Starting phenix.real_space_refine on Sat May 24 22:37:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jyk_36724/05_2025/8jyk_36724.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jyk_36724/05_2025/8jyk_36724.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jyk_36724/05_2025/8jyk_36724.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jyk_36724/05_2025/8jyk_36724.map" model { file = "/net/cci-nas-00/data/ceres_data/8jyk_36724/05_2025/8jyk_36724.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jyk_36724/05_2025/8jyk_36724.cif" } resolution = 2.59 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= 0.001 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 111 5.16 5 C 16341 2.51 5 N 4203 2.21 5 O 4983 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 25638 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 8294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8294 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 57, 'TRANS': 1003} Chain breaks: 6 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" 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: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "E" Number of atoms: 8294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8294 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 57, 'TRANS': 1003} Chain breaks: 6 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: "E" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "I" Number of atoms: 8294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8294 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 57, 'TRANS': 1003} Chain breaks: 6 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: "I" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 15.14, per 1000 atoms: 0.59 Number of scatterers: 25638 At special positions: 0 Unit cell: (137.685, 130.65, 164.82, 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 111 16.00 O 4983 8.00 N 4203 7.00 C 16341 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=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.04 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.04 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.04 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.03 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.03 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.02 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E 840 " - pdb=" SG CYS E 851 " distance=2.03 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.03 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 166 " distance=2.04 Simple disulfide: pdb=" SG CYS I 291 " - pdb=" SG CYS I 301 " distance=2.03 Simple disulfide: pdb=" SG CYS I 336 " - pdb=" SG CYS I 361 " distance=2.03 Simple disulfide: pdb=" SG CYS I 379 " - pdb=" SG CYS I 432 " distance=2.03 Simple disulfide: pdb=" SG CYS I 391 " - pdb=" SG CYS I 525 " distance=2.04 Simple disulfide: pdb=" SG CYS I 480 " - pdb=" SG CYS I 488 " distance=2.03 Simple disulfide: pdb=" SG CYS I 538 " - pdb=" SG CYS I 590 " distance=2.04 Simple disulfide: pdb=" SG CYS I 617 " - pdb=" SG CYS I 649 " distance=2.03 Simple disulfide: pdb=" SG CYS I 662 " - pdb=" SG CYS I 671 " distance=2.03 Simple disulfide: pdb=" SG CYS I 738 " - pdb=" SG CYS I 760 " distance=2.03 Simple disulfide: pdb=" SG CYS I 743 " - pdb=" SG CYS I 749 " distance=2.03 Simple disulfide: pdb=" SG CYS I 840 " - pdb=" SG CYS I 851 " distance=2.03 Simple disulfide: pdb=" SG CYS I1032 " - pdb=" SG CYS I1043 " distance=2.03 Simple disulfide: pdb=" SG CYS I1082 " - pdb=" SG CYS I1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 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-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG A1311 " - " ASN A1134 " " NAG A1312 " - " ASN A 616 " " NAG B 1 " - " ASN A 717 " " NAG C 1 " - " ASN A 801 " " NAG D 1 " - " ASN A1098 " " NAG E1301 " - " ASN E 61 " " NAG E1302 " - " ASN E 122 " " NAG E1303 " - " ASN E 165 " " NAG E1304 " - " ASN E 234 " " NAG E1305 " - " ASN E 282 " " NAG E1306 " - " ASN E 331 " " NAG E1307 " - " ASN E 343 " " NAG E1308 " - " ASN E 657 " " NAG E1309 " - " ASN E 709 " " NAG E1310 " - " ASN E1074 " " NAG E1311 " - " ASN E1134 " " NAG E1312 " - " ASN E 616 " " NAG F 1 " - " ASN E 717 " " NAG G 1 " - " ASN E 801 " " NAG H 1 " - " ASN E1098 " " NAG I1301 " - " ASN I 61 " " NAG I1302 " - " ASN I 122 " " NAG I1303 " - " ASN I 165 " " NAG I1304 " - " ASN I 234 " " NAG I1305 " - " ASN I 282 " " NAG I1306 " - " ASN I 331 " " NAG I1307 " - " ASN I 343 " " NAG I1308 " - " ASN I 657 " " NAG I1309 " - " ASN I 709 " " NAG I1310 " - " ASN I1074 " " NAG I1311 " - " ASN I1134 " " NAG I1312 " - " ASN I 616 " " NAG J 1 " - " ASN I 717 " " NAG K 1 " - " ASN I 801 " " NAG L 1 " - " ASN I1098 " Time building additional restraints: 6.99 Conformation dependent library (CDL) restraints added in 3.6 seconds 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5970 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 42 sheets defined 25.6% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.55 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 342 removed outlier: 4.074A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 337 through 342' Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.752A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.680A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.822A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.747A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.563A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.588A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 843 removed outlier: 4.271A pdb=" N ASP A 843 " --> pdb=" O ASP A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 855 removed outlier: 3.579A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.068A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.177A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.591A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.505A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (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 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.635A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 304 Processing helix chain 'E' and resid 337 through 342 removed outlier: 4.073A pdb=" N VAL E 341 " --> pdb=" O PRO E 337 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE E 342 " --> pdb=" O PHE E 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 337 through 342' Processing helix chain 'E' and resid 364 through 371 removed outlier: 3.752A pdb=" N VAL E 367 " --> pdb=" O ASP E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 387 Processing helix chain 'E' and resid 403 through 410 removed outlier: 3.680A pdb=" N VAL E 407 " --> pdb=" O GLY E 404 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N SER E 408 " --> pdb=" O ASN E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 502 through 506 removed outlier: 3.822A pdb=" N GLN E 506 " --> pdb=" O VAL E 503 " (cutoff:3.500A) Processing helix chain 'E' and resid 737 through 744 Processing helix chain 'E' and resid 746 through 754 removed outlier: 3.747A pdb=" N SER E 750 " --> pdb=" O SER E 746 " (cutoff:3.500A) Processing helix chain 'E' and resid 758 through 783 removed outlier: 3.563A pdb=" N GLN E 762 " --> pdb=" O SER E 758 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP E 775 " --> pdb=" O ALA E 771 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 826 removed outlier: 3.587A pdb=" N VAL E 826 " --> pdb=" O LEU E 822 " (cutoff:3.500A) Processing helix chain 'E' and resid 835 through 843 removed outlier: 4.271A pdb=" N ASP E 843 " --> pdb=" O ASP E 839 " (cutoff:3.500A) Processing helix chain 'E' and resid 848 through 855 removed outlier: 3.578A pdb=" N ALA E 852 " --> pdb=" O ASP E 848 " (cutoff:3.500A) Processing helix chain 'E' and resid 866 through 885 Processing helix chain 'E' and resid 886 through 891 removed outlier: 4.067A pdb=" N GLY E 891 " --> pdb=" O PHE E 888 " (cutoff:3.500A) Processing helix chain 'E' and resid 897 through 909 Processing helix chain 'E' and resid 912 through 918 removed outlier: 4.176A pdb=" N LEU E 916 " --> pdb=" O THR E 912 " (cutoff:3.500A) Processing helix chain 'E' and resid 919 through 941 removed outlier: 3.591A pdb=" N ILE E 934 " --> pdb=" O ALA E 930 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLN E 935 " --> pdb=" O ILE E 931 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASP E 936 " --> pdb=" O GLY E 932 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR E 941 " --> pdb=" O SER E 937 " (cutoff:3.500A) Processing helix chain 'E' and resid 945 through 965 removed outlier: 3.505A pdb=" N GLN E 949 " --> pdb=" O LEU E 945 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL E 951 " --> pdb=" O LYS E 947 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL E 952 " --> pdb=" O LEU E 948 " (cutoff:3.500A) Processing helix chain 'E' and resid 966 through 968 No H-bonds generated for 'chain 'E' and resid 966 through 968' Processing helix chain 'E' and resid 976 through 984 Processing helix chain 'E' and resid 985 through 1033 removed outlier: 4.635A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN E 992 " --> pdb=" O GLU E 988 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG E 995 " --> pdb=" O VAL E 991 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU E 996 " --> pdb=" O GLN E 992 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL E1033 " --> pdb=" O MET E1029 " (cutoff:3.500A) Processing helix chain 'I' and resid 294 through 304 Processing helix chain 'I' and resid 337 through 342 removed outlier: 4.073A pdb=" N VAL I 341 " --> pdb=" O PRO I 337 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE I 342 " --> pdb=" O PHE I 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 337 through 342' Processing helix chain 'I' and resid 364 through 371 removed outlier: 3.751A pdb=" N VAL I 367 " --> pdb=" O ASP I 364 " (cutoff:3.500A) Processing helix chain 'I' and resid 383 through 387 Processing helix chain 'I' and resid 403 through 410 removed outlier: 3.680A pdb=" N VAL I 407 " --> pdb=" O GLY I 404 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N SER I 408 " --> pdb=" O ASN I 405 " (cutoff:3.500A) Processing helix chain 'I' and resid 416 through 422 Processing helix chain 'I' and resid 502 through 506 removed outlier: 3.822A pdb=" N GLN I 506 " --> pdb=" O VAL I 503 " (cutoff:3.500A) Processing helix chain 'I' and resid 737 through 744 Processing helix chain 'I' and resid 746 through 754 removed outlier: 3.747A pdb=" N SER I 750 " --> pdb=" O SER I 746 " (cutoff:3.500A) Processing helix chain 'I' and resid 758 through 783 removed outlier: 3.563A pdb=" N GLN I 762 " --> pdb=" O SER I 758 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP I 775 " --> pdb=" O ALA I 771 " (cutoff:3.500A) Processing helix chain 'I' and resid 816 through 826 removed outlier: 3.588A pdb=" N VAL I 826 " --> pdb=" O LEU I 822 " (cutoff:3.500A) Processing helix chain 'I' and resid 835 through 843 removed outlier: 4.271A pdb=" N ASP I 843 " --> pdb=" O ASP I 839 " (cutoff:3.500A) Processing helix chain 'I' and resid 848 through 855 removed outlier: 3.578A pdb=" N ALA I 852 " --> pdb=" O ASP I 848 " (cutoff:3.500A) Processing helix chain 'I' and resid 866 through 885 Processing helix chain 'I' and resid 886 through 891 removed outlier: 4.067A pdb=" N GLY I 891 " --> pdb=" O PHE I 888 " (cutoff:3.500A) Processing helix chain 'I' and resid 897 through 909 Processing helix chain 'I' and resid 912 through 918 removed outlier: 4.177A pdb=" N LEU I 916 " --> pdb=" O THR I 912 " (cutoff:3.500A) Processing helix chain 'I' and resid 919 through 941 removed outlier: 3.591A pdb=" N ILE I 934 " --> pdb=" O ALA I 930 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLN I 935 " --> pdb=" O ILE I 931 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASP I 936 " --> pdb=" O GLY I 932 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR I 941 " --> pdb=" O SER I 937 " (cutoff:3.500A) Processing helix chain 'I' and resid 945 through 965 removed outlier: 3.505A pdb=" N GLN I 949 " --> pdb=" O LEU I 945 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL I 951 " --> pdb=" O LYS I 947 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL I 952 " --> pdb=" O LEU I 948 " (cutoff:3.500A) Processing helix chain 'I' and resid 966 through 968 No H-bonds generated for 'chain 'I' and resid 966 through 968' Processing helix chain 'I' and resid 976 through 984 Processing helix chain 'I' and resid 985 through 1033 removed outlier: 4.635A pdb=" N VAL I 991 " --> pdb=" O PRO I 987 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN I 992 " --> pdb=" O GLU I 988 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG I 995 " --> pdb=" O VAL I 991 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU I 996 " --> pdb=" O GLN I 992 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL I1033 " --> pdb=" O MET I1029 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 23 through 30 removed outlier: 8.378A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.934A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 140 through 141 removed outlier: 3.721A pdb=" N LEU A 241 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE A 106 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.245A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.538A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.523A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=10, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.030A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.879A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.600A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=14, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=15, first strand: chain 'E' and resid 23 through 30 removed outlier: 8.377A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N PHE E 201 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASP E 228 " --> pdb=" O PHE E 201 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE E 203 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N HIS E 207 " --> pdb=" O ALA E 222 " (cutoff:3.500A) removed outlier: 8.995A pdb=" N ALA E 222 " --> pdb=" O HIS E 207 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL E 36 " --> pdb=" O LEU E 223 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'E' and resid 48 through 55 removed outlier: 3.934A pdb=" N ASP E 287 " --> pdb=" O LYS E 278 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'E' and resid 140 through 141 removed outlier: 3.722A pdb=" N LEU E 241 " --> pdb=" O GLY E 103 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N GLY E 103 " --> pdb=" O LEU E 241 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA E 243 " --> pdb=" O ILE E 101 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE E 101 " --> pdb=" O ALA E 243 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ARG E 102 " --> pdb=" O ASN E 121 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ASN E 121 " --> pdb=" O ARG E 102 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE E 106 " --> pdb=" O LEU E 117 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LYS E 129 " --> pdb=" O LEU E 118 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'E' and resid 311 through 319 removed outlier: 5.245A pdb=" N ILE E 312 " --> pdb=" O THR E 599 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N THR E 599 " --> pdb=" O ILE E 312 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N GLN E 314 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL E 597 " --> pdb=" O GLN E 314 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER E 316 " --> pdb=" O VAL E 595 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'E' and resid 325 through 328 removed outlier: 3.538A pdb=" N ALA E 575 " --> pdb=" O GLY E 566 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'E' and resid 354 through 358 Processing sheet with id=21, first strand: chain 'E' and resid 361 through 362 removed outlier: 6.522A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL E 524 " --> pdb=" O PHE E 392 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'E' and resid 452 through 453 Processing sheet with id=23, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=24, first strand: chain 'E' and resid 654 through 655 removed outlier: 6.030A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'E' and resid 711 through 728 removed outlier: 6.878A pdb=" N SER E 711 " --> pdb=" O THR E1076 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR E1076 " --> pdb=" O SER E 711 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA E 713 " --> pdb=" O ASN E1074 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ASN E1074 " --> pdb=" O ALA E 713 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N GLU E1072 " --> pdb=" O PRO E 715 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N TYR E1067 " --> pdb=" O HIS E1048 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N HIS E1048 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'E' and resid 733 through 736 removed outlier: 4.600A pdb=" N LYS E 733 " --> pdb=" O LEU E 861 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'E' and resid 1120 through 1121 Processing sheet with id=28, first strand: chain 'E' and resid 1094 through 1097 Processing sheet with id=29, first strand: chain 'I' and resid 23 through 30 removed outlier: 8.377A pdb=" N ASN I 61 " --> pdb=" O TYR I 269 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N TYR I 269 " --> pdb=" O ASN I 61 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N PHE I 201 " --> pdb=" O ASP I 228 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASP I 228 " --> pdb=" O PHE I 201 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE I 203 " --> pdb=" O LEU I 226 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N HIS I 207 " --> pdb=" O ALA I 222 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N ALA I 222 " --> pdb=" O HIS I 207 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL I 36 " --> pdb=" O LEU I 223 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'I' and resid 48 through 55 removed outlier: 3.934A pdb=" N ASP I 287 " --> pdb=" O LYS I 278 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'I' and resid 140 through 141 removed outlier: 3.721A pdb=" N LEU I 241 " --> pdb=" O GLY I 103 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N GLY I 103 " --> pdb=" O LEU I 241 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA I 243 " --> pdb=" O ILE I 101 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE I 101 " --> pdb=" O ALA I 243 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ARG I 102 " --> pdb=" O ASN I 121 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ASN I 121 " --> pdb=" O ARG I 102 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE I 106 " --> pdb=" O LEU I 117 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LYS I 129 " --> pdb=" O LEU I 118 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'I' and resid 311 through 319 removed outlier: 5.246A pdb=" N ILE I 312 " --> pdb=" O THR I 599 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N THR I 599 " --> pdb=" O ILE I 312 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N GLN I 314 " --> pdb=" O VAL I 597 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL I 597 " --> pdb=" O GLN I 314 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER I 316 " --> pdb=" O VAL I 595 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY I 594 " --> pdb=" O GLN I 613 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'I' and resid 325 through 328 removed outlier: 3.537A pdb=" N ALA I 575 " --> pdb=" O GLY I 566 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'I' and resid 354 through 358 Processing sheet with id=35, first strand: chain 'I' and resid 361 through 362 removed outlier: 6.523A pdb=" N CYS I 361 " --> pdb=" O CYS I 525 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL I 524 " --> pdb=" O PHE I 392 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'I' and resid 452 through 453 Processing sheet with id=37, first strand: chain 'I' and resid 473 through 474 Processing sheet with id=38, first strand: chain 'I' and resid 654 through 655 removed outlier: 6.029A pdb=" N GLU I 654 " --> pdb=" O ALA I 694 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N THR I 696 " --> pdb=" O GLU I 654 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'I' and resid 711 through 728 removed outlier: 6.878A pdb=" N SER I 711 " --> pdb=" O THR I1076 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR I1076 " --> pdb=" O SER I 711 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA I 713 " --> pdb=" O ASN I1074 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ASN I1074 " --> pdb=" O ALA I 713 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N GLU I1072 " --> pdb=" O PRO I 715 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N TYR I1067 " --> pdb=" O HIS I1048 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N HIS I1048 " --> pdb=" O TYR I1067 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'I' and resid 733 through 736 removed outlier: 4.600A pdb=" N LYS I 733 " --> pdb=" O LEU I 861 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'I' and resid 1120 through 1121 Processing sheet with id=42, first strand: chain 'I' and resid 1094 through 1097 996 hydrogen bonds defined for protein. 2664 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: 12.19 Time building geometry restraints manager: 7.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8133 1.34 - 1.47: 6564 1.47 - 1.59: 11397 1.59 - 1.71: 0 1.71 - 1.83: 135 Bond restraints: 26229 Sorted by residual: bond pdb=" C1 NAG I1308 " pdb=" O5 NAG I1308 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.04e+00 bond pdb=" C1 NAG E1308 " pdb=" O5 NAG E1308 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.01e+00 bond pdb=" C1 NAG A1308 " pdb=" O5 NAG A1308 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.01e+00 bond pdb=" C1 NAG E1307 " pdb=" O5 NAG E1307 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.73e+00 bond pdb=" C1 NAG A1307 " pdb=" O5 NAG A1307 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.59e+00 ... (remaining 26224 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 35094 1.96 - 3.92: 585 3.92 - 5.87: 27 5.87 - 7.83: 3 7.83 - 9.79: 3 Bond angle restraints: 35712 Sorted by residual: angle pdb=" N THR A 108 " pdb=" CA THR A 108 " pdb=" C THR A 108 " ideal model delta sigma weight residual 114.56 110.93 3.63 1.27e+00 6.20e-01 8.19e+00 angle pdb=" N THR I 108 " pdb=" CA THR I 108 " pdb=" C THR I 108 " ideal model delta sigma weight residual 114.56 110.93 3.63 1.27e+00 6.20e-01 8.15e+00 angle pdb=" N THR E 108 " pdb=" CA THR E 108 " pdb=" C THR E 108 " ideal model delta sigma weight residual 114.56 110.94 3.62 1.27e+00 6.20e-01 8.11e+00 angle pdb=" C PHE I 342 " pdb=" N ASN I 343 " pdb=" CA ASN I 343 " ideal model delta sigma weight residual 121.54 126.89 -5.35 1.91e+00 2.74e-01 7.85e+00 angle pdb=" CA LEU E 118 " pdb=" CB LEU E 118 " pdb=" CG LEU E 118 " ideal model delta sigma weight residual 116.30 126.09 -9.79 3.50e+00 8.16e-02 7.82e+00 ... (remaining 35707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.37: 14688 16.37 - 32.74: 1204 32.74 - 49.11: 305 49.11 - 65.48: 99 65.48 - 81.85: 42 Dihedral angle restraints: 16338 sinusoidal: 7062 harmonic: 9276 Sorted by residual: dihedral pdb=" CB CYS I1082 " pdb=" SG CYS I1082 " pdb=" SG CYS I1126 " pdb=" CB CYS I1126 " ideal model delta sinusoidal sigma weight residual -86.00 -144.55 58.55 1 1.00e+01 1.00e-02 4.59e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -144.52 58.52 1 1.00e+01 1.00e-02 4.59e+01 dihedral pdb=" CB CYS E1082 " pdb=" SG CYS E1082 " pdb=" SG CYS E1126 " pdb=" CB CYS E1126 " ideal model delta sinusoidal sigma weight residual -86.00 -144.50 58.50 1 1.00e+01 1.00e-02 4.58e+01 ... (remaining 16335 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 3632 0.069 - 0.138: 562 0.138 - 0.206: 9 0.206 - 0.275: 0 0.275 - 0.344: 3 Chirality restraints: 4206 Sorted by residual: chirality pdb=" C1 NAG A1309 " pdb=" ND2 ASN A 709 " pdb=" C2 NAG A1309 " pdb=" O5 NAG A1309 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" C1 NAG E1309 " pdb=" ND2 ASN E 709 " pdb=" C2 NAG E1309 " pdb=" O5 NAG E1309 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" C1 NAG I1309 " pdb=" ND2 ASN I 709 " pdb=" C2 NAG I1309 " pdb=" O5 NAG I1309 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.92e+00 ... (remaining 4203 not shown) Planarity restraints: 4593 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 208 " 0.029 5.00e-02 4.00e+02 4.36e-02 3.05e+00 pdb=" N PRO A 209 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 209 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 209 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR I 208 " 0.029 5.00e-02 4.00e+02 4.36e-02 3.05e+00 pdb=" N PRO I 209 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO I 209 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO I 209 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 208 " 0.028 5.00e-02 4.00e+02 4.35e-02 3.03e+00 pdb=" N PRO E 209 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO E 209 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 209 " 0.024 5.00e-02 4.00e+02 ... (remaining 4590 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1870 2.74 - 3.28: 23697 3.28 - 3.82: 39246 3.82 - 4.36: 46280 4.36 - 4.90: 83759 Nonbonded interactions: 194852 Sorted by model distance: nonbonded pdb=" NZ LYS I 811 " pdb=" OG SER I 813 " model vdw 2.202 3.120 nonbonded pdb=" NZ LYS E 811 " pdb=" OG SER E 813 " model vdw 2.202 3.120 nonbonded pdb=" NZ LYS A 811 " pdb=" OG SER A 813 " model vdw 2.202 3.120 nonbonded pdb=" O THR E 393 " pdb=" OG1 THR E 523 " model vdw 2.205 3.040 nonbonded pdb=" O THR I 393 " pdb=" OG1 THR I 523 " model vdw 2.205 3.040 ... (remaining 194847 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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 individual isotropic 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: 5.530 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: 1.040 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 60.700 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 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 : 0.003 0.035 26325 Z= 0.156 Angle : 0.589 10.782 35958 Z= 0.290 Chirality : 0.046 0.344 4206 Planarity : 0.004 0.044 4548 Dihedral : 13.582 81.848 10242 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.20 (0.15), residues: 3141 helix: 2.09 (0.21), residues: 723 sheet: 1.07 (0.18), residues: 729 loop : -1.26 (0.14), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 436 HIS 0.002 0.000 HIS I1064 PHE 0.016 0.001 PHE I 906 TYR 0.015 0.001 TYR E1067 ARG 0.002 0.000 ARG E 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00583 ( 45) link_NAG-ASN : angle 3.55925 ( 135) link_BETA1-4 : bond 0.00408 ( 9) link_BETA1-4 : angle 0.78474 ( 27) hydrogen bonds : bond 0.12816 ( 996) hydrogen bonds : angle 6.30614 ( 2664) SS BOND : bond 0.00371 ( 42) SS BOND : angle 1.15608 ( 84) covalent geometry : bond 0.00311 (26229) covalent geometry : angle 0.54578 (35712) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 2.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 849 LEU cc_start: 0.7835 (mt) cc_final: 0.7584 (mt) REVERT: E 52 GLN cc_start: 0.8215 (tm-30) cc_final: 0.7945 (tm-30) REVERT: E 489 TYR cc_start: 0.7326 (m-80) cc_final: 0.6936 (m-80) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 1.1756 time to fit residues: 233.5039 Evaluate side-chains 75 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 2.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 0.8980 chunk 241 optimal weight: 4.9990 chunk 133 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 chunk 162 optimal weight: 0.9980 chunk 128 optimal weight: 7.9990 chunk 249 optimal weight: 9.9990 chunk 96 optimal weight: 3.9990 chunk 151 optimal weight: 8.9990 chunk 185 optimal weight: 1.9990 chunk 288 optimal weight: 0.5980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.105804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.071249 restraints weight = 50669.274| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 3.00 r_work: 0.2969 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.0823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26325 Z= 0.135 Angle : 0.589 12.182 35958 Z= 0.296 Chirality : 0.046 0.319 4206 Planarity : 0.004 0.054 4548 Dihedral : 7.000 57.469 4548 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.68 % Allowed : 5.12 % Favored : 94.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.39 (0.15), residues: 3141 helix: 2.40 (0.21), residues: 711 sheet: 1.30 (0.19), residues: 741 loop : -1.26 (0.14), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 436 HIS 0.003 0.001 HIS A1064 PHE 0.019 0.001 PHE A 906 TYR 0.022 0.001 TYR I 170 ARG 0.010 0.000 ARG I 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00487 ( 45) link_NAG-ASN : angle 3.48996 ( 135) link_BETA1-4 : bond 0.00217 ( 9) link_BETA1-4 : angle 0.99854 ( 27) hydrogen bonds : bond 0.05810 ( 996) hydrogen bonds : angle 5.29469 ( 2664) SS BOND : bond 0.00342 ( 42) SS BOND : angle 1.45930 ( 84) covalent geometry : bond 0.00309 (26229) covalent geometry : angle 0.54564 (35712) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 2.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 849 LEU cc_start: 0.7688 (mt) cc_final: 0.7398 (mt) REVERT: E 52 GLN cc_start: 0.8323 (tm-30) cc_final: 0.8037 (tm-30) REVERT: E 189 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8101 (tm) REVERT: I 189 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8235 (tm) REVERT: I 319 ARG cc_start: 0.8739 (ttm110) cc_final: 0.8411 (ptm160) REVERT: I 427 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7858 (t0) REVERT: I 571 ASP cc_start: 0.8489 (t0) cc_final: 0.8230 (t0) outliers start: 19 outliers final: 7 residues processed: 104 average time/residue: 1.1761 time to fit residues: 148.1039 Evaluate side-chains 85 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 3.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 427 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 165 optimal weight: 1.9990 chunk 237 optimal weight: 0.9990 chunk 145 optimal weight: 4.9990 chunk 224 optimal weight: 2.9990 chunk 298 optimal weight: 0.0020 chunk 220 optimal weight: 10.0000 chunk 198 optimal weight: 2.9990 chunk 208 optimal weight: 4.9990 chunk 151 optimal weight: 8.9990 chunk 294 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 overall best weight: 1.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 613 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.104795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.069904 restraints weight = 50716.531| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 3.00 r_work: 0.2939 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 26325 Z= 0.136 Angle : 0.575 11.885 35958 Z= 0.292 Chirality : 0.046 0.291 4206 Planarity : 0.004 0.075 4548 Dihedral : 6.452 56.628 4548 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.12 % Allowed : 6.13 % Favored : 92.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.38 (0.15), residues: 3141 helix: 2.52 (0.21), residues: 693 sheet: 1.29 (0.19), residues: 738 loop : -1.28 (0.14), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 436 HIS 0.003 0.001 HIS A1064 PHE 0.028 0.001 PHE A 906 TYR 0.019 0.001 TYR E 170 ARG 0.008 0.000 ARG A 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00475 ( 45) link_NAG-ASN : angle 3.29899 ( 135) link_BETA1-4 : bond 0.00259 ( 9) link_BETA1-4 : angle 0.99912 ( 27) hydrogen bonds : bond 0.06201 ( 996) hydrogen bonds : angle 5.23068 ( 2664) SS BOND : bond 0.00323 ( 42) SS BOND : angle 1.54938 ( 84) covalent geometry : bond 0.00313 (26229) covalent geometry : angle 0.53437 (35712) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 87 time to evaluate : 2.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 THR cc_start: 0.7086 (m) cc_final: 0.6568 (p) REVERT: A 849 LEU cc_start: 0.7672 (mt) cc_final: 0.7371 (mt) REVERT: E 52 GLN cc_start: 0.8328 (tm-30) cc_final: 0.7973 (tm-30) REVERT: E 189 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.8069 (tm) REVERT: I 319 ARG cc_start: 0.8697 (ttm110) cc_final: 0.8358 (ptm160) REVERT: I 427 ASP cc_start: 0.8098 (OUTLIER) cc_final: 0.7827 (t0) REVERT: I 571 ASP cc_start: 0.8456 (t0) cc_final: 0.8168 (t0) outliers start: 31 outliers final: 13 residues processed: 112 average time/residue: 1.2044 time to fit residues: 161.6941 Evaluate side-chains 91 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 2.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain I residue 130 VAL Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 415 THR Chi-restraints excluded: chain I residue 427 ASP Chi-restraints excluded: chain I residue 525 CYS Chi-restraints excluded: chain I residue 635 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 178 optimal weight: 1.9990 chunk 308 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 140 optimal weight: 0.3980 chunk 268 optimal weight: 0.3980 chunk 163 optimal weight: 0.0040 chunk 83 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 128 optimal weight: 0.7980 chunk 139 optimal weight: 9.9990 chunk 143 optimal weight: 7.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.106176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.071771 restraints weight = 51098.874| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.98 r_work: 0.2979 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 26325 Z= 0.105 Angle : 0.545 11.561 35958 Z= 0.273 Chirality : 0.045 0.297 4206 Planarity : 0.004 0.060 4548 Dihedral : 5.982 55.735 4548 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.05 % Allowed : 7.28 % Favored : 91.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.45 (0.15), residues: 3141 helix: 2.53 (0.21), residues: 696 sheet: 1.31 (0.18), residues: 759 loop : -1.24 (0.14), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 436 HIS 0.002 0.000 HIS E 69 PHE 0.013 0.001 PHE I 168 TYR 0.018 0.001 TYR I 170 ARG 0.007 0.000 ARG E 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00476 ( 45) link_NAG-ASN : angle 3.25115 ( 135) link_BETA1-4 : bond 0.00305 ( 9) link_BETA1-4 : angle 0.94108 ( 27) hydrogen bonds : bond 0.05175 ( 996) hydrogen bonds : angle 5.09684 ( 2664) SS BOND : bond 0.00311 ( 42) SS BOND : angle 1.38139 ( 84) covalent geometry : bond 0.00222 (26229) covalent geometry : angle 0.50397 (35712) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 77 time to evaluate : 2.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 THR cc_start: 0.7049 (m) cc_final: 0.6621 (p) REVERT: A 200 TYR cc_start: 0.7484 (m-80) cc_final: 0.7139 (m-80) REVERT: E 52 GLN cc_start: 0.8332 (tm-30) cc_final: 0.8045 (tm-30) REVERT: E 189 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8099 (tm) REVERT: I 189 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8306 (tm) REVERT: I 319 ARG cc_start: 0.8682 (ttm110) cc_final: 0.8400 (ptm160) REVERT: I 427 ASP cc_start: 0.8091 (OUTLIER) cc_final: 0.7826 (t0) REVERT: I 516 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8479 (mt-10) outliers start: 29 outliers final: 14 residues processed: 104 average time/residue: 1.1927 time to fit residues: 149.6870 Evaluate side-chains 91 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 3.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 635 VAL Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain I residue 130 VAL Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 427 ASP Chi-restraints excluded: chain I residue 516 GLU Chi-restraints excluded: chain I residue 525 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 298 optimal weight: 0.5980 chunk 157 optimal weight: 0.7980 chunk 275 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 263 optimal weight: 8.9990 chunk 146 optimal weight: 4.9990 chunk 235 optimal weight: 4.9990 chunk 220 optimal weight: 8.9990 chunk 43 optimal weight: 4.9990 chunk 136 optimal weight: 4.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN I 613 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.102715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.067684 restraints weight = 51044.379| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.99 r_work: 0.2883 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 26325 Z= 0.209 Angle : 0.637 11.037 35958 Z= 0.326 Chirality : 0.048 0.264 4206 Planarity : 0.004 0.046 4548 Dihedral : 6.187 57.667 4548 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.19 % Allowed : 8.32 % Favored : 90.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.23 (0.15), residues: 3141 helix: 2.36 (0.21), residues: 693 sheet: 1.24 (0.19), residues: 732 loop : -1.38 (0.14), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 886 HIS 0.005 0.001 HIS A1064 PHE 0.031 0.002 PHE I 906 TYR 0.020 0.001 TYR I1067 ARG 0.010 0.000 ARG A 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00401 ( 45) link_NAG-ASN : angle 3.26538 ( 135) link_BETA1-4 : bond 0.00172 ( 9) link_BETA1-4 : angle 1.10497 ( 27) hydrogen bonds : bond 0.07600 ( 996) hydrogen bonds : angle 5.35237 ( 2664) SS BOND : bond 0.00530 ( 42) SS BOND : angle 2.02358 ( 84) covalent geometry : bond 0.00510 (26229) covalent geometry : angle 0.59798 (35712) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 82 time to evaluate : 2.639 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8208 (tm) REVERT: A 200 TYR cc_start: 0.7497 (m-80) cc_final: 0.7245 (m-80) REVERT: A 988 GLU cc_start: 0.8314 (tp30) cc_final: 0.7861 (tp30) REVERT: E 52 GLN cc_start: 0.8365 (tm-30) cc_final: 0.7965 (tm-30) REVERT: E 988 GLU cc_start: 0.8299 (tp30) cc_final: 0.7599 (tp30) REVERT: I 319 ARG cc_start: 0.8664 (ttm110) cc_final: 0.8363 (ptm160) REVERT: I 427 ASP cc_start: 0.8070 (OUTLIER) cc_final: 0.7802 (t0) REVERT: I 988 GLU cc_start: 0.8401 (tp30) cc_final: 0.7866 (tp30) outliers start: 33 outliers final: 18 residues processed: 112 average time/residue: 1.2422 time to fit residues: 166.0354 Evaluate side-chains 94 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 2.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 635 VAL Chi-restraints excluded: chain E residue 705 VAL Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain I residue 130 VAL Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 415 THR Chi-restraints excluded: chain I residue 427 ASP Chi-restraints excluded: chain I residue 525 CYS Chi-restraints excluded: chain I residue 635 VAL Chi-restraints excluded: chain I residue 1092 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 29 optimal weight: 2.9990 chunk 230 optimal weight: 9.9990 chunk 143 optimal weight: 2.9990 chunk 210 optimal weight: 5.9990 chunk 188 optimal weight: 0.9990 chunk 300 optimal weight: 0.5980 chunk 159 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 228 optimal weight: 5.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.103827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.068903 restraints weight = 50598.720| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.98 r_work: 0.2917 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26325 Z= 0.143 Angle : 0.587 10.768 35958 Z= 0.299 Chirality : 0.046 0.273 4206 Planarity : 0.004 0.060 4548 Dihedral : 6.001 56.368 4548 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.23 % Allowed : 8.86 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.24 (0.15), residues: 3141 helix: 2.40 (0.21), residues: 693 sheet: 1.24 (0.18), residues: 732 loop : -1.38 (0.14), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 886 HIS 0.003 0.001 HIS I 66 PHE 0.014 0.001 PHE I 906 TYR 0.017 0.001 TYR A1067 ARG 0.017 0.000 ARG E 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00405 ( 45) link_NAG-ASN : angle 3.15482 ( 135) link_BETA1-4 : bond 0.00269 ( 9) link_BETA1-4 : angle 1.00764 ( 27) hydrogen bonds : bond 0.06402 ( 996) hydrogen bonds : angle 5.23518 ( 2664) SS BOND : bond 0.00352 ( 42) SS BOND : angle 1.65127 ( 84) covalent geometry : bond 0.00332 (26229) covalent geometry : angle 0.55004 (35712) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 82 time to evaluate : 2.932 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 841 LEU cc_start: 0.7322 (OUTLIER) cc_final: 0.7120 (pp) REVERT: A 988 GLU cc_start: 0.8280 (tp30) cc_final: 0.7836 (tp30) REVERT: E 52 GLN cc_start: 0.8397 (tm-30) cc_final: 0.8103 (tm-30) REVERT: E 189 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8205 (tm) REVERT: E 988 GLU cc_start: 0.8272 (tp30) cc_final: 0.7579 (tp30) REVERT: I 319 ARG cc_start: 0.8672 (ttm110) cc_final: 0.8384 (ptm160) REVERT: I 427 ASP cc_start: 0.8073 (OUTLIER) cc_final: 0.7805 (t0) REVERT: I 571 ASP cc_start: 0.8484 (t0) cc_final: 0.8199 (t0) REVERT: I 988 GLU cc_start: 0.8369 (tp30) cc_final: 0.7852 (tp30) outliers start: 34 outliers final: 18 residues processed: 113 average time/residue: 1.0874 time to fit residues: 150.3530 Evaluate side-chains 96 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 2.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 635 VAL Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain I residue 130 VAL Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 427 ASP Chi-restraints excluded: chain I residue 525 CYS Chi-restraints excluded: chain I residue 635 VAL Chi-restraints excluded: chain I residue 705 VAL Chi-restraints excluded: chain I residue 1092 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 241 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 145 optimal weight: 0.9980 chunk 125 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 149 optimal weight: 0.5980 chunk 295 optimal weight: 0.9980 chunk 128 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E1002 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.105214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.070639 restraints weight = 51037.169| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.98 r_work: 0.2954 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 26325 Z= 0.113 Angle : 0.555 11.007 35958 Z= 0.280 Chirality : 0.045 0.270 4206 Planarity : 0.004 0.057 4548 Dihedral : 5.748 55.949 4548 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.12 % Allowed : 8.97 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.31 (0.15), residues: 3141 helix: 2.46 (0.20), residues: 696 sheet: 1.24 (0.18), residues: 753 loop : -1.35 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 886 HIS 0.002 0.001 HIS I 69 PHE 0.012 0.001 PHE I 168 TYR 0.016 0.001 TYR A1067 ARG 0.011 0.000 ARG E 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00403 ( 45) link_NAG-ASN : angle 3.01026 ( 135) link_BETA1-4 : bond 0.00288 ( 9) link_BETA1-4 : angle 0.92725 ( 27) hydrogen bonds : bond 0.05439 ( 996) hydrogen bonds : angle 5.11553 ( 2664) SS BOND : bond 0.00352 ( 42) SS BOND : angle 1.46724 ( 84) covalent geometry : bond 0.00247 (26229) covalent geometry : angle 0.51929 (35712) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 82 time to evaluate : 2.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 841 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.7127 (pp) REVERT: E 189 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8210 (tm) REVERT: I 189 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8324 (tm) REVERT: I 319 ARG cc_start: 0.8653 (ttm110) cc_final: 0.8384 (ptm160) REVERT: I 427 ASP cc_start: 0.8057 (OUTLIER) cc_final: 0.7793 (t0) REVERT: I 571 ASP cc_start: 0.8463 (t0) cc_final: 0.8195 (t0) outliers start: 31 outliers final: 15 residues processed: 110 average time/residue: 1.0758 time to fit residues: 143.7484 Evaluate side-chains 97 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 2.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 705 VAL Chi-restraints excluded: chain I residue 130 VAL Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 427 ASP Chi-restraints excluded: chain I residue 525 CYS Chi-restraints excluded: chain I residue 635 VAL Chi-restraints excluded: chain I residue 705 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 82 optimal weight: 1.9990 chunk 158 optimal weight: 4.9990 chunk 199 optimal weight: 0.7980 chunk 296 optimal weight: 0.2980 chunk 171 optimal weight: 2.9990 chunk 239 optimal weight: 7.9990 chunk 181 optimal weight: 10.0000 chunk 206 optimal weight: 2.9990 chunk 175 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 264 optimal weight: 7.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E1002 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.104588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.069824 restraints weight = 50739.987| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.98 r_work: 0.2940 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26325 Z= 0.127 Angle : 0.570 13.390 35958 Z= 0.287 Chirality : 0.045 0.255 4206 Planarity : 0.004 0.051 4548 Dihedral : 5.750 56.482 4548 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.08 % Allowed : 9.23 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.31 (0.15), residues: 3141 helix: 2.51 (0.21), residues: 693 sheet: 1.24 (0.18), residues: 753 loop : -1.37 (0.14), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 886 HIS 0.004 0.001 HIS I 69 PHE 0.012 0.001 PHE I 906 TYR 0.017 0.001 TYR A1067 ARG 0.012 0.000 ARG A 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00359 ( 45) link_NAG-ASN : angle 2.92556 ( 135) link_BETA1-4 : bond 0.00281 ( 9) link_BETA1-4 : angle 0.93115 ( 27) hydrogen bonds : bond 0.05885 ( 996) hydrogen bonds : angle 5.11172 ( 2664) SS BOND : bond 0.00342 ( 42) SS BOND : angle 1.62631 ( 84) covalent geometry : bond 0.00291 (26229) covalent geometry : angle 0.53652 (35712) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 83 time to evaluate : 2.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 841 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.7114 (pp) REVERT: A 988 GLU cc_start: 0.8245 (tp30) cc_final: 0.7766 (tp30) REVERT: E 189 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8210 (tm) REVERT: E 834 ILE cc_start: 0.7711 (OUTLIER) cc_final: 0.7510 (pp) REVERT: I 319 ARG cc_start: 0.8650 (ttm110) cc_final: 0.8385 (ptm160) REVERT: I 427 ASP cc_start: 0.8054 (OUTLIER) cc_final: 0.7788 (t0) REVERT: I 571 ASP cc_start: 0.8549 (t0) cc_final: 0.8300 (t0) outliers start: 30 outliers final: 19 residues processed: 110 average time/residue: 1.0788 time to fit residues: 145.4357 Evaluate side-chains 103 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 2.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 635 VAL Chi-restraints excluded: chain E residue 705 VAL Chi-restraints excluded: chain E residue 834 ILE Chi-restraints excluded: chain I residue 130 VAL Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 427 ASP Chi-restraints excluded: chain I residue 525 CYS Chi-restraints excluded: chain I residue 635 VAL Chi-restraints excluded: chain I residue 705 VAL Chi-restraints excluded: chain I residue 1092 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 260 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 296 optimal weight: 0.8980 chunk 275 optimal weight: 1.9990 chunk 224 optimal weight: 8.9990 chunk 244 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 272 optimal weight: 7.9990 chunk 281 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.104361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.069563 restraints weight = 50924.652| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.99 r_work: 0.2932 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26325 Z= 0.132 Angle : 0.570 10.722 35958 Z= 0.289 Chirality : 0.045 0.248 4206 Planarity : 0.004 0.054 4548 Dihedral : 5.765 56.445 4548 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.08 % Allowed : 9.33 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.30 (0.15), residues: 3141 helix: 2.49 (0.21), residues: 693 sheet: 1.22 (0.18), residues: 753 loop : -1.37 (0.14), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 886 HIS 0.003 0.001 HIS A 66 PHE 0.012 0.001 PHE I 906 TYR 0.017 0.001 TYR A1067 ARG 0.013 0.000 ARG A 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00340 ( 45) link_NAG-ASN : angle 2.86236 ( 135) link_BETA1-4 : bond 0.00275 ( 9) link_BETA1-4 : angle 0.91813 ( 27) hydrogen bonds : bond 0.06024 ( 996) hydrogen bonds : angle 5.11722 ( 2664) SS BOND : bond 0.00344 ( 42) SS BOND : angle 1.65022 ( 84) covalent geometry : bond 0.00304 (26229) covalent geometry : angle 0.53788 (35712) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 85 time to evaluate : 2.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 841 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.7120 (pp) REVERT: A 988 GLU cc_start: 0.8263 (tp30) cc_final: 0.7783 (tp30) REVERT: E 189 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8208 (tm) REVERT: E 200 TYR cc_start: 0.7632 (m-80) cc_final: 0.7362 (m-80) REVERT: I 319 ARG cc_start: 0.8644 (ttm110) cc_final: 0.8387 (ptm160) REVERT: I 427 ASP cc_start: 0.8049 (OUTLIER) cc_final: 0.7782 (t0) REVERT: I 571 ASP cc_start: 0.8548 (t0) cc_final: 0.8295 (t0) outliers start: 30 outliers final: 17 residues processed: 111 average time/residue: 1.1253 time to fit residues: 151.6320 Evaluate side-chains 101 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 2.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 635 VAL Chi-restraints excluded: chain E residue 705 VAL Chi-restraints excluded: chain I residue 130 VAL Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 427 ASP Chi-restraints excluded: chain I residue 525 CYS Chi-restraints excluded: chain I residue 635 VAL Chi-restraints excluded: chain I residue 705 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 70 optimal weight: 0.0020 chunk 244 optimal weight: 0.9980 chunk 5 optimal weight: 0.0270 chunk 25 optimal weight: 0.9990 chunk 214 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 300 optimal weight: 0.6980 chunk 137 optimal weight: 1.9990 chunk 80 optimal weight: 0.0370 chunk 275 optimal weight: 1.9990 overall best weight: 0.3524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.107268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.073203 restraints weight = 50726.919| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.97 r_work: 0.3013 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 26325 Z= 0.096 Angle : 0.536 14.451 35958 Z= 0.266 Chirality : 0.044 0.264 4206 Planarity : 0.004 0.051 4548 Dihedral : 5.494 55.215 4548 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.61 % Allowed : 9.84 % Favored : 89.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.47 (0.15), residues: 3141 helix: 2.53 (0.21), residues: 696 sheet: 1.35 (0.18), residues: 762 loop : -1.25 (0.14), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 436 HIS 0.002 0.000 HIS I 69 PHE 0.013 0.001 PHE I 168 TYR 0.016 0.001 TYR E1067 ARG 0.013 0.000 ARG E 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00402 ( 45) link_NAG-ASN : angle 2.77718 ( 135) link_BETA1-4 : bond 0.00374 ( 9) link_BETA1-4 : angle 0.86086 ( 27) hydrogen bonds : bond 0.04368 ( 996) hydrogen bonds : angle 4.94262 ( 2664) SS BOND : bond 0.00316 ( 42) SS BOND : angle 1.09045 ( 84) covalent geometry : bond 0.00196 (26229) covalent geometry : angle 0.50712 (35712) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 2.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7569 (mtm110) cc_final: 0.7188 (mtp-110) REVERT: A 841 LEU cc_start: 0.7392 (OUTLIER) cc_final: 0.7183 (pp) REVERT: E 189 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8185 (tm) REVERT: I 189 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8321 (tm) REVERT: I 319 ARG cc_start: 0.8605 (ttm110) cc_final: 0.8373 (ptm160) REVERT: I 740 MET cc_start: 0.8885 (mmm) cc_final: 0.8547 (ttm) outliers start: 17 outliers final: 11 residues processed: 102 average time/residue: 1.1824 time to fit residues: 148.1925 Evaluate side-chains 96 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 2.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 635 VAL Chi-restraints excluded: chain E residue 705 VAL Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 525 CYS Chi-restraints excluded: chain I residue 705 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 312 optimal weight: 0.2980 chunk 300 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 202 optimal weight: 2.9990 chunk 42 optimal weight: 0.2980 chunk 288 optimal weight: 4.9990 chunk 238 optimal weight: 1.9990 chunk 260 optimal weight: 2.9990 chunk 306 optimal weight: 1.9990 chunk 302 optimal weight: 0.5980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.106633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.072360 restraints weight = 50847.254| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.99 r_work: 0.2995 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 26325 Z= 0.099 Angle : 0.538 13.719 35958 Z= 0.267 Chirality : 0.044 0.244 4206 Planarity : 0.004 0.057 4548 Dihedral : 5.447 56.041 4548 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.65 % Allowed : 9.91 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.51 (0.15), residues: 3141 helix: 2.63 (0.21), residues: 696 sheet: 1.38 (0.18), residues: 756 loop : -1.23 (0.14), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 436 HIS 0.002 0.000 HIS A 66 PHE 0.015 0.001 PHE I 168 TYR 0.016 0.001 TYR A1067 ARG 0.014 0.000 ARG E 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00337 ( 45) link_NAG-ASN : angle 2.69582 ( 135) link_BETA1-4 : bond 0.00317 ( 9) link_BETA1-4 : angle 0.83783 ( 27) hydrogen bonds : bond 0.04705 ( 996) hydrogen bonds : angle 4.89690 ( 2664) SS BOND : bond 0.00300 ( 42) SS BOND : angle 1.26685 ( 84) covalent geometry : bond 0.00211 (26229) covalent geometry : angle 0.50930 (35712) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20224.51 seconds wall clock time: 348 minutes 21.02 seconds (20901.02 seconds total)