Starting phenix.real_space_refine on Fri May 30 08:31:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jyn_36727/05_2025/8jyn_36727.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jyn_36727/05_2025/8jyn_36727.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jyn_36727/05_2025/8jyn_36727.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jyn_36727/05_2025/8jyn_36727.map" model { file = "/net/cci-nas-00/data/ceres_data/8jyn_36727/05_2025/8jyn_36727.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jyn_36727/05_2025/8jyn_36727.cif" } resolution = 3.04 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= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4890 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 133 5.16 5 C 18503 2.51 5 N 4727 2.21 5 O 5637 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: 29000 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 7893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1010, 7893 Classifications: {'peptide': 1010} Link IDs: {'PTRANS': 54, 'TRANS': 955} Chain breaks: 7 Chain: "B" Number of atoms: 7714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 985, 7714 Classifications: {'peptide': 985} Link IDs: {'PTRANS': 51, 'TRANS': 933} Chain breaks: 8 Chain: "C" Number of atoms: 7717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 986, 7717 Classifications: {'peptide': 986} Link IDs: {'PTRANS': 52, 'TRANS': 933} Chain breaks: 8 Chain: "D" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 15.91, per 1000 atoms: 0.55 Number of scatterers: 29000 At special positions: 0 Unit cell: (139.695, 152.76, 239.19, 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 133 16.00 O 5637 8.00 N 4727 7.00 C 18503 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.04 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " 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 ALPHA1-3 " BMA N 3 " - " MAN N 4 " ALPHA1-6 " BMA N 3 " - " MAN N 5 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " 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 616 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A1074 " " NAG A1310 " - " ASN A1098 " " NAG A1311 " - " ASN A1134 " " NAG A1312 " - " ASN A 331 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B1098 " " NAG B1310 " - " ASN B1134 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C1098 " " NAG C1310 " - " ASN C1134 " " NAG D 701 " - " ASN D 322 " " NAG D 702 " - " ASN D 432 " " NAG D 703 " - " ASN D 53 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN B 717 " " NAG H 1 " - " ASN B 801 " " NAG I 1 " - " ASN C 165 " " NAG J 1 " - " ASN C 717 " " NAG K 1 " - " ASN C 801 " " NAG L 1 " - " ASN D 546 " " NAG M 1 " - " ASN D 90 " " NAG N 1 " - " ASN D 103 " Time building additional restraints: 7.78 Conformation dependent library (CDL) restraints added in 3.6 seconds 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6726 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 47 sheets defined 31.6% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.91 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.515A pdb=" N GLU A 406 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.501A pdb=" N ASN A 422 " --> pdb=" O ILE A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.744A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 827 removed outlier: 4.200A pdb=" N THR A 827 " --> pdb=" O PHE A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.137A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.720A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.950A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.321A 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 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.289A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 removed outlier: 3.549A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 372 removed outlier: 3.715A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA B 372 " --> pdb=" O ILE B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 3.561A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.826A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.133A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.559A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.872A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.161A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 removed outlier: 3.686A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 372 removed outlier: 3.760A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ALA C 372 " --> pdb=" O ILE C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.051A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.849A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.073A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.630A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.883A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.064A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'D' and resid 20 through 53 removed outlier: 4.364A pdb=" N HIS D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU D 35 " --> pdb=" O LYS D 31 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 80 Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 84 through 88 removed outlier: 3.885A pdb=" N GLU D 87 " --> pdb=" O PRO D 84 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE D 88 " --> pdb=" O LEU D 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 84 through 88' Processing helix chain 'D' and resid 92 through 103 removed outlier: 3.569A pdb=" N GLN D 96 " --> pdb=" O THR D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 130 Processing helix chain 'D' and resid 147 through 155 Processing helix chain 'D' and resid 157 through 194 removed outlier: 3.646A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N GLN D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 3.627A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 220 through 233 removed outlier: 3.843A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 252 removed outlier: 4.049A pdb=" N ASN D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 303 through 318 removed outlier: 3.733A pdb=" N VAL D 318 " --> pdb=" O PHE D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 331 removed outlier: 3.705A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.697A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.616A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU D 410 " --> pdb=" O GLU D 406 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER D 411 " --> pdb=" O ILE D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 422 Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.536A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 466 removed outlier: 4.305A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 482 Processing helix chain 'D' and resid 498 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 533 removed outlier: 4.164A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLN D 524 " --> pdb=" O LEU D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 559 removed outlier: 3.793A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.626A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.336A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 8.973A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.145A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 101 through 107 removed outlier: 4.738A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 120 through 121 removed outlier: 3.654A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.856A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 4.248A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.842A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.723A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.207A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.820A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.956A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 713 removed outlier: 3.758A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 717 through 728 removed outlier: 3.522A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.786A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.577A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.538A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 169 through 172 removed outlier: 3.585A pdb=" N LYS B 129 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.997A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 327 removed outlier: 6.858A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 356 through 358 Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.173A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.775A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.778A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1121 Processing sheet with id=AD4, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 29 removed outlier: 3.557A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.596A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.947A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.941A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 169 through 172 Processing sheet with id=AD8, first strand: chain 'C' and resid 140 through 141 Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.037A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.579A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL C 510 " --> pdb=" O PHE C 400 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'C' and resid 538 through 543 removed outlier: 3.693A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.229A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.850A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.651A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.604A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1121 Processing sheet with id=AE8, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AE9, first strand: chain 'D' and resid 131 through 132 removed outlier: 3.606A pdb=" N VAL D 132 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU D 142 " --> pdb=" O VAL D 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.827A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'D' and resid 347 through 350 1147 hydrogen bonds defined for protein. 3186 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: 11.52 Time building geometry restraints manager: 8.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 9176 1.35 - 1.47: 7801 1.47 - 1.60: 12519 1.60 - 1.72: 0 1.72 - 1.85: 181 Bond restraints: 29677 Sorted by residual: bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.488 -0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" C1 NAG B1306 " pdb=" O5 NAG B1306 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.52e+01 bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.94e+00 bond pdb=" C1 NAG A1309 " pdb=" O5 NAG A1309 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.11e+00 bond pdb=" C1 NAG C1308 " pdb=" O5 NAG C1308 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 2.99e+00 ... (remaining 29672 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 39477 1.61 - 3.23: 775 3.23 - 4.84: 83 4.84 - 6.45: 20 6.45 - 8.07: 7 Bond angle restraints: 40362 Sorted by residual: angle pdb=" N GLY B 526 " pdb=" CA GLY B 526 " pdb=" C GLY B 526 " ideal model delta sigma weight residual 112.34 119.87 -7.53 2.04e+00 2.40e-01 1.36e+01 angle pdb=" N GLY C 526 " pdb=" CA GLY C 526 " pdb=" C GLY C 526 " ideal model delta sigma weight residual 112.34 118.44 -6.10 2.04e+00 2.40e-01 8.95e+00 angle pdb=" N THR A 236 " pdb=" CA THR A 236 " pdb=" C THR A 236 " ideal model delta sigma weight residual 114.56 110.95 3.61 1.27e+00 6.20e-01 8.07e+00 angle pdb=" C PRO D 135 " pdb=" N ASP D 136 " pdb=" CA ASP D 136 " ideal model delta sigma weight residual 121.54 126.94 -5.40 1.91e+00 2.74e-01 8.00e+00 angle pdb=" C ILE A 197 " pdb=" N ASP A 198 " pdb=" CA ASP A 198 " ideal model delta sigma weight residual 121.54 126.83 -5.29 1.91e+00 2.74e-01 7.67e+00 ... (remaining 40357 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.27: 17413 23.27 - 46.55: 870 46.55 - 69.82: 104 69.82 - 93.10: 37 93.10 - 116.37: 14 Dihedral angle restraints: 18438 sinusoidal: 8000 harmonic: 10438 Sorted by residual: dihedral pdb=" CB CYS D 133 " pdb=" SG CYS D 133 " pdb=" SG CYS D 141 " pdb=" CB CYS D 141 " ideal model delta sinusoidal sigma weight residual 93.00 28.92 64.08 1 1.00e+01 1.00e-02 5.40e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -143.04 57.04 1 1.00e+01 1.00e-02 4.38e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -138.85 52.85 1 1.00e+01 1.00e-02 3.80e+01 ... (remaining 18435 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.136: 4669 0.136 - 0.272: 21 0.272 - 0.408: 4 0.408 - 0.544: 2 0.544 - 0.681: 3 Chirality restraints: 4699 Sorted by residual: chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN D 103 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.72 -0.68 2.00e-01 2.50e+01 1.16e+01 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN B 801 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.37e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 801 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.66e+00 ... (remaining 4696 not shown) Planarity restraints: 5175 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 801 " 0.039 2.00e-02 2.50e+03 3.62e-02 1.64e+01 pdb=" CG ASN A 801 " -0.040 2.00e-02 2.50e+03 pdb=" OD1 ASN A 801 " 0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN A 801 " -0.042 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 801 " 0.038 2.00e-02 2.50e+03 3.50e-02 1.53e+01 pdb=" CG ASN B 801 " -0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN B 801 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN B 801 " -0.041 2.00e-02 2.50e+03 pdb=" C1 NAG H 1 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 165 " -0.002 2.00e-02 2.50e+03 1.58e-02 3.12e+00 pdb=" CG ASN A 165 " 0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN A 165 " -0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN A 165 " 0.014 2.00e-02 2.50e+03 pdb=" C1 NAG A1303 " -0.015 2.00e-02 2.50e+03 ... (remaining 5172 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2369 2.74 - 3.28: 27894 3.28 - 3.82: 45164 3.82 - 4.36: 51694 4.36 - 4.90: 93203 Nonbonded interactions: 220324 Sorted by model distance: nonbonded pdb=" NZ LYS B 811 " pdb=" OG SER B 813 " model vdw 2.203 3.120 nonbonded pdb=" OD2 ASP A 142 " pdb=" OG SER A 155 " model vdw 2.218 3.040 nonbonded pdb=" NZ LYS A 811 " pdb=" OG SER A 813 " model vdw 2.240 3.120 nonbonded pdb=" OG SER B 735 " pdb=" OG1 THR B 859 " model vdw 2.255 3.040 nonbonded pdb=" OG1 THR A 500 " pdb=" OH TYR D 41 " model vdw 2.271 3.040 ... (remaining 220319 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 25 through 65 or resid 86 through 177 or resid 188 through \ 469 or resid 490 through 620 or resid 640 through 675 or resid 690 through 827 \ or resid 855 through 1139 or resid 1301 through 1310)) selection = (chain 'B' and (resid 25 through 65 or resid 86 through 177 or resid 188 through \ 620 or resid 640 through 1139 or resid 1301 through 1310)) selection = (chain 'C' and (resid 25 through 65 or resid 86 through 469 or resid 490 through \ 675 or resid 690 through 827 or resid 855 through 1139 or resid 1301 through 13 \ 10)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' 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: 2.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.180 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: 0.230 Process input model: 63.540 Find NCS groups from input model: 1.640 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 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 0.082 29776 Z= 0.155 Angle : 0.576 12.303 40619 Z= 0.272 Chirality : 0.048 0.681 4699 Planarity : 0.003 0.044 5130 Dihedral : 13.707 116.371 11592 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.69 % Favored : 96.28 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % 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: 0.42 (0.14), residues: 3523 helix: 2.00 (0.17), residues: 1004 sheet: 0.96 (0.20), residues: 702 loop : -1.04 (0.14), residues: 1817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 886 HIS 0.003 0.000 HIS B 339 PHE 0.027 0.001 PHE B 906 TYR 0.012 0.001 TYR B1067 ARG 0.004 0.000 ARG D 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00641 ( 45) link_NAG-ASN : angle 3.55174 ( 135) link_ALPHA1-6 : bond 0.00421 ( 1) link_ALPHA1-6 : angle 1.58765 ( 3) link_BETA1-4 : bond 0.00324 ( 12) link_BETA1-4 : angle 1.73553 ( 36) link_ALPHA1-3 : bond 0.00354 ( 1) link_ALPHA1-3 : angle 1.52854 ( 3) hydrogen bonds : bond 0.21536 ( 1147) hydrogen bonds : angle 7.21272 ( 3186) SS BOND : bond 0.00315 ( 40) SS BOND : angle 1.19406 ( 80) covalent geometry : bond 0.00322 (29677) covalent geometry : angle 0.53515 (40362) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 3.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 TRP cc_start: 0.2811 (p-90) cc_final: 0.2098 (p-90) REVERT: A 392 PHE cc_start: 0.6501 (m-10) cc_final: 0.5433 (m-10) REVERT: A 515 PHE cc_start: 0.5656 (m-80) cc_final: 0.5298 (m-10) REVERT: B 160 TYR cc_start: 0.8082 (p90) cc_final: 0.7665 (p90) REVERT: B 354 ASN cc_start: 0.7644 (m110) cc_final: 0.7389 (t0) REVERT: B 398 ASP cc_start: 0.7424 (m-30) cc_final: 0.7037 (t0) REVERT: B 436 TRP cc_start: 0.4058 (p90) cc_final: 0.3555 (p90) REVERT: B 452 LEU cc_start: 0.8019 (mp) cc_final: 0.7419 (mt) REVERT: B 589 PRO cc_start: 0.8174 (Cg_exo) cc_final: 0.7912 (Cg_endo) REVERT: B 979 ASP cc_start: 0.8461 (t70) cc_final: 0.8151 (t0) REVERT: C 357 ARG cc_start: 0.7095 (ttm170) cc_final: 0.6855 (ttm170) REVERT: C 528 LYS cc_start: 0.8053 (pttm) cc_final: 0.7420 (ptmm) outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.4040 time to fit residues: 176.0395 Evaluate side-chains 176 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 3.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 300 optimal weight: 6.9990 chunk 269 optimal weight: 0.9980 chunk 149 optimal weight: 0.3980 chunk 92 optimal weight: 3.9990 chunk 182 optimal weight: 4.9990 chunk 144 optimal weight: 20.0000 chunk 279 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 169 optimal weight: 1.9990 chunk 207 optimal weight: 6.9990 chunk 323 optimal weight: 20.0000 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 207 HIS ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS D 121 ASN D 417 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.143058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.081765 restraints weight = 64212.379| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 3.70 r_work: 0.2822 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 29776 Z= 0.212 Angle : 0.651 12.172 40619 Z= 0.327 Chirality : 0.049 0.477 4699 Planarity : 0.004 0.045 5130 Dihedral : 8.946 108.878 5058 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.03 % Favored : 95.94 % Rotamer: Outliers : 0.57 % Allowed : 5.03 % Favored : 94.39 % 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: 0.29 (0.14), residues: 3523 helix: 1.89 (0.16), residues: 1032 sheet: 0.92 (0.19), residues: 730 loop : -1.23 (0.14), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 353 HIS 0.006 0.001 HIS D 535 PHE 0.029 0.002 PHE B 906 TYR 0.020 0.001 TYR B1067 ARG 0.004 0.000 ARG D 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00575 ( 45) link_NAG-ASN : angle 3.48014 ( 135) link_ALPHA1-6 : bond 0.00402 ( 1) link_ALPHA1-6 : angle 2.50461 ( 3) link_BETA1-4 : bond 0.00261 ( 12) link_BETA1-4 : angle 1.75816 ( 36) link_ALPHA1-3 : bond 0.00528 ( 1) link_ALPHA1-3 : angle 1.92667 ( 3) hydrogen bonds : bond 0.06584 ( 1147) hydrogen bonds : angle 5.40351 ( 3186) SS BOND : bond 0.00360 ( 40) SS BOND : angle 1.54966 ( 80) covalent geometry : bond 0.00507 (29677) covalent geometry : angle 0.61475 (40362) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 200 time to evaluate : 2.999 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7423 (m-80) cc_final: 0.7178 (m-80) REVERT: A 168 PHE cc_start: 0.6363 (t80) cc_final: 0.6019 (t80) REVERT: A 353 TRP cc_start: 0.4989 (p-90) cc_final: 0.2748 (p-90) REVERT: A 515 PHE cc_start: 0.7036 (m-80) cc_final: 0.6579 (m-10) REVERT: B 160 TYR cc_start: 0.8314 (p90) cc_final: 0.7857 (p90) REVERT: B 398 ASP cc_start: 0.7055 (m-30) cc_final: 0.6362 (p0) REVERT: B 423 TYR cc_start: 0.7612 (t80) cc_final: 0.7356 (t80) REVERT: B 449 TYR cc_start: 0.8549 (m-80) cc_final: 0.8321 (t80) REVERT: C 235 ILE cc_start: 0.5894 (mm) cc_final: 0.5626 (mm) REVERT: C 357 ARG cc_start: 0.7011 (ttm170) cc_final: 0.6750 (ttm170) REVERT: C 528 LYS cc_start: 0.8181 (pttm) cc_final: 0.7528 (ttpp) REVERT: D 231 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7219 (pt0) REVERT: D 329 GLU cc_start: 0.7047 (mm-30) cc_final: 0.6803 (mm-30) REVERT: D 455 MET cc_start: 0.6336 (tmm) cc_final: 0.5766 (ptm) outliers start: 18 outliers final: 13 residues processed: 208 average time/residue: 0.3572 time to fit residues: 124.1425 Evaluate side-chains 189 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 176 time to evaluate : 2.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain D residue 280 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 52 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 274 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 337 optimal weight: 8.9990 chunk 218 optimal weight: 5.9990 chunk 319 optimal weight: 20.0000 chunk 165 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS B1088 HIS ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 524 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.143342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.080916 restraints weight = 64418.708| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 3.40 r_work: 0.2855 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29776 Z= 0.148 Angle : 0.592 12.365 40619 Z= 0.293 Chirality : 0.046 0.413 4699 Planarity : 0.004 0.045 5130 Dihedral : 7.976 107.048 5058 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.41 % Favored : 96.57 % Rotamer: Outliers : 0.83 % Allowed : 7.58 % Favored : 91.59 % 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: 0.32 (0.14), residues: 3523 helix: 1.96 (0.16), residues: 1030 sheet: 0.92 (0.19), residues: 741 loop : -1.24 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 353 HIS 0.004 0.001 HIS D 535 PHE 0.022 0.001 PHE B 906 TYR 0.016 0.001 TYR B1067 ARG 0.008 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00806 ( 45) link_NAG-ASN : angle 3.27419 ( 135) link_ALPHA1-6 : bond 0.00622 ( 1) link_ALPHA1-6 : angle 1.75306 ( 3) link_BETA1-4 : bond 0.00394 ( 12) link_BETA1-4 : angle 1.72267 ( 36) link_ALPHA1-3 : bond 0.01171 ( 1) link_ALPHA1-3 : angle 1.57968 ( 3) hydrogen bonds : bond 0.05662 ( 1147) hydrogen bonds : angle 4.98701 ( 3186) SS BOND : bond 0.00289 ( 40) SS BOND : angle 1.38439 ( 80) covalent geometry : bond 0.00341 (29677) covalent geometry : angle 0.55693 (40362) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 180 time to evaluate : 3.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 TRP cc_start: 0.5010 (p-90) cc_final: 0.2678 (p-90) REVERT: A 515 PHE cc_start: 0.7159 (m-80) cc_final: 0.6849 (m-10) REVERT: B 160 TYR cc_start: 0.8245 (p90) cc_final: 0.7836 (p90) REVERT: B 175 PHE cc_start: 0.7706 (m-80) cc_final: 0.7420 (m-10) REVERT: B 398 ASP cc_start: 0.6988 (m-30) cc_final: 0.6594 (p0) REVERT: C 357 ARG cc_start: 0.7326 (ttm170) cc_final: 0.7003 (ttm170) REVERT: C 528 LYS cc_start: 0.8208 (pttm) cc_final: 0.7590 (ttpp) REVERT: C 904 TYR cc_start: 0.8822 (m-80) cc_final: 0.8498 (m-10) REVERT: D 231 GLU cc_start: 0.7573 (mm-30) cc_final: 0.7259 (pt0) REVERT: D 332 MET cc_start: 0.4098 (ppp) cc_final: 0.3887 (ppp) REVERT: D 455 MET cc_start: 0.6384 (tmm) cc_final: 0.5878 (ptm) REVERT: D 579 MET cc_start: 0.2893 (mtt) cc_final: 0.2212 (mmm) outliers start: 26 outliers final: 15 residues processed: 198 average time/residue: 0.3686 time to fit residues: 123.9264 Evaluate side-chains 179 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 164 time to evaluate : 3.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain D residue 410 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 124 optimal weight: 0.9980 chunk 352 optimal weight: 0.3980 chunk 32 optimal weight: 0.9980 chunk 325 optimal weight: 20.0000 chunk 113 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 350 optimal weight: 7.9990 chunk 164 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS D 472 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.143973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.084920 restraints weight = 64941.835| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 3.69 r_work: 0.2866 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29776 Z= 0.113 Angle : 0.571 14.805 40619 Z= 0.278 Chirality : 0.046 0.403 4699 Planarity : 0.004 0.046 5130 Dihedral : 7.347 105.912 5058 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.66 % Favored : 96.31 % Rotamer: Outliers : 0.92 % Allowed : 8.57 % Favored : 90.51 % 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 (0.14), residues: 3523 helix: 2.00 (0.16), residues: 1038 sheet: 0.94 (0.19), residues: 739 loop : -1.20 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 353 HIS 0.003 0.001 HIS D 535 PHE 0.023 0.001 PHE A 133 TYR 0.015 0.001 TYR D 50 ARG 0.006 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00816 ( 45) link_NAG-ASN : angle 3.27223 ( 135) link_ALPHA1-6 : bond 0.00908 ( 1) link_ALPHA1-6 : angle 1.72218 ( 3) link_BETA1-4 : bond 0.00419 ( 12) link_BETA1-4 : angle 1.61687 ( 36) link_ALPHA1-3 : bond 0.00835 ( 1) link_ALPHA1-3 : angle 1.37960 ( 3) hydrogen bonds : bond 0.04893 ( 1147) hydrogen bonds : angle 4.73770 ( 3186) SS BOND : bond 0.00248 ( 40) SS BOND : angle 1.26932 ( 80) covalent geometry : bond 0.00248 (29677) covalent geometry : angle 0.53571 (40362) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 3.293 Fit side-chains revert: symmetry clash REVERT: A 515 PHE cc_start: 0.7253 (m-80) cc_final: 0.6925 (m-10) REVERT: B 160 TYR cc_start: 0.8211 (p90) cc_final: 0.7775 (p90) REVERT: C 340 GLU cc_start: 0.8874 (mp0) cc_final: 0.8300 (pm20) REVERT: C 357 ARG cc_start: 0.7208 (ttm170) cc_final: 0.7002 (ttm110) REVERT: C 528 LYS cc_start: 0.8207 (pttm) cc_final: 0.7601 (ttpp) REVERT: C 904 TYR cc_start: 0.8633 (m-80) cc_final: 0.8318 (m-10) REVERT: D 231 GLU cc_start: 0.7543 (mm-30) cc_final: 0.7236 (pt0) REVERT: D 323 MET cc_start: 0.6172 (mmt) cc_final: 0.5732 (tpp) REVERT: D 332 MET cc_start: 0.4038 (ppp) cc_final: 0.3822 (ppp) REVERT: D 376 MET cc_start: 0.7982 (tpp) cc_final: 0.7453 (mtp) REVERT: D 455 MET cc_start: 0.6357 (tmm) cc_final: 0.5776 (ptm) REVERT: D 579 MET cc_start: 0.1041 (mtt) cc_final: 0.0725 (mmt) outliers start: 29 outliers final: 18 residues processed: 191 average time/residue: 0.3717 time to fit residues: 119.6568 Evaluate side-chains 179 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 161 time to evaluate : 3.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 410 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 100 optimal weight: 0.8980 chunk 46 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 143 optimal weight: 9.9990 chunk 289 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 317 optimal weight: 40.0000 chunk 41 optimal weight: 7.9990 chunk 109 optimal weight: 20.0000 chunk 295 optimal weight: 5.9990 chunk 203 optimal weight: 7.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS A 901 GLN B 690 GLN C 544 ASN C 564 GLN C 804 GLN D 345 HIS D 472 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.139141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.075745 restraints weight = 64123.017| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 3.21 r_work: 0.2767 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.077 29776 Z= 0.371 Angle : 0.783 11.385 40619 Z= 0.396 Chirality : 0.053 0.569 4699 Planarity : 0.005 0.051 5130 Dihedral : 7.839 106.182 5058 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.39 % Favored : 94.58 % Rotamer: Outliers : 1.53 % Allowed : 9.78 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.14), residues: 3523 helix: 1.38 (0.16), residues: 1042 sheet: 0.35 (0.19), residues: 710 loop : -1.43 (0.14), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 353 HIS 0.009 0.002 HIS C1064 PHE 0.029 0.003 PHE A 58 TYR 0.021 0.002 TYR B1067 ARG 0.005 0.001 ARG C 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00596 ( 45) link_NAG-ASN : angle 3.64124 ( 135) link_ALPHA1-6 : bond 0.01037 ( 1) link_ALPHA1-6 : angle 1.71327 ( 3) link_BETA1-4 : bond 0.00575 ( 12) link_BETA1-4 : angle 2.14749 ( 36) link_ALPHA1-3 : bond 0.00854 ( 1) link_ALPHA1-3 : angle 1.03784 ( 3) hydrogen bonds : bond 0.08248 ( 1147) hydrogen bonds : angle 5.28562 ( 3186) SS BOND : bond 0.00536 ( 40) SS BOND : angle 2.13998 ( 80) covalent geometry : bond 0.00924 (29677) covalent geometry : angle 0.74805 (40362) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 167 time to evaluate : 3.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 PRO cc_start: 0.8041 (Cg_endo) cc_final: 0.7834 (Cg_exo) REVERT: A 515 PHE cc_start: 0.7647 (m-80) cc_final: 0.7299 (m-10) REVERT: A 1118 ASP cc_start: 0.8759 (p0) cc_final: 0.8426 (t0) REVERT: B 106 PHE cc_start: 0.8436 (m-10) cc_final: 0.8182 (m-10) REVERT: B 464 PHE cc_start: 0.8897 (m-80) cc_final: 0.8684 (m-80) REVERT: B 895 GLN cc_start: 0.9304 (OUTLIER) cc_final: 0.9095 (pm20) REVERT: C 314 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.8327 (tp-100) REVERT: C 528 LYS cc_start: 0.8194 (pttm) cc_final: 0.7591 (ptmm) REVERT: D 231 GLU cc_start: 0.7573 (mm-30) cc_final: 0.7325 (pt0) REVERT: D 249 MET cc_start: 0.3300 (mmm) cc_final: 0.2915 (mmt) REVERT: D 323 MET cc_start: 0.6724 (mmt) cc_final: 0.6292 (mmt) REVERT: D 376 MET cc_start: 0.8040 (tpp) cc_final: 0.7422 (mtp) REVERT: D 557 MET cc_start: 0.8474 (tpt) cc_final: 0.8071 (mmp) REVERT: D 579 MET cc_start: 0.1026 (mtt) cc_final: 0.0137 (mmm) outliers start: 48 outliers final: 32 residues processed: 206 average time/residue: 0.3688 time to fit residues: 127.9728 Evaluate side-chains 191 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 157 time to evaluate : 3.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 280 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 317 optimal weight: 30.0000 chunk 215 optimal weight: 0.7980 chunk 301 optimal weight: 5.9990 chunk 320 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 chunk 198 optimal weight: 0.8980 chunk 128 optimal weight: 7.9990 chunk 324 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 334 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C1088 HIS D 373 HIS ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.140006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.078250 restraints weight = 64393.052| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 3.58 r_work: 0.2780 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 29776 Z= 0.235 Angle : 0.656 11.313 40619 Z= 0.328 Chirality : 0.048 0.503 4699 Planarity : 0.004 0.057 5130 Dihedral : 7.371 106.394 5058 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.29 % Favored : 95.69 % Rotamer: Outliers : 1.59 % Allowed : 10.80 % Favored : 87.61 % 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: -0.18 (0.14), residues: 3523 helix: 1.55 (0.16), residues: 1043 sheet: 0.44 (0.19), residues: 718 loop : -1.44 (0.14), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 436 HIS 0.006 0.001 HIS C1064 PHE 0.025 0.002 PHE A 168 TYR 0.020 0.001 TYR B1067 ARG 0.004 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00488 ( 45) link_NAG-ASN : angle 3.36211 ( 135) link_ALPHA1-6 : bond 0.01023 ( 1) link_ALPHA1-6 : angle 1.63655 ( 3) link_BETA1-4 : bond 0.00430 ( 12) link_BETA1-4 : angle 1.73457 ( 36) link_ALPHA1-3 : bond 0.00971 ( 1) link_ALPHA1-3 : angle 1.24643 ( 3) hydrogen bonds : bond 0.06520 ( 1147) hydrogen bonds : angle 4.97758 ( 3186) SS BOND : bond 0.00304 ( 40) SS BOND : angle 1.77565 ( 80) covalent geometry : bond 0.00576 (29677) covalent geometry : angle 0.62081 (40362) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 162 time to evaluate : 3.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 515 PHE cc_start: 0.7732 (m-80) cc_final: 0.7451 (m-10) REVERT: B 160 TYR cc_start: 0.8305 (p90) cc_final: 0.7657 (p90) REVERT: B 339 HIS cc_start: 0.8968 (OUTLIER) cc_final: 0.8729 (m90) REVERT: C 528 LYS cc_start: 0.8172 (pttm) cc_final: 0.7704 (ttpp) REVERT: C 904 TYR cc_start: 0.8819 (m-80) cc_final: 0.8538 (m-80) REVERT: D 231 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7315 (pt0) REVERT: D 557 MET cc_start: 0.8455 (tpt) cc_final: 0.8085 (mmp) REVERT: D 579 MET cc_start: 0.1102 (mtt) cc_final: 0.0218 (mmm) outliers start: 50 outliers final: 34 residues processed: 200 average time/residue: 0.3641 time to fit residues: 122.6381 Evaluate side-chains 185 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 150 time to evaluate : 3.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 339 HIS Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 280 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 137 optimal weight: 9.9990 chunk 111 optimal weight: 5.9990 chunk 112 optimal weight: 8.9990 chunk 200 optimal weight: 0.8980 chunk 181 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 302 optimal weight: 0.9990 chunk 344 optimal weight: 7.9990 chunk 104 optimal weight: 2.9990 chunk 308 optimal weight: 8.9990 chunk 231 optimal weight: 6.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN D 58 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.139818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.077275 restraints weight = 64336.830| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 3.25 r_work: 0.2796 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 29776 Z= 0.221 Angle : 0.654 12.246 40619 Z= 0.325 Chirality : 0.048 0.475 4699 Planarity : 0.004 0.053 5130 Dihedral : 7.082 104.883 5058 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.83 % Favored : 95.15 % Rotamer: Outliers : 1.59 % Allowed : 11.56 % Favored : 86.85 % 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: -0.15 (0.14), residues: 3523 helix: 1.62 (0.16), residues: 1044 sheet: 0.46 (0.19), residues: 728 loop : -1.48 (0.14), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 436 HIS 0.005 0.001 HIS B1064 PHE 0.017 0.002 PHE A 392 TYR 0.018 0.001 TYR B1067 ARG 0.005 0.000 ARG D 245 Details of bonding type rmsd link_NAG-ASN : bond 0.00481 ( 45) link_NAG-ASN : angle 3.28054 ( 135) link_ALPHA1-6 : bond 0.00910 ( 1) link_ALPHA1-6 : angle 1.18064 ( 3) link_BETA1-4 : bond 0.00462 ( 12) link_BETA1-4 : angle 1.63820 ( 36) link_ALPHA1-3 : bond 0.00869 ( 1) link_ALPHA1-3 : angle 1.16384 ( 3) hydrogen bonds : bond 0.06354 ( 1147) hydrogen bonds : angle 4.89230 ( 3186) SS BOND : bond 0.00343 ( 40) SS BOND : angle 1.74017 ( 80) covalent geometry : bond 0.00542 (29677) covalent geometry : angle 0.62142 (40362) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 161 time to evaluate : 2.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 515 PHE cc_start: 0.7757 (m-80) cc_final: 0.7172 (m-10) REVERT: A 1118 ASP cc_start: 0.8746 (p0) cc_final: 0.8325 (t0) REVERT: B 160 TYR cc_start: 0.8388 (p90) cc_final: 0.7726 (p90) REVERT: B 339 HIS cc_start: 0.9008 (OUTLIER) cc_final: 0.8773 (m90) REVERT: B 453 TYR cc_start: 0.6591 (p90) cc_final: 0.6363 (p90) REVERT: C 271 GLN cc_start: 0.8444 (tp-100) cc_final: 0.8161 (tp40) REVERT: C 528 LYS cc_start: 0.8090 (pttm) cc_final: 0.7745 (ttpp) REVERT: C 904 TYR cc_start: 0.8777 (m-80) cc_final: 0.8540 (m-80) REVERT: D 231 GLU cc_start: 0.7636 (mm-30) cc_final: 0.7359 (pt0) REVERT: D 323 MET cc_start: 0.6245 (mmt) cc_final: 0.5824 (mmt) REVERT: D 366 MET cc_start: 0.3638 (tpp) cc_final: 0.2710 (mmm) REVERT: D 376 MET cc_start: 0.7995 (tpp) cc_final: 0.7427 (ttm) REVERT: D 557 MET cc_start: 0.8443 (tpt) cc_final: 0.8083 (mmm) REVERT: D 579 MET cc_start: 0.0212 (mtt) cc_final: -0.0490 (mmm) outliers start: 50 outliers final: 37 residues processed: 200 average time/residue: 0.3488 time to fit residues: 118.6293 Evaluate side-chains 190 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 152 time to evaluate : 3.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 339 HIS Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 280 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 339 optimal weight: 20.0000 chunk 198 optimal weight: 0.9990 chunk 197 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 185 optimal weight: 1.9990 chunk 307 optimal weight: 20.0000 chunk 186 optimal weight: 0.9980 chunk 15 optimal weight: 0.0870 chunk 1 optimal weight: 3.9990 chunk 68 optimal weight: 0.0770 chunk 247 optimal weight: 1.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN A 207 HIS A 901 GLN C 394 ASN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.142057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.081170 restraints weight = 64778.430| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 3.41 r_work: 0.2863 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 29776 Z= 0.105 Angle : 0.572 11.316 40619 Z= 0.281 Chirality : 0.045 0.412 4699 Planarity : 0.004 0.048 5130 Dihedral : 6.552 104.064 5058 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.38 % Favored : 96.59 % Rotamer: Outliers : 1.15 % Allowed : 12.17 % Favored : 86.69 % 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: 0.18 (0.14), residues: 3523 helix: 1.97 (0.16), residues: 1034 sheet: 0.74 (0.19), residues: 735 loop : -1.37 (0.14), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 436 HIS 0.002 0.001 HIS B1064 PHE 0.020 0.001 PHE A 168 TYR 0.013 0.001 TYR A1067 ARG 0.004 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00528 ( 45) link_NAG-ASN : angle 3.03452 ( 135) link_ALPHA1-6 : bond 0.01087 ( 1) link_ALPHA1-6 : angle 1.48212 ( 3) link_BETA1-4 : bond 0.00426 ( 12) link_BETA1-4 : angle 1.39985 ( 36) link_ALPHA1-3 : bond 0.00737 ( 1) link_ALPHA1-3 : angle 1.38512 ( 3) hydrogen bonds : bond 0.04656 ( 1147) hydrogen bonds : angle 4.60547 ( 3186) SS BOND : bond 0.00334 ( 40) SS BOND : angle 1.31836 ( 80) covalent geometry : bond 0.00222 (29677) covalent geometry : angle 0.54180 (40362) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 160 time to evaluate : 3.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 515 PHE cc_start: 0.7689 (m-80) cc_final: 0.7284 (m-10) REVERT: B 160 TYR cc_start: 0.8336 (p90) cc_final: 0.7696 (p90) REVERT: B 339 HIS cc_start: 0.8959 (OUTLIER) cc_final: 0.8725 (m90) REVERT: B 421 TYR cc_start: 0.8757 (m-10) cc_final: 0.8531 (m-10) REVERT: C 116 SER cc_start: 0.7523 (m) cc_final: 0.7243 (p) REVERT: C 271 GLN cc_start: 0.8448 (tp-100) cc_final: 0.8154 (tp40) REVERT: C 528 LYS cc_start: 0.8082 (pttm) cc_final: 0.7772 (ttpp) REVERT: C 787 GLN cc_start: 0.9392 (OUTLIER) cc_final: 0.8852 (mt0) REVERT: D 86 GLN cc_start: 0.7502 (tp40) cc_final: 0.7003 (pm20) REVERT: D 231 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7358 (pt0) REVERT: D 323 MET cc_start: 0.6352 (mmt) cc_final: 0.5483 (mmt) REVERT: D 366 MET cc_start: 0.3713 (tpp) cc_final: 0.2801 (mmm) REVERT: D 376 MET cc_start: 0.7917 (tpp) cc_final: 0.7145 (mtp) REVERT: D 557 MET cc_start: 0.8465 (tpt) cc_final: 0.8098 (mmm) REVERT: D 579 MET cc_start: 0.0123 (mtt) cc_final: -0.0501 (mmm) outliers start: 36 outliers final: 25 residues processed: 185 average time/residue: 0.3622 time to fit residues: 114.0611 Evaluate side-chains 176 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 149 time to evaluate : 3.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 339 HIS Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 280 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 52 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 199 optimal weight: 9.9990 chunk 183 optimal weight: 5.9990 chunk 142 optimal weight: 10.0000 chunk 182 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 329 optimal weight: 20.0000 chunk 104 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN C 394 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.139793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.076938 restraints weight = 64527.712| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 3.10 r_work: 0.2812 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 29776 Z= 0.223 Angle : 0.638 11.080 40619 Z= 0.317 Chirality : 0.047 0.459 4699 Planarity : 0.004 0.047 5130 Dihedral : 6.653 102.340 5058 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.74 % Favored : 95.23 % Rotamer: Outliers : 1.40 % Allowed : 12.17 % Favored : 86.43 % 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: 0.04 (0.14), residues: 3523 helix: 1.83 (0.16), residues: 1038 sheet: 0.58 (0.19), residues: 738 loop : -1.41 (0.14), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 436 HIS 0.005 0.001 HIS B1064 PHE 0.013 0.002 PHE C 92 TYR 0.018 0.001 TYR B 904 ARG 0.004 0.000 ARG B1000 Details of bonding type rmsd link_NAG-ASN : bond 0.00467 ( 45) link_NAG-ASN : angle 3.21879 ( 135) link_ALPHA1-6 : bond 0.00731 ( 1) link_ALPHA1-6 : angle 1.27681 ( 3) link_BETA1-4 : bond 0.00432 ( 12) link_BETA1-4 : angle 1.55120 ( 36) link_ALPHA1-3 : bond 0.00802 ( 1) link_ALPHA1-3 : angle 1.27101 ( 3) hydrogen bonds : bond 0.06286 ( 1147) hydrogen bonds : angle 4.81188 ( 3186) SS BOND : bond 0.00372 ( 40) SS BOND : angle 1.71342 ( 80) covalent geometry : bond 0.00551 (29677) covalent geometry : angle 0.60586 (40362) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 159 time to evaluate : 3.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 515 PHE cc_start: 0.7740 (m-80) cc_final: 0.7156 (m-10) REVERT: B 160 TYR cc_start: 0.8426 (p90) cc_final: 0.7754 (p90) REVERT: B 339 HIS cc_start: 0.8990 (OUTLIER) cc_final: 0.8767 (m90) REVERT: C 116 SER cc_start: 0.7744 (m) cc_final: 0.7518 (p) REVERT: C 271 GLN cc_start: 0.8478 (tp-100) cc_final: 0.8172 (tp40) REVERT: C 528 LYS cc_start: 0.8012 (pttm) cc_final: 0.7728 (ttpp) REVERT: C 787 GLN cc_start: 0.9433 (OUTLIER) cc_final: 0.8912 (mt0) REVERT: C 904 TYR cc_start: 0.8769 (m-80) cc_final: 0.8484 (m-80) REVERT: C 990 GLU cc_start: 0.8872 (tt0) cc_final: 0.8588 (tm-30) REVERT: D 231 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7384 (pt0) REVERT: D 366 MET cc_start: 0.3805 (tpp) cc_final: 0.2936 (mmm) REVERT: D 376 MET cc_start: 0.7807 (tpp) cc_final: 0.7022 (mtp) REVERT: D 557 MET cc_start: 0.8406 (tpt) cc_final: 0.8089 (mmm) REVERT: D 579 MET cc_start: 0.0140 (mtt) cc_final: -0.0456 (mmm) outliers start: 44 outliers final: 33 residues processed: 192 average time/residue: 0.3549 time to fit residues: 115.7135 Evaluate side-chains 190 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 155 time to evaluate : 3.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 339 HIS Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 280 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 33 optimal weight: 7.9990 chunk 237 optimal weight: 6.9990 chunk 270 optimal weight: 0.6980 chunk 271 optimal weight: 0.7980 chunk 229 optimal weight: 0.0470 chunk 251 optimal weight: 0.6980 chunk 140 optimal weight: 9.9990 chunk 336 optimal weight: 1.9990 chunk 282 optimal weight: 6.9990 chunk 351 optimal weight: 0.9990 chunk 213 optimal weight: 0.8980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS C 394 ASN C 992 GLN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.142046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.082168 restraints weight = 64550.810| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 3.57 r_work: 0.2855 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 29776 Z= 0.108 Angle : 0.567 10.863 40619 Z= 0.278 Chirality : 0.045 0.401 4699 Planarity : 0.004 0.051 5130 Dihedral : 6.262 101.906 5058 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.32 % Favored : 96.65 % Rotamer: Outliers : 1.11 % Allowed : 12.32 % Favored : 86.56 % 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: 0.25 (0.14), residues: 3523 helix: 2.05 (0.17), residues: 1033 sheet: 0.70 (0.19), residues: 763 loop : -1.33 (0.14), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 436 HIS 0.003 0.001 HIS B1064 PHE 0.018 0.001 PHE A 168 TYR 0.013 0.001 TYR A1067 ARG 0.003 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00512 ( 45) link_NAG-ASN : angle 2.98365 ( 135) link_ALPHA1-6 : bond 0.00780 ( 1) link_ALPHA1-6 : angle 1.33054 ( 3) link_BETA1-4 : bond 0.00442 ( 12) link_BETA1-4 : angle 1.35942 ( 36) link_ALPHA1-3 : bond 0.00696 ( 1) link_ALPHA1-3 : angle 1.37030 ( 3) hydrogen bonds : bond 0.04559 ( 1147) hydrogen bonds : angle 4.56668 ( 3186) SS BOND : bond 0.00321 ( 40) SS BOND : angle 1.28224 ( 80) covalent geometry : bond 0.00236 (29677) covalent geometry : angle 0.53672 (40362) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 162 time to evaluate : 3.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 515 PHE cc_start: 0.7736 (m-80) cc_final: 0.7139 (m-10) REVERT: B 160 TYR cc_start: 0.8359 (p90) cc_final: 0.7702 (p90) REVERT: B 339 HIS cc_start: 0.8923 (OUTLIER) cc_final: 0.8695 (m90) REVERT: B 364 ASP cc_start: 0.8724 (m-30) cc_final: 0.7774 (t0) REVERT: B 421 TYR cc_start: 0.8831 (m-80) cc_final: 0.8432 (m-10) REVERT: C 116 SER cc_start: 0.7835 (m) cc_final: 0.7589 (p) REVERT: C 200 TYR cc_start: 0.8600 (m-80) cc_final: 0.8247 (m-80) REVERT: C 271 GLN cc_start: 0.8468 (tp-100) cc_final: 0.8180 (tp40) REVERT: C 528 LYS cc_start: 0.8020 (pttm) cc_final: 0.7747 (ttpp) REVERT: C 787 GLN cc_start: 0.9403 (OUTLIER) cc_final: 0.8877 (mt0) REVERT: C 904 TYR cc_start: 0.8688 (m-80) cc_final: 0.8462 (m-10) REVERT: D 86 GLN cc_start: 0.7390 (tp40) cc_final: 0.6910 (pm20) REVERT: D 231 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7386 (pt0) REVERT: D 323 MET cc_start: 0.6359 (mmt) cc_final: 0.5812 (mmt) REVERT: D 366 MET cc_start: 0.3898 (tpp) cc_final: 0.2815 (mmm) REVERT: D 376 MET cc_start: 0.7847 (tpp) cc_final: 0.7064 (mtp) REVERT: D 455 MET cc_start: 0.6508 (tmm) cc_final: 0.6064 (ppp) REVERT: D 557 MET cc_start: 0.8382 (tpt) cc_final: 0.8084 (mmm) REVERT: D 579 MET cc_start: -0.0028 (mtt) cc_final: -0.0464 (mmm) outliers start: 35 outliers final: 30 residues processed: 186 average time/residue: 0.3692 time to fit residues: 117.1545 Evaluate side-chains 188 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 156 time to evaluate : 3.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 339 HIS Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 280 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 283 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 352 optimal weight: 10.0000 chunk 317 optimal weight: 2.9990 chunk 147 optimal weight: 0.0470 chunk 129 optimal weight: 0.4980 chunk 124 optimal weight: 0.0370 chunk 54 optimal weight: 0.5980 chunk 132 optimal weight: 8.9990 chunk 30 optimal weight: 6.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 755 GLN C 394 ASN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.142777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.083196 restraints weight = 64782.305| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 3.66 r_work: 0.2873 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 29776 Z= 0.101 Angle : 0.548 10.463 40619 Z= 0.269 Chirality : 0.044 0.371 4699 Planarity : 0.004 0.050 5130 Dihedral : 5.958 98.888 5058 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.83 % Favored : 96.14 % Rotamer: Outliers : 1.02 % Allowed : 12.74 % Favored : 86.24 % 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: 0.37 (0.14), residues: 3523 helix: 2.17 (0.17), residues: 1034 sheet: 0.79 (0.19), residues: 757 loop : -1.27 (0.14), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 436 HIS 0.002 0.000 HIS B1064 PHE 0.022 0.001 PHE B 456 TYR 0.026 0.001 TYR B 453 ARG 0.009 0.000 ARG B 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00511 ( 45) link_NAG-ASN : angle 2.77910 ( 135) link_ALPHA1-6 : bond 0.00608 ( 1) link_ALPHA1-6 : angle 1.22668 ( 3) link_BETA1-4 : bond 0.00413 ( 12) link_BETA1-4 : angle 1.31998 ( 36) link_ALPHA1-3 : bond 0.00681 ( 1) link_ALPHA1-3 : angle 1.37328 ( 3) hydrogen bonds : bond 0.04185 ( 1147) hydrogen bonds : angle 4.42747 ( 3186) SS BOND : bond 0.00273 ( 40) SS BOND : angle 1.13109 ( 80) covalent geometry : bond 0.00220 (29677) covalent geometry : angle 0.52141 (40362) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24756.51 seconds wall clock time: 425 minutes 54.33 seconds (25554.33 seconds total)