual 112.43 105.51 6.92 9.20e-01 1.18e+00 5.66e+01 angle pdb=" N ILE C 909 " pdb=" CA ILE C 909 " pdb=" C ILE C 909 " ideal model delta sigma weight residual 112.43 105.52 6.91 9.20e-01 1.18e+00 5.64e+01 ... (remaining 40993 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 17025 17.94 - 35.87: 1198 35.87 - 53.81: 198 53.81 - 71.74: 62 71.74 - 89.68: 39 Dihedral angle restraints: 18522 sinusoidal: 7827 harmonic: 10695 Sorted by residual: dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual -86.00 -175.68 89.68 1 1.00e+01 1.00e-02 9.55e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual -86.00 -175.14 89.14 1 1.00e+01 1.00e-02 9.46e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual -86.00 -175.12 89.12 1 1.00e+01 1.00e-02 9.45e+01 ... (remaining 18519 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 3009 0.105 - 0.209: 1350 0.209 - 0.314: 346 0.314 - 0.419: 65 0.419 - 0.523: 15 Chirality restraints: 4785 Sorted by residual: chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.32e+01 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.18e+01 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.10e+01 ... (remaining 4782 not shown) Planarity restraints: 5247 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 1 " 0.231 2.00e-02 2.50e+03 1.94e-01 4.71e+02 pdb=" C7 NAG J 1 " -0.062 2.00e-02 2.50e+03 pdb=" C8 NAG J 1 " 0.160 2.00e-02 2.50e+03 pdb=" N2 NAG J 1 " -0.325 2.00e-02 2.50e+03 pdb=" O7 NAG J 1 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 1 " 0.215 2.00e-02 2.50e+03 1.80e-01 4.06e+02 pdb=" C7 NAG E 1 " -0.057 2.00e-02 2.50e+03 pdb=" C8 NAG E 1 " 0.151 2.00e-02 2.50e+03 pdb=" N2 NAG E 1 " -0.300 2.00e-02 2.50e+03 pdb=" O7 NAG E 1 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG O 1 " 0.212 2.00e-02 2.50e+03 1.78e-01 3.97e+02 pdb=" C7 NAG O 1 " -0.057 2.00e-02 2.50e+03 pdb=" C8 NAG O 1 " 0.150 2.00e-02 2.50e+03 pdb=" N2 NAG O 1 " -0.296 2.00e-02 2.50e+03 pdb=" O7 NAG O 1 " -0.008 2.00e-02 2.50e+03 ... (remaining 5244 not shown) Histogram of nonbonded interaction distances: 1.08 - 1.85: 10 1.85 - 2.61: 281 2.61 - 3.37: 36372 3.37 - 4.14: 73090 4.14 - 4.90: 124434 Nonbonded interactions: 234187 Sorted by model distance: nonbonded pdb=" O PHE A 486 " pdb=" OH TYR U 102 " model vdw 1.083 3.040 nonbonded pdb=" O PHE B 486 " pdb=" OH TYR S 102 " model vdw 1.104 3.040 nonbonded pdb=" O PHE C 486 " pdb=" OH TYR W 102 " model vdw 1.109 3.040 nonbonded pdb=" OG1 THR B 912 " pdb=" NE2 GLN B1106 " model vdw 1.809 3.120 nonbonded pdb=" CD1 ILE U 51 " pdb=" CB MET U 70 " model vdw 1.812 3.860 ... (remaining 234182 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: 0.19 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'S' selection = chain 'U' selection = chain 'W' } ncs_group { reference = chain 'T' selection = chain 'V' selection = chain 'X' } 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: 10.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.290 Check model and map are aligned: 0.230 Set scattering table: 0.280 Process input model: 74.700 Find NCS groups from input model: 2.460 Set up NCS constraints: 0.230 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:3.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 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 : 0.012 0.463 30229 Z= 0.837 Angle : 1.803 15.969 41235 Z= 1.156 Chirality : 0.123 0.523 4785 Planarity : 0.012 0.194 5208 Dihedral : 13.283 87.812 11544 Min Nonbonded Distance : 1.083 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.79 % Favored : 95.12 % Rotamer: Outliers : 1.03 % Allowed : 4.19 % Favored : 94.77 % Cbeta Deviations : 1.49 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 (0.13), residues: 3630 helix: -0.55 (0.17), residues: 666 sheet: -0.07 (0.15), residues: 969 loop : -0.89 (0.13), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.009 TRP S 50 HIS 0.019 0.005 HIS B1064 PHE 0.055 0.010 PHE A 888 TYR 0.067 0.009 TYR W 102 ARG 0.041 0.003 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.01407 ( 39) link_NAG-ASN : angle 4.40258 ( 117) link_BETA1-4 : bond 0.02230 ( 12) link_BETA1-4 : angle 4.43261 ( 36) hydrogen bonds : bond 0.21027 ( 1165) hydrogen bonds : angle 7.98400 ( 3204) SS BOND : bond 0.02681 ( 42) SS BOND : angle 2.82716 ( 84) covalent geometry : bond 0.01028 (30129) covalent geometry : angle 1.78315 (40998) Misc. bond : bond 0.35514 ( 7) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 411 time to evaluate : 3.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LEU cc_start: 0.8160 (mp) cc_final: 0.7854 (mt) REVERT: A 242 LEU cc_start: 0.7676 (mt) cc_final: 0.7227 (mt) REVERT: A 394 ASN cc_start: 0.9154 (m-40) cc_final: 0.8859 (t0) REVERT: A 417 LYS cc_start: 0.9047 (mmtt) cc_final: 0.8805 (mtpt) REVERT: A 979 ASP cc_start: 0.9057 (m-30) cc_final: 0.8640 (t0) REVERT: A 1092 GLU cc_start: 0.9409 (mt-10) cc_final: 0.9012 (pm20) REVERT: B 110 LEU cc_start: 0.8358 (mp) cc_final: 0.8001 (mt) REVERT: B 114 THR cc_start: 0.8889 (t) cc_final: 0.8675 (p) REVERT: B 276 LEU cc_start: 0.9303 (tp) cc_final: 0.9094 (tp) REVERT: B 390 LEU cc_start: 0.8529 (tp) cc_final: 0.8276 (mt) REVERT: B 394 ASN cc_start: 0.9125 (m-40) cc_final: 0.8822 (t0) REVERT: B 979 ASP cc_start: 0.9066 (m-30) cc_final: 0.8629 (t0) REVERT: B 1092 GLU cc_start: 0.9459 (mt-10) cc_final: 0.9168 (pm20) REVERT: C 110 LEU cc_start: 0.8067 (mp) cc_final: 0.7672 (mt) REVERT: C 242 LEU cc_start: 0.7612 (mt) cc_final: 0.7345 (mt) REVERT: C 390 LEU cc_start: 0.8542 (tp) cc_final: 0.8301 (mt) REVERT: C 394 ASN cc_start: 0.9110 (m-40) cc_final: 0.8903 (t0) REVERT: C 417 LYS cc_start: 0.9087 (mmtt) cc_final: 0.8868 (mtpt) REVERT: C 979 ASP cc_start: 0.9114 (m-30) cc_final: 0.8668 (t70) REVERT: C 1092 GLU cc_start: 0.9431 (mt-10) cc_final: 0.9139 (pm20) REVERT: S 89 ASP cc_start: 0.9538 (m-30) cc_final: 0.9254 (p0) REVERT: T 49 MET cc_start: 0.8273 (mmm) cc_final: 0.7858 (mmm) REVERT: U 54 ILE cc_start: 0.9144 (OUTLIER) cc_final: 0.8910 (mp) REVERT: U 82 GLU cc_start: 0.8545 (tt0) cc_final: 0.8266 (tp30) REVERT: U 89 ASP cc_start: 0.9545 (m-30) cc_final: 0.9302 (p0) REVERT: V 49 MET cc_start: 0.8202 (mmm) cc_final: 0.7782 (mmm) REVERT: V 63 ARG cc_start: 0.7734 (ptt90) cc_final: 0.7478 (ptt180) REVERT: W 89 ASP cc_start: 0.9519 (m-30) cc_final: 0.9281 (p0) REVERT: X 49 MET cc_start: 0.8180 (mmm) cc_final: 0.7711 (mmm) REVERT: X 63 ARG cc_start: 0.7658 (ptt90) cc_final: 0.6732 (ppt170) outliers start: 33 outliers final: 3 residues processed: 434 average time/residue: 0.4715 time to fit residues: 306.9867 Evaluate side-chains 186 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 182 time to evaluate : 3.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain U residue 54 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 309 optimal weight: 5.9990 chunk 277 optimal weight: 0.6980 chunk 153 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 187 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 286 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 174 optimal weight: 0.9980 chunk 213 optimal weight: 3.9990 chunk 332 optimal weight: 10.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 207 HIS A 474 GLN B 207 HIS B 321 GLN B 474 GLN C 66 HIS C 207 HIS C 360 ASN C 474 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN ** S 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 43 GLN ** S 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 3 GLN ** U 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 43 GLN ** U 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 3 GLN ** W 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 43 GLN ** W 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 55 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.084924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.054754 restraints weight = 127170.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.056639 restraints weight = 58893.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.057832 restraints weight = 36966.910| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.135 30229 Z= 0.178 Angle : 0.760 24.235 41235 Z= 0.387 Chirality : 0.048 0.272 4785 Planarity : 0.012 0.453 5208 Dihedral : 6.227 114.928 5099 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.40 % Favored : 97.52 % Rotamer: Outliers : 1.56 % Allowed : 8.51 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.22 (0.13), residues: 3630 helix: 1.22 (0.20), residues: 684 sheet: 0.03 (0.14), residues: 1056 loop : -0.73 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP W 104 HIS 0.013 0.001 HIS U 100 PHE 0.029 0.002 PHE B 486 TYR 0.044 0.002 TYR U 102 ARG 0.029 0.001 ARG C 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00578 ( 39) link_NAG-ASN : angle 2.52307 ( 117) link_BETA1-4 : bond 0.00495 ( 12) link_BETA1-4 : angle 2.00781 ( 36) hydrogen bonds : bond 0.06802 ( 1165) hydrogen bonds : angle 6.14053 ( 3204) SS BOND : bond 0.01203 ( 42) SS BOND : angle 1.30359 ( 84) covalent geometry : bond 0.00388 (30129) covalent geometry : angle 0.74514 (40998) Misc. bond : bond 0.00463 ( 7) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 201 time to evaluate : 3.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.7546 (tp) cc_final: 0.7113 (mp) REVERT: A 417 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8477 (mtmt) REVERT: A 505 TYR cc_start: 0.8778 (OUTLIER) cc_final: 0.8463 (t80) REVERT: B 276 LEU cc_start: 0.9390 (tp) cc_final: 0.9184 (tp) REVERT: C 117 LEU cc_start: 0.7673 (tp) cc_final: 0.7188 (mt) REVERT: C 417 LYS cc_start: 0.8928 (mmtt) cc_final: 0.8518 (mtpt) REVERT: C 505 TYR cc_start: 0.8791 (OUTLIER) cc_final: 0.8444 (t80) REVERT: C 900 MET cc_start: 0.8597 (mtp) cc_final: 0.8157 (mtm) REVERT: S 70 MET cc_start: 0.6305 (mpp) cc_final: 0.4780 (mmt) REVERT: T 38 TYR cc_start: 0.6464 (m-80) cc_final: 0.6001 (m-80) REVERT: T 63 ARG cc_start: 0.8180 (ptt180) cc_final: 0.7777 (ptt180) REVERT: T 85 GLU cc_start: 0.7184 (tm-30) cc_final: 0.6512 (mt-10) REVERT: U 70 MET cc_start: 0.6465 (mtt) cc_final: 0.4941 (mmt) REVERT: U 101 THR cc_start: 0.7433 (OUTLIER) cc_final: 0.7209 (m) REVERT: V 38 TYR cc_start: 0.6559 (m-80) cc_final: 0.6314 (m-80) REVERT: V 85 GLU cc_start: 0.7256 (tm-30) cc_final: 0.6695 (mt-10) REVERT: W 70 MET cc_start: 0.7333 (mtt) cc_final: 0.6589 (mtt) REVERT: W 101 THR cc_start: 0.7211 (OUTLIER) cc_final: 0.6927 (m) REVERT: X 38 TYR cc_start: 0.6500 (m-80) cc_final: 0.6214 (m-80) outliers start: 50 outliers final: 15 residues processed: 244 average time/residue: 0.4841 time to fit residues: 177.7633 Evaluate side-chains 151 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 3.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 72 ARG Chi-restraints excluded: chain U residue 72 ARG Chi-restraints excluded: chain U residue 101 THR Chi-restraints excluded: chain V residue 72 THR Chi-restraints excluded: chain W residue 7 SER Chi-restraints excluded: chain W residue 72 ARG Chi-restraints excluded: chain W residue 101 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 144 optimal weight: 10.0000 chunk 71 optimal weight: 9.9990 chunk 158 optimal weight: 1.9990 chunk 210 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 316 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 362 optimal weight: 30.0000 chunk 326 optimal weight: 9.9990 chunk 220 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN B 388 ASN B1135 ASN C 388 ASN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 52 ASN ** S 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 52 ASN ** V 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 52 ASN ** W 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 33 ASN ** 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 = 0.3740 r_free = 0.3740 target = 0.078216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.048246 restraints weight = 129229.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.049897 restraints weight = 63353.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.050892 restraints weight = 40964.321| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 30229 Z= 0.302 Angle : 0.821 26.590 41235 Z= 0.417 Chirality : 0.049 0.337 4785 Planarity : 0.010 0.381 5208 Dihedral : 6.337 154.159 5094 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.82 % Allowed : 8.70 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -0.38 (0.13), residues: 3630 helix: 1.49 (0.21), residues: 639 sheet: -0.09 (0.15), residues: 1038 loop : -0.92 (0.13), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.003 TRP S 104 HIS 0.012 0.002 HIS A1064 PHE 0.030 0.002 PHE C 486 TYR 0.043 0.002 TYR S 102 ARG 0.034 0.001 ARG B 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00595 ( 39) link_NAG-ASN : angle 2.16832 ( 117) link_BETA1-4 : bond 0.00524 ( 12) link_BETA1-4 : angle 1.84620 ( 36) hydrogen bonds : bond 0.07465 ( 1165) hydrogen bonds : angle 6.07411 ( 3204) SS BOND : bond 0.00295 ( 42) SS BOND : angle 1.45508 ( 84) covalent geometry : bond 0.00698 (30129) covalent geometry : angle 0.81023 (40998) Misc. bond : bond 0.00583 ( 7) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 139 time to evaluate : 3.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 505 TYR cc_start: 0.8841 (OUTLIER) cc_final: 0.8632 (t80) REVERT: C 417 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8653 (mtpt) REVERT: C 505 TYR cc_start: 0.8818 (OUTLIER) cc_final: 0.8604 (t80) REVERT: S 70 MET cc_start: 0.6461 (mpp) cc_final: 0.5648 (mmm) REVERT: T 63 ARG cc_start: 0.8177 (ptt180) cc_final: 0.7740 (ptt180) REVERT: T 85 GLU cc_start: 0.7237 (tm-30) cc_final: 0.6695 (mt-10) REVERT: U 70 MET cc_start: 0.6868 (mtt) cc_final: 0.5567 (mtt) REVERT: V 63 ARG cc_start: 0.8192 (ptt180) cc_final: 0.7741 (ptm160) REVERT: W 48 MET cc_start: 0.7090 (mmm) cc_final: 0.6794 (mpp) REVERT: X 63 ARG cc_start: 0.8026 (ptt90) cc_final: 0.7402 (ptt180) outliers start: 90 outliers final: 50 residues processed: 222 average time/residue: 0.4918 time to fit residues: 167.9680 Evaluate side-chains 169 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 116 time to evaluate : 3.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain T residue 51 TYR Chi-restraints excluded: chain U residue 72 ARG Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 51 TYR Chi-restraints excluded: chain X residue 5 THR Chi-restraints excluded: chain X residue 51 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 106 optimal weight: 8.9990 chunk 48 optimal weight: 0.9980 chunk 335 optimal weight: 50.0000 chunk 183 optimal weight: 4.9990 chunk 297 optimal weight: 3.9990 chunk 328 optimal weight: 3.9990 chunk 285 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 chunk 259 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 3 GLN ** W 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.078701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.049107 restraints weight = 129118.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.050782 restraints weight = 62565.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.051863 restraints weight = 40328.883| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.4394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 30229 Z= 0.186 Angle : 0.667 24.618 41235 Z= 0.336 Chirality : 0.046 0.215 4785 Planarity : 0.009 0.273 5208 Dihedral : 5.983 160.304 5094 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.91 % Allowed : 10.74 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -0.29 (0.13), residues: 3630 helix: 1.82 (0.21), residues: 660 sheet: -0.08 (0.15), residues: 1056 loop : -0.97 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP S 104 HIS 0.004 0.001 HIS A1064 PHE 0.020 0.002 PHE A 486 TYR 0.037 0.001 TYR S 102 ARG 0.027 0.001 ARG C 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00421 ( 39) link_NAG-ASN : angle 1.83656 ( 117) link_BETA1-4 : bond 0.00425 ( 12) link_BETA1-4 : angle 1.55384 ( 36) hydrogen bonds : bond 0.05923 ( 1165) hydrogen bonds : angle 5.58994 ( 3204) SS BOND : bond 0.00240 ( 42) SS BOND : angle 1.20513 ( 84) covalent geometry : bond 0.00435 (30129) covalent geometry : angle 0.65779 (40998) Misc. bond : bond 0.00585 ( 7) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 119 time to evaluate : 3.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 505 TYR cc_start: 0.8782 (OUTLIER) cc_final: 0.8528 (t80) REVERT: B 403 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.7940 (ttm-80) REVERT: C 505 TYR cc_start: 0.8765 (OUTLIER) cc_final: 0.8511 (t80) REVERT: S 19 LYS cc_start: 0.7857 (OUTLIER) cc_final: 0.7318 (tptp) REVERT: S 70 MET cc_start: 0.6077 (mpp) cc_final: 0.4697 (mmt) REVERT: S 82 GLU cc_start: 0.8118 (tt0) cc_final: 0.7829 (tm-30) REVERT: T 63 ARG cc_start: 0.8249 (ptt180) cc_final: 0.7805 (ptt180) REVERT: T 85 GLU cc_start: 0.7216 (tm-30) cc_final: 0.6704 (mt-10) REVERT: U 70 MET cc_start: 0.6739 (mtt) cc_final: 0.5101 (mtt) REVERT: U 82 GLU cc_start: 0.8254 (tt0) cc_final: 0.7878 (tm-30) outliers start: 61 outliers final: 29 residues processed: 175 average time/residue: 0.4869 time to fit residues: 131.2187 Evaluate side-chains 138 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 105 time to evaluate : 3.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain S residue 13 LYS Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain U residue 13 LYS Chi-restraints excluded: chain U residue 72 ARG Chi-restraints excluded: chain X residue 51 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 299 optimal weight: 1.9990 chunk 171 optimal weight: 0.3980 chunk 174 optimal weight: 0.8980 chunk 337 optimal weight: 3.9990 chunk 153 optimal weight: 7.9990 chunk 312 optimal weight: 40.0000 chunk 61 optimal weight: 5.9990 chunk 139 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 chunk 69 optimal weight: 0.1980 chunk 44 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 52 ASN S 100 HIS ** U 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 100 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.079405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.049948 restraints weight = 128196.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.051648 restraints weight = 61964.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 71)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.052730 restraints weight = 39746.083| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.4616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 30229 Z= 0.122 Angle : 0.606 22.190 41235 Z= 0.305 Chirality : 0.044 0.200 4785 Planarity : 0.007 0.217 5208 Dihedral : 5.716 170.357 5094 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.82 % Allowed : 11.39 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -0.10 (0.14), residues: 3630 helix: 2.10 (0.21), residues: 663 sheet: 0.07 (0.15), residues: 1044 loop : -0.92 (0.13), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP U 104 HIS 0.003 0.001 HIS B1064 PHE 0.012 0.001 PHE A 168 TYR 0.031 0.001 TYR W 102 ARG 0.024 0.001 ARG B 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00356 ( 39) link_NAG-ASN : angle 1.68188 ( 117) link_BETA1-4 : bond 0.00348 ( 12) link_BETA1-4 : angle 1.46876 ( 36) hydrogen bonds : bond 0.05214 ( 1165) hydrogen bonds : angle 5.28118 ( 3204) SS BOND : bond 0.00215 ( 42) SS BOND : angle 1.01231 ( 84) covalent geometry : bond 0.00272 (30129) covalent geometry : angle 0.59773 (40998) Misc. bond : bond 0.00381 ( 7) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 118 time to evaluate : 3.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.8014 (ttm-80) REVERT: A 505 TYR cc_start: 0.8784 (OUTLIER) cc_final: 0.8317 (t80) REVERT: B 117 LEU cc_start: 0.7905 (tp) cc_final: 0.7486 (mt) REVERT: B 403 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.8113 (ttm-80) REVERT: C 403 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7928 (ttm-80) REVERT: C 505 TYR cc_start: 0.8779 (OUTLIER) cc_final: 0.8345 (t80) REVERT: S 19 LYS cc_start: 0.7713 (OUTLIER) cc_final: 0.7161 (tptp) REVERT: S 70 MET cc_start: 0.6182 (mpp) cc_final: 0.5578 (mmm) REVERT: S 82 GLU cc_start: 0.8096 (tt0) cc_final: 0.7850 (tm-30) REVERT: T 85 GLU cc_start: 0.7281 (tm-30) cc_final: 0.6804 (mt-10) REVERT: V 49 MET cc_start: 0.6955 (ptt) cc_final: 0.6565 (ptt) outliers start: 58 outliers final: 27 residues processed: 175 average time/residue: 0.4551 time to fit residues: 125.9338 Evaluate side-chains 138 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 105 time to evaluate : 3.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 100 HIS Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 72 ARG Chi-restraints excluded: chain W residue 51 ILE Chi-restraints excluded: chain W residue 100 HIS Chi-restraints excluded: chain X residue 51 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 285 optimal weight: 4.9990 chunk 232 optimal weight: 0.9990 chunk 282 optimal weight: 3.9990 chunk 235 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 144 optimal weight: 8.9990 chunk 299 optimal weight: 4.9990 chunk 180 optimal weight: 2.9990 chunk 347 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 100 HIS W 105 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.079256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.049810 restraints weight = 127003.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.051507 restraints weight = 61359.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.052592 restraints weight = 39370.261| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.4805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 30229 Z= 0.137 Angle : 0.611 23.522 41235 Z= 0.306 Chirality : 0.044 0.199 4785 Planarity : 0.007 0.321 5208 Dihedral : 5.567 166.755 5094 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.75 % Allowed : 11.33 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.08 (0.14), residues: 3630 helix: 2.19 (0.21), residues: 666 sheet: 0.05 (0.15), residues: 1071 loop : -0.94 (0.14), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP U 104 HIS 0.020 0.001 HIS W 100 PHE 0.012 0.001 PHE C 543 TYR 0.030 0.001 TYR U 102 ARG 0.025 0.001 ARG A 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00312 ( 39) link_NAG-ASN : angle 1.64652 ( 117) link_BETA1-4 : bond 0.00267 ( 12) link_BETA1-4 : angle 1.45160 ( 36) hydrogen bonds : bond 0.05131 ( 1165) hydrogen bonds : angle 5.20650 ( 3204) SS BOND : bond 0.00303 ( 42) SS BOND : angle 1.29802 ( 84) covalent geometry : bond 0.00313 (30129) covalent geometry : angle 0.60214 (40998) Misc. bond : bond 0.00476 ( 7) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 119 time to evaluate : 3.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.7977 (tp) cc_final: 0.7581 (mp) REVERT: A 403 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7962 (ttm-80) REVERT: A 505 TYR cc_start: 0.8800 (OUTLIER) cc_final: 0.8303 (t80) REVERT: A 532 ASN cc_start: 0.9029 (t0) cc_final: 0.8815 (t0) REVERT: B 117 LEU cc_start: 0.7994 (tp) cc_final: 0.7558 (mp) REVERT: B 403 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.8039 (ttm-80) REVERT: B 532 ASN cc_start: 0.9054 (t0) cc_final: 0.8765 (t0) REVERT: C 403 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7917 (ttm-80) REVERT: C 505 TYR cc_start: 0.8755 (OUTLIER) cc_final: 0.8277 (t80) REVERT: S 19 LYS cc_start: 0.7770 (OUTLIER) cc_final: 0.7276 (tptp) REVERT: S 70 MET cc_start: 0.5864 (mpp) cc_final: 0.5279 (mmm) REVERT: S 82 GLU cc_start: 0.8097 (tt0) cc_final: 0.7814 (tm-30) REVERT: S 98 ARG cc_start: 0.6462 (tmm-80) cc_final: 0.6078 (ttp80) REVERT: T 85 GLU cc_start: 0.7273 (tm-30) cc_final: 0.6808 (mt-10) REVERT: V 63 ARG cc_start: 0.7919 (ptt180) cc_final: 0.7238 (ptm160) outliers start: 56 outliers final: 33 residues processed: 172 average time/residue: 0.4546 time to fit residues: 123.0787 Evaluate side-chains 147 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 108 time to evaluate : 3.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 72 ARG Chi-restraints excluded: chain U residue 72 ARG Chi-restraints excluded: chain V residue 51 TYR Chi-restraints excluded: chain W residue 51 ILE Chi-restraints excluded: chain X residue 51 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 323 optimal weight: 9.9990 chunk 183 optimal weight: 4.9990 chunk 259 optimal weight: 0.0000 chunk 261 optimal weight: 4.9990 chunk 320 optimal weight: 9.9990 chunk 210 optimal weight: 0.8980 chunk 150 optimal weight: 8.9990 chunk 118 optimal weight: 6.9990 chunk 365 optimal weight: 6.9990 chunk 206 optimal weight: 9.9990 chunk 134 optimal weight: 1.9990 overall best weight: 2.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 GLN C 901 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 100 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.076371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.046876 restraints weight = 128203.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.048415 restraints weight = 66722.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.049395 restraints weight = 44593.257| |-----------------------------------------------------------------------------| r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.5195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 30229 Z= 0.216 Angle : 0.655 21.987 41235 Z= 0.332 Chirality : 0.045 0.213 4785 Planarity : 0.007 0.231 5208 Dihedral : 5.862 165.964 5094 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.00 % Allowed : 11.11 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -0.24 (0.14), residues: 3630 helix: 2.02 (0.21), residues: 663 sheet: -0.02 (0.15), residues: 1050 loop : -1.04 (0.13), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP U 104 HIS 0.008 0.001 HIS W 100 PHE 0.015 0.001 PHE B 92 TYR 0.018 0.002 TYR W 102 ARG 0.024 0.001 ARG B 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00376 ( 39) link_NAG-ASN : angle 1.77912 ( 117) link_BETA1-4 : bond 0.00252 ( 12) link_BETA1-4 : angle 1.54288 ( 36) hydrogen bonds : bond 0.06002 ( 1165) hydrogen bonds : angle 5.40544 ( 3204) SS BOND : bond 0.00400 ( 42) SS BOND : angle 1.47948 ( 84) covalent geometry : bond 0.00503 (30129) covalent geometry : angle 0.64507 (40998) Misc. bond : bond 0.00481 ( 7) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 111 time to evaluate : 3.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.8031 (ttm-80) REVERT: A 505 TYR cc_start: 0.8958 (OUTLIER) cc_final: 0.8334 (t80) REVERT: A 532 ASN cc_start: 0.9113 (t0) cc_final: 0.8877 (t0) REVERT: B 117 LEU cc_start: 0.8221 (tp) cc_final: 0.7679 (mp) REVERT: B 403 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.8011 (ttm-80) REVERT: B 532 ASN cc_start: 0.9043 (t0) cc_final: 0.8797 (t0) REVERT: C 403 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7927 (ttm-80) REVERT: C 505 TYR cc_start: 0.8940 (OUTLIER) cc_final: 0.8369 (t80) REVERT: S 70 MET cc_start: 0.6213 (mpp) cc_final: 0.5428 (mmm) REVERT: W 98 ARG cc_start: 0.6499 (tmm-80) cc_final: 0.5885 (tmm-80) outliers start: 64 outliers final: 37 residues processed: 173 average time/residue: 0.4263 time to fit residues: 118.8336 Evaluate side-chains 148 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 106 time to evaluate : 3.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain S residue 72 ARG Chi-restraints excluded: chain U residue 72 ARG Chi-restraints excluded: chain V residue 51 TYR Chi-restraints excluded: chain W residue 51 ILE Chi-restraints excluded: chain X residue 51 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 98 optimal weight: 3.9990 chunk 236 optimal weight: 9.9990 chunk 292 optimal weight: 0.9990 chunk 151 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 207 optimal weight: 10.0000 chunk 223 optimal weight: 6.9990 chunk 214 optimal weight: 0.8980 chunk 36 optimal weight: 9.9990 chunk 74 optimal weight: 1.9990 chunk 281 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 901 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN ** S 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 100 HIS W 3 GLN X 81 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.075975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.046947 restraints weight = 127627.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.049224 restraints weight = 67602.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.049433 restraints weight = 37815.314| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.5416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 30229 Z= 0.171 Angle : 0.607 18.778 41235 Z= 0.310 Chirality : 0.045 0.192 4785 Planarity : 0.007 0.203 5208 Dihedral : 5.772 164.611 5094 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.60 % Allowed : 11.92 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -0.16 (0.14), residues: 3630 helix: 2.21 (0.21), residues: 660 sheet: -0.03 (0.15), residues: 1053 loop : -0.98 (0.14), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP S 104 HIS 0.005 0.001 HIS B1064 PHE 0.031 0.001 PHE B 486 TYR 0.021 0.001 TYR C 904 ARG 0.020 0.001 ARG A 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00312 ( 39) link_NAG-ASN : angle 1.65736 ( 117) link_BETA1-4 : bond 0.00255 ( 12) link_BETA1-4 : angle 1.45835 ( 36) hydrogen bonds : bond 0.05520 ( 1165) hydrogen bonds : angle 5.27647 ( 3204) SS BOND : bond 0.00283 ( 42) SS BOND : angle 1.35075 ( 84) covalent geometry : bond 0.00396 (30129) covalent geometry : angle 0.59806 (40998) Misc. bond : bond 0.00427 ( 7) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 112 time to evaluate : 3.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.8139 (ttm-80) REVERT: A 505 TYR cc_start: 0.8908 (OUTLIER) cc_final: 0.8300 (t80) REVERT: A 532 ASN cc_start: 0.8948 (t0) cc_final: 0.8735 (t0) REVERT: B 117 LEU cc_start: 0.8142 (tp) cc_final: 0.7626 (mp) REVERT: B 403 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.8064 (ttm-80) REVERT: B 532 ASN cc_start: 0.9024 (t0) cc_final: 0.8785 (t0) REVERT: C 403 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.8039 (ttm-80) REVERT: C 434 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8684 (tp) REVERT: C 505 TYR cc_start: 0.8911 (OUTLIER) cc_final: 0.8320 (t80) REVERT: S 70 MET cc_start: 0.5856 (mpp) cc_final: 0.5472 (mmm) REVERT: U 51 ILE cc_start: 0.4630 (OUTLIER) cc_final: 0.4280 (mt) REVERT: U 70 MET cc_start: 0.6293 (mmt) cc_final: 0.5288 (mmm) REVERT: X 63 ARG cc_start: 0.7572 (ppt-90) cc_final: 0.7368 (ppt-90) REVERT: X 81 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7881 (pm20) outliers start: 51 outliers final: 33 residues processed: 161 average time/residue: 0.4392 time to fit residues: 113.1976 Evaluate side-chains 147 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 106 time to evaluate : 2.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain S residue 72 ARG Chi-restraints excluded: chain U residue 51 ILE Chi-restraints excluded: chain U residue 72 ARG Chi-restraints excluded: chain V residue 51 TYR Chi-restraints excluded: chain W residue 51 ILE Chi-restraints excluded: chain X residue 51 TYR Chi-restraints excluded: chain X residue 81 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 272 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 263 optimal weight: 4.9990 chunk 118 optimal weight: 6.9990 chunk 75 optimal weight: 0.6980 chunk 156 optimal weight: 6.9990 chunk 313 optimal weight: 30.0000 chunk 236 optimal weight: 10.0000 chunk 248 optimal weight: 6.9990 chunk 353 optimal weight: 2.9990 chunk 201 optimal weight: 3.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 ASN C 901 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 100 HIS X 81 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.075244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.045238 restraints weight = 127923.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.046860 restraints weight = 64786.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.047908 restraints weight = 42883.039| |-----------------------------------------------------------------------------| r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.5633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 30229 Z= 0.213 Angle : 0.653 19.623 41235 Z= 0.331 Chirality : 0.046 0.424 4785 Planarity : 0.007 0.186 5208 Dihedral : 5.960 164.828 5094 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.60 % Allowed : 12.27 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.28 (0.14), residues: 3630 helix: 2.11 (0.21), residues: 660 sheet: -0.08 (0.15), residues: 1026 loop : -1.07 (0.13), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP S 104 HIS 0.006 0.001 HIS A1064 PHE 0.033 0.002 PHE B 486 TYR 0.018 0.001 TYR U 102 ARG 0.031 0.001 ARG B 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00329 ( 39) link_NAG-ASN : angle 1.73944 ( 117) link_BETA1-4 : bond 0.00214 ( 12) link_BETA1-4 : angle 1.50066 ( 36) hydrogen bonds : bond 0.05791 ( 1165) hydrogen bonds : angle 5.35778 ( 3204) SS BOND : bond 0.00315 ( 42) SS BOND : angle 1.46138 ( 84) covalent geometry : bond 0.00495 (30129) covalent geometry : angle 0.64372 (40998) Misc. bond : bond 0.00360 ( 7) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 114 time to evaluate : 3.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.8106 (ttm-80) REVERT: A 505 TYR cc_start: 0.8972 (OUTLIER) cc_final: 0.8282 (t80) REVERT: B 117 LEU cc_start: 0.8289 (tp) cc_final: 0.7711 (mp) REVERT: B 403 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.8028 (ttm-80) REVERT: C 403 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7966 (ttm-80) REVERT: C 434 ILE cc_start: 0.9056 (OUTLIER) cc_final: 0.8704 (tp) REVERT: C 505 TYR cc_start: 0.8961 (OUTLIER) cc_final: 0.8313 (t80) REVERT: S 70 MET cc_start: 0.6148 (mpp) cc_final: 0.5564 (mmm) REVERT: U 51 ILE cc_start: 0.4540 (OUTLIER) cc_final: 0.4234 (mt) REVERT: U 70 MET cc_start: 0.6772 (mmt) cc_final: 0.5567 (mmm) outliers start: 51 outliers final: 38 residues processed: 163 average time/residue: 0.4468 time to fit residues: 116.1285 Evaluate side-chains 151 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 106 time to evaluate : 3.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain S residue 72 ARG Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 51 ILE Chi-restraints excluded: chain U residue 72 ARG Chi-restraints excluded: chain V residue 51 TYR Chi-restraints excluded: chain W residue 7 SER Chi-restraints excluded: chain W residue 51 ILE Chi-restraints excluded: chain X residue 51 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 315 optimal weight: 8.9990 chunk 111 optimal weight: 10.0000 chunk 357 optimal weight: 50.0000 chunk 184 optimal weight: 0.0980 chunk 71 optimal weight: 0.0050 chunk 279 optimal weight: 0.4980 chunk 61 optimal weight: 2.9990 chunk 126 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 290 optimal weight: 0.8980 chunk 127 optimal weight: 7.9990 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 901 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 41 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.077184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.048052 restraints weight = 128644.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.049693 restraints weight = 63869.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 74)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.050748 restraints weight = 41615.206| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.5745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 30229 Z= 0.117 Angle : 0.599 21.272 41235 Z= 0.303 Chirality : 0.045 0.321 4785 Planarity : 0.006 0.165 5208 Dihedral : 5.725 160.765 5094 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.28 % Allowed : 12.77 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -0.02 (0.14), residues: 3630 helix: 2.40 (0.21), residues: 660 sheet: 0.02 (0.15), residues: 1047 loop : -0.89 (0.14), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP U 104 HIS 0.003 0.001 HIS B1064 PHE 0.030 0.001 PHE C 486 TYR 0.019 0.001 TYR B 266 ARG 0.023 0.001 ARG A 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00341 ( 39) link_NAG-ASN : angle 1.57161 ( 117) link_BETA1-4 : bond 0.00408 ( 12) link_BETA1-4 : angle 1.39692 ( 36) hydrogen bonds : bond 0.04991 ( 1165) hydrogen bonds : angle 5.10987 ( 3204) SS BOND : bond 0.00561 ( 42) SS BOND : angle 1.28451 ( 84) covalent geometry : bond 0.00258 (30129) covalent geometry : angle 0.59055 (40998) Misc. bond : bond 0.00361 ( 7) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 117 time to evaluate : 3.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.8145 (ttm-80) REVERT: A 505 TYR cc_start: 0.8863 (OUTLIER) cc_final: 0.8235 (t80) REVERT: B 117 LEU cc_start: 0.8278 (tp) cc_final: 0.7717 (mp) REVERT: C 117 LEU cc_start: 0.8200 (tp) cc_final: 0.7707 (mp) REVERT: C 403 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7970 (ttm-80) REVERT: C 434 ILE cc_start: 0.9083 (OUTLIER) cc_final: 0.8758 (tp) REVERT: C 505 TYR cc_start: 0.8879 (OUTLIER) cc_final: 0.8243 (t80) REVERT: S 70 MET cc_start: 0.6036 (mpp) cc_final: 0.5640 (mmm) REVERT: U 48 MET cc_start: 0.6541 (mmm) cc_final: 0.6317 (mmm) REVERT: U 51 ILE cc_start: 0.4346 (OUTLIER) cc_final: 0.4015 (mt) REVERT: U 70 MET cc_start: 0.6044 (mmt) cc_final: 0.4941 (mmm) REVERT: V 49 MET cc_start: 0.7047 (ptt) cc_final: 0.6786 (ptt) outliers start: 41 outliers final: 30 residues processed: 156 average time/residue: 0.4112 time to fit residues: 103.6885 Evaluate side-chains 145 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 109 time to evaluate : 3.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain S residue 72 ARG Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 51 ILE Chi-restraints excluded: chain U residue 72 ARG Chi-restraints excluded: chain V residue 51 TYR Chi-restraints excluded: chain W residue 51 ILE Chi-restraints excluded: chain X residue 51 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 221 optimal weight: 7.9990 chunk 260 optimal weight: 2.9990 chunk 286 optimal weight: 0.8980 chunk 270 optimal weight: 0.6980 chunk 142 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 chunk 137 optimal weight: 6.9990 chunk 129 optimal weight: 0.9990 chunk 165 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN ** S 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 55 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.076041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.047097 restraints weight = 126085.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.049322 restraints weight = 66924.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.049488 restraints weight = 37738.830| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.5879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 30229 Z= 0.146 Angle : 0.602 19.583 41235 Z= 0.304 Chirality : 0.044 0.263 4785 Planarity : 0.006 0.161 5208 Dihedral : 5.745 161.167 5094 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.25 % Allowed : 12.77 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -0.02 (0.14), residues: 3630 helix: 2.42 (0.21), residues: 660 sheet: 0.01 (0.15), residues: 1050 loop : -0.90 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP U 104 HIS 0.004 0.001 HIS B1064 PHE 0.029 0.001 PHE B 486 TYR 0.011 0.001 TYR B1067 ARG 0.032 0.001 ARG C 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00260 ( 39) link_NAG-ASN : angle 1.60095 ( 117) link_BETA1-4 : bond 0.00235 ( 12) link_BETA1-4 : angle 1.43144 ( 36) hydrogen bonds : bond 0.05083 ( 1165) hydrogen bonds : angle 5.10614 ( 3204) SS BOND : bond 0.00404 ( 42) SS BOND : angle 1.30790 ( 84) covalent geometry : bond 0.00338 (30129) covalent geometry : angle 0.59285 (40998) Misc. bond : bond 0.00336 ( 7) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11057.15 seconds wall clock time: 194 minutes 26.68 seconds (11666.68 seconds total)