Starting phenix.real_space_refine on Tue Aug 26 04:24:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jyn_36727/08_2025/8jyn_36727.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jyn_36727/08_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_36727/08_2025/8jyn_36727.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jyn_36727/08_2025/8jyn_36727.map" model { file = "/net/cci-nas-00/data/ceres_data/8jyn_36727/08_2025/8jyn_36727.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jyn_36727/08_2025/8jyn_36727.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 6.80, per 1000 atoms: 0.23 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: 2.54 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.2 microseconds 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: 1.41 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: 5.87 Time building geometry restraints manager: 3.36 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 1310)) selection = (chain 'B' and (resid 25 through 65 or resid 86 through 177 or resid 188 through \ 620 or resid 640 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 1310)) } 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: 3.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 27.290 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.090 ------------------------------------------------------------------------------- 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 : 4.48 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG D 204 TYR 0.012 0.001 TYR B1067 PHE 0.027 0.001 PHE B 906 TRP 0.013 0.001 TRP C 886 HIS 0.003 0.000 HIS B 339 Details of bonding type rmsd covalent geometry : bond 0.00322 (29677) covalent geometry : angle 0.53515 (40362) SS BOND : bond 0.00315 ( 40) SS BOND : angle 1.19406 ( 80) hydrogen bonds : bond 0.21536 ( 1147) hydrogen bonds : angle 7.21272 ( 3186) link_ALPHA1-3 : bond 0.00354 ( 1) link_ALPHA1-3 : angle 1.52854 ( 3) 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_NAG-ASN : bond 0.00641 ( 45) link_NAG-ASN : angle 3.55174 ( 135) *********************** 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 : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 TRP cc_start: 0.2811 (p-90) cc_final: 0.2099 (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: 0.6834 (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: 0.1862 time to fit residues: 80.8903 Evaluate side-chains 174 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 20.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS 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 = 0.4190 r_free = 0.4190 target = 0.142684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.080605 restraints weight = 64441.499| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 3.66 r_work: 0.2831 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 29776 Z= 0.228 Angle : 0.677 12.665 40619 Z= 0.340 Chirality : 0.050 0.474 4699 Planarity : 0.005 0.048 5130 Dihedral : 8.816 108.349 5058 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.34 % Favored : 95.63 % Rotamer: Outliers : 0.61 % Allowed : 5.76 % Favored : 93.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.14), residues: 3523 helix: 1.81 (0.16), residues: 1027 sheet: 0.81 (0.19), residues: 726 loop : -1.28 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 177 TYR 0.022 0.002 TYR B1067 PHE 0.035 0.002 PHE B 906 TRP 0.025 0.002 TRP C 353 HIS 0.006 0.001 HIS D 535 Details of bonding type rmsd covalent geometry : bond 0.00552 (29677) covalent geometry : angle 0.64081 (40362) SS BOND : bond 0.00389 ( 40) SS BOND : angle 1.67298 ( 80) hydrogen bonds : bond 0.06718 ( 1147) hydrogen bonds : angle 5.35570 ( 3186) link_ALPHA1-3 : bond 0.00881 ( 1) link_ALPHA1-3 : angle 2.38842 ( 3) link_ALPHA1-6 : bond 0.00301 ( 1) link_ALPHA1-6 : angle 1.98861 ( 3) link_BETA1-4 : bond 0.00378 ( 12) link_BETA1-4 : angle 1.92504 ( 36) link_NAG-ASN : bond 0.00730 ( 45) link_NAG-ASN : angle 3.48859 ( 135) *********************** 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 216 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 197 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 PHE cc_start: 0.6611 (t80) cc_final: 0.6255 (t80) REVERT: A 353 TRP cc_start: 0.4987 (p-90) cc_final: 0.2717 (p-90) REVERT: A 515 PHE cc_start: 0.7077 (m-80) cc_final: 0.6645 (m-10) REVERT: B 160 TYR cc_start: 0.8277 (p90) cc_final: 0.7830 (p90) REVERT: B 398 ASP cc_start: 0.7068 (m-30) cc_final: 0.6484 (p0) REVERT: B 423 TYR cc_start: 0.7754 (t80) cc_final: 0.7482 (t80) REVERT: B 449 TYR cc_start: 0.8459 (m-80) cc_final: 0.8239 (t80) REVERT: C 235 ILE cc_start: 0.6028 (mm) cc_final: 0.5784 (mm) REVERT: C 357 ARG cc_start: 0.7131 (ttm170) cc_final: 0.6890 (ttm110) REVERT: C 528 LYS cc_start: 0.8190 (pttm) cc_final: 0.7552 (ttpp) REVERT: D 231 GLU cc_start: 0.7543 (mm-30) cc_final: 0.7224 (pt0) REVERT: D 329 GLU cc_start: 0.7098 (mm-30) cc_final: 0.6849 (mm-30) REVERT: D 455 MET cc_start: 0.6460 (tmm) cc_final: 0.5882 (ptm) outliers start: 19 outliers final: 12 residues processed: 208 average time/residue: 0.1690 time to fit residues: 58.4007 Evaluate side-chains 185 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 173 time to evaluate : 0.994 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 31 optimal weight: 9.9990 chunk 146 optimal weight: 9.9990 chunk 176 optimal weight: 0.9990 chunk 254 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 267 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 244 optimal weight: 9.9990 chunk 23 optimal weight: 0.3980 chunk 102 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 524 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.143747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.083304 restraints weight = 64684.300| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 3.82 r_work: 0.2854 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29776 Z= 0.129 Angle : 0.581 10.912 40619 Z= 0.285 Chirality : 0.046 0.405 4699 Planarity : 0.004 0.046 5130 Dihedral : 7.784 106.941 5058 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.24 % Favored : 96.74 % Rotamer: Outliers : 0.83 % Allowed : 7.99 % Favored : 91.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.14), residues: 3523 helix: 1.95 (0.16), residues: 1037 sheet: 0.94 (0.19), residues: 740 loop : -1.25 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 357 TYR 0.014 0.001 TYR B1067 PHE 0.019 0.001 PHE B 106 TRP 0.023 0.001 TRP C 353 HIS 0.004 0.001 HIS D 535 Details of bonding type rmsd covalent geometry : bond 0.00291 (29677) covalent geometry : angle 0.54766 (40362) SS BOND : bond 0.00287 ( 40) SS BOND : angle 1.32345 ( 80) hydrogen bonds : bond 0.05303 ( 1147) hydrogen bonds : angle 4.88242 ( 3186) link_ALPHA1-3 : bond 0.01017 ( 1) link_ALPHA1-3 : angle 1.22101 ( 3) link_ALPHA1-6 : bond 0.00831 ( 1) link_ALPHA1-6 : angle 1.78174 ( 3) link_BETA1-4 : bond 0.00484 ( 12) link_BETA1-4 : angle 1.67115 ( 36) link_NAG-ASN : bond 0.00637 ( 45) link_NAG-ASN : angle 3.15869 ( 135) *********************** 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 204 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 178 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 515 PHE cc_start: 0.7162 (m-80) cc_final: 0.6840 (m-10) REVERT: B 160 TYR cc_start: 0.8206 (p90) cc_final: 0.7766 (p90) REVERT: B 398 ASP cc_start: 0.6781 (m-30) cc_final: 0.6524 (p0) REVERT: B 423 TYR cc_start: 0.7625 (t80) cc_final: 0.7378 (t80) REVERT: C 235 ILE cc_start: 0.6091 (mm) cc_final: 0.5887 (mm) REVERT: C 528 LYS cc_start: 0.8162 (pttm) cc_final: 0.7585 (ttpp) REVERT: C 904 TYR cc_start: 0.8659 (m-80) cc_final: 0.8279 (m-10) REVERT: D 231 GLU cc_start: 0.7554 (mm-30) cc_final: 0.7238 (pt0) REVERT: D 383 MET cc_start: 0.6365 (mtm) cc_final: 0.6109 (mtm) REVERT: D 579 MET cc_start: 0.2272 (mtt) cc_final: 0.1865 (mmt) outliers start: 26 outliers final: 16 residues processed: 196 average time/residue: 0.1579 time to fit residues: 52.8600 Evaluate side-chains 177 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 161 time to evaluate : 1.046 ------------------------------------------------------------------------------- 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 118 LEU Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 389 ASP 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 C residue 976 VAL Chi-restraints excluded: chain D residue 280 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 51 optimal weight: 3.9990 chunk 45 optimal weight: 0.4980 chunk 272 optimal weight: 0.9990 chunk 230 optimal weight: 7.9990 chunk 337 optimal weight: 30.0000 chunk 168 optimal weight: 0.9980 chunk 299 optimal weight: 30.0000 chunk 157 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 C 394 ASN C 544 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.143716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.084773 restraints weight = 64573.750| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 3.92 r_work: 0.2844 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 29776 Z= 0.119 Angle : 0.573 12.820 40619 Z= 0.279 Chirality : 0.046 0.403 4699 Planarity : 0.004 0.046 5130 Dihedral : 7.284 105.620 5058 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.75 % Favored : 96.22 % Rotamer: Outliers : 0.92 % Allowed : 9.08 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.14), residues: 3523 helix: 1.97 (0.16), residues: 1034 sheet: 0.93 (0.19), residues: 741 loop : -1.24 (0.14), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 357 TYR 0.015 0.001 TYR D 50 PHE 0.020 0.001 PHE B 106 TRP 0.024 0.001 TRP C 353 HIS 0.003 0.001 HIS D 535 Details of bonding type rmsd covalent geometry : bond 0.00269 (29677) covalent geometry : angle 0.53755 (40362) SS BOND : bond 0.00259 ( 40) SS BOND : angle 1.26891 ( 80) hydrogen bonds : bond 0.04975 ( 1147) hydrogen bonds : angle 4.72201 ( 3186) link_ALPHA1-3 : bond 0.01059 ( 1) link_ALPHA1-3 : angle 1.57717 ( 3) link_ALPHA1-6 : bond 0.00818 ( 1) link_ALPHA1-6 : angle 1.62852 ( 3) link_BETA1-4 : bond 0.00426 ( 12) link_BETA1-4 : angle 1.62913 ( 36) link_NAG-ASN : bond 0.00518 ( 45) link_NAG-ASN : angle 3.26202 ( 135) *********************** 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 197 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 1.026 Fit side-chains revert: symmetry clash REVERT: A 515 PHE cc_start: 0.7297 (m-80) cc_final: 0.6977 (m-10) REVERT: B 160 TYR cc_start: 0.8240 (p90) cc_final: 0.7807 (p90) REVERT: B 423 TYR cc_start: 0.7642 (t80) cc_final: 0.7363 (t80) REVERT: C 340 GLU cc_start: 0.8900 (mp0) cc_final: 0.8343 (pm20) REVERT: C 528 LYS cc_start: 0.8200 (pttm) cc_final: 0.7610 (ttpp) REVERT: C 904 TYR cc_start: 0.8609 (m-80) cc_final: 0.8294 (m-10) REVERT: D 231 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7257 (pt0) REVERT: D 249 MET cc_start: 0.3148 (mmm) cc_final: 0.2827 (mmt) REVERT: D 323 MET cc_start: 0.6071 (mmt) cc_final: 0.5056 (tpp) REVERT: D 376 MET cc_start: 0.7996 (tpp) cc_final: 0.7426 (mtp) REVERT: D 455 MET cc_start: 0.6354 (tmm) cc_final: 0.5759 (ptm) REVERT: D 579 MET cc_start: 0.1221 (mtt) cc_final: 0.0837 (mmt) outliers start: 29 outliers final: 22 residues processed: 188 average time/residue: 0.1618 time to fit residues: 51.6983 Evaluate side-chains 177 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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 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 389 ASP 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 233 ILE 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 973 ILE 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 348 optimal weight: 4.9990 chunk 350 optimal weight: 7.9990 chunk 135 optimal weight: 10.0000 chunk 276 optimal weight: 4.9990 chunk 151 optimal weight: 4.9990 chunk 290 optimal weight: 4.9990 chunk 292 optimal weight: 0.9990 chunk 194 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 58 optimal weight: 0.3980 chunk 234 optimal weight: 20.0000 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.141644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.080377 restraints weight = 64254.976| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 3.42 r_work: 0.2821 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 29776 Z= 0.198 Angle : 0.616 11.118 40619 Z= 0.308 Chirality : 0.047 0.445 4699 Planarity : 0.004 0.047 5130 Dihedral : 7.080 104.930 5058 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.09 % Favored : 95.88 % Rotamer: Outliers : 1.21 % Allowed : 9.87 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.14), residues: 3523 helix: 1.82 (0.16), residues: 1043 sheet: 0.76 (0.19), residues: 743 loop : -1.29 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1091 TYR 0.017 0.001 TYR B1067 PHE 0.015 0.002 PHE A 133 TRP 0.021 0.001 TRP C 353 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00481 (29677) covalent geometry : angle 0.58435 (40362) SS BOND : bond 0.00281 ( 40) SS BOND : angle 1.55455 ( 80) hydrogen bonds : bond 0.06190 ( 1147) hydrogen bonds : angle 4.83794 ( 3186) link_ALPHA1-3 : bond 0.01516 ( 1) link_ALPHA1-3 : angle 1.57403 ( 3) link_ALPHA1-6 : bond 0.00969 ( 1) link_ALPHA1-6 : angle 1.56393 ( 3) link_BETA1-4 : bond 0.00478 ( 12) link_BETA1-4 : angle 1.70632 ( 36) link_NAG-ASN : bond 0.00480 ( 45) link_NAG-ASN : angle 3.15076 ( 135) *********************** 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 202 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 164 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 PHE cc_start: 0.7215 (t80) cc_final: 0.6753 (t80) REVERT: A 515 PHE cc_start: 0.7517 (m-80) cc_final: 0.7141 (m-10) REVERT: B 106 PHE cc_start: 0.8213 (m-10) cc_final: 0.7959 (m-10) REVERT: B 160 TYR cc_start: 0.8379 (p90) cc_final: 0.7813 (p90) REVERT: B 423 TYR cc_start: 0.7752 (t80) cc_final: 0.7439 (t80) REVERT: C 528 LYS cc_start: 0.8233 (pttm) cc_final: 0.7658 (ttpp) REVERT: C 904 TYR cc_start: 0.8839 (m-80) cc_final: 0.8548 (m-80) REVERT: D 231 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7316 (pt0) REVERT: D 249 MET cc_start: 0.3420 (mmm) cc_final: 0.3124 (mmt) REVERT: D 323 MET cc_start: 0.6163 (mmt) cc_final: 0.4762 (tpp) REVERT: D 376 MET cc_start: 0.8172 (tpp) cc_final: 0.7440 (mtp) REVERT: D 557 MET cc_start: 0.8430 (tpt) cc_final: 0.7997 (mmt) REVERT: D 579 MET cc_start: 0.1013 (mtt) cc_final: -0.0001 (mmm) outliers start: 38 outliers final: 24 residues processed: 195 average time/residue: 0.1789 time to fit residues: 59.0807 Evaluate side-chains 179 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 155 time to evaluate : 1.137 ------------------------------------------------------------------------------- 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 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 A residue 1096 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 353 TRP 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 C residue 51 THR Chi-restraints excluded: chain C residue 270 LEU 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 976 VAL Chi-restraints excluded: chain C residue 1096 VAL 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 215 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 110 optimal weight: 9.9990 chunk 280 optimal weight: 2.9990 chunk 199 optimal weight: 10.0000 chunk 258 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 187 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 172 optimal weight: 0.6980 chunk 101 optimal weight: 0.0870 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS B 173 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS ** D 373 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 = 0.4198 r_free = 0.4198 target = 0.143256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.083533 restraints weight = 64329.255| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 3.81 r_work: 0.2844 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 29776 Z= 0.107 Angle : 0.558 11.440 40619 Z= 0.273 Chirality : 0.045 0.397 4699 Planarity : 0.004 0.045 5130 Dihedral : 6.570 104.424 5058 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.24 % Favored : 96.74 % Rotamer: Outliers : 1.18 % Allowed : 10.67 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.14), residues: 3523 helix: 2.09 (0.16), residues: 1026 sheet: 0.85 (0.19), residues: 752 loop : -1.22 (0.14), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 357 TYR 0.013 0.001 TYR C1067 PHE 0.017 0.001 PHE A 133 TRP 0.021 0.001 TRP C 353 HIS 0.003 0.001 HIS D 373 Details of bonding type rmsd covalent geometry : bond 0.00234 (29677) covalent geometry : angle 0.52707 (40362) SS BOND : bond 0.00238 ( 40) SS BOND : angle 1.24231 ( 80) hydrogen bonds : bond 0.04722 ( 1147) hydrogen bonds : angle 4.59026 ( 3186) link_ALPHA1-3 : bond 0.01181 ( 1) link_ALPHA1-3 : angle 1.54309 ( 3) link_ALPHA1-6 : bond 0.00814 ( 1) link_ALPHA1-6 : angle 1.29222 ( 3) link_BETA1-4 : bond 0.00420 ( 12) link_BETA1-4 : angle 1.42800 ( 36) link_NAG-ASN : bond 0.00518 ( 45) link_NAG-ASN : angle 2.99286 ( 135) *********************** 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 206 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 169 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 515 PHE cc_start: 0.7493 (m-80) cc_final: 0.7133 (m-10) REVERT: B 160 TYR cc_start: 0.8279 (p90) cc_final: 0.7788 (p90) REVERT: B 423 TYR cc_start: 0.7540 (t80) cc_final: 0.7187 (t80) REVERT: B 449 TYR cc_start: 0.8824 (OUTLIER) cc_final: 0.8261 (t80) REVERT: C 528 LYS cc_start: 0.8155 (pttm) cc_final: 0.7673 (ttpp) REVERT: D 86 GLN cc_start: 0.7365 (tp40) cc_final: 0.6839 (pm20) REVERT: D 231 GLU cc_start: 0.7600 (mm-30) cc_final: 0.7291 (pt0) REVERT: D 323 MET cc_start: 0.6124 (mmt) cc_final: 0.4634 (tpp) REVERT: D 376 MET cc_start: 0.8250 (tpp) cc_final: 0.7518 (mtp) REVERT: D 455 MET cc_start: 0.6547 (tmm) cc_final: 0.5999 (ppp) REVERT: D 557 MET cc_start: 0.8393 (tpt) cc_final: 0.7992 (mmt) REVERT: D 579 MET cc_start: 0.0491 (mtt) cc_final: -0.0065 (mmm) outliers start: 37 outliers final: 19 residues processed: 198 average time/residue: 0.1795 time to fit residues: 59.7311 Evaluate side-chains 170 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 1.008 ------------------------------------------------------------------------------- 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 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 B residue 118 LEU Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 449 TYR 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 C residue 51 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 916 LEU 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 213 optimal weight: 8.9990 chunk 329 optimal weight: 0.5980 chunk 310 optimal weight: 10.0000 chunk 355 optimal weight: 0.7980 chunk 309 optimal weight: 30.0000 chunk 118 optimal weight: 0.3980 chunk 296 optimal weight: 3.9990 chunk 319 optimal weight: 5.9990 chunk 128 optimal weight: 10.0000 chunk 194 optimal weight: 0.7980 chunk 135 optimal weight: 10.0000 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS B 173 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 GLN ** 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 = 0.4189 r_free = 0.4189 target = 0.142587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.082212 restraints weight = 64543.591| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 3.50 r_work: 0.2855 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29776 Z= 0.129 Angle : 0.566 10.909 40619 Z= 0.279 Chirality : 0.045 0.395 4699 Planarity : 0.004 0.058 5130 Dihedral : 6.307 103.251 5058 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.89 % Favored : 96.08 % Rotamer: Outliers : 1.18 % Allowed : 11.15 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.14), residues: 3523 helix: 2.12 (0.17), residues: 1028 sheet: 0.84 (0.19), residues: 761 loop : -1.23 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 357 TYR 0.015 0.001 TYR B1067 PHE 0.017 0.001 PHE A 133 TRP 0.021 0.001 TRP C 353 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00303 (29677) covalent geometry : angle 0.53593 (40362) SS BOND : bond 0.00294 ( 40) SS BOND : angle 1.33859 ( 80) hydrogen bonds : bond 0.04994 ( 1147) hydrogen bonds : angle 4.57857 ( 3186) link_ALPHA1-3 : bond 0.00986 ( 1) link_ALPHA1-3 : angle 1.35728 ( 3) link_ALPHA1-6 : bond 0.00941 ( 1) link_ALPHA1-6 : angle 1.29674 ( 3) link_BETA1-4 : bond 0.00435 ( 12) link_BETA1-4 : angle 1.43217 ( 36) link_NAG-ASN : bond 0.00488 ( 45) link_NAG-ASN : angle 2.98978 ( 135) *********************** 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 195 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 158 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 515 PHE cc_start: 0.7539 (m-80) cc_final: 0.7149 (m-10) REVERT: B 160 TYR cc_start: 0.8279 (p90) cc_final: 0.7761 (p90) REVERT: B 177 MET cc_start: 0.4398 (ppp) cc_final: 0.4015 (ppp) REVERT: B 423 TYR cc_start: 0.7597 (t80) cc_final: 0.7305 (t80) REVERT: B 449 TYR cc_start: 0.8823 (OUTLIER) cc_final: 0.8161 (t80) REVERT: C 904 TYR cc_start: 0.8785 (m-80) cc_final: 0.8553 (m-10) REVERT: D 86 GLN cc_start: 0.7297 (tp40) cc_final: 0.6768 (pm20) REVERT: D 231 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7324 (pt0) REVERT: D 249 MET cc_start: 0.3216 (mmp) cc_final: 0.3008 (mmp) REVERT: D 323 MET cc_start: 0.6100 (mmt) cc_final: 0.5432 (mmt) REVERT: D 360 MET cc_start: 0.0854 (ttp) cc_final: 0.0444 (ppp) REVERT: D 366 MET cc_start: 0.3667 (tpp) cc_final: 0.2912 (mmm) REVERT: D 376 MET cc_start: 0.8310 (tpp) cc_final: 0.7534 (mtp) REVERT: D 557 MET cc_start: 0.8472 (tpt) cc_final: 0.8030 (mmt) REVERT: D 579 MET cc_start: 0.0205 (mtt) cc_final: -0.0229 (mmm) outliers start: 37 outliers final: 24 residues processed: 184 average time/residue: 0.1803 time to fit residues: 55.9135 Evaluate side-chains 178 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 1.145 ------------------------------------------------------------------------------- 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 878 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 449 TYR 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 C residue 51 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 375 PHE 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 190 MET 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 7 optimal weight: 0.0170 chunk 67 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 303 optimal weight: 20.0000 chunk 325 optimal weight: 20.0000 chunk 280 optimal weight: 3.9990 chunk 190 optimal weight: 2.9990 chunk 169 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 311 optimal weight: 20.0000 overall best weight: 1.7624 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 345 HIS ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.141785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.081191 restraints weight = 64581.539| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 3.68 r_work: 0.2814 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 29776 Z= 0.152 Angle : 0.581 10.897 40619 Z= 0.287 Chirality : 0.046 0.414 4699 Planarity : 0.004 0.052 5130 Dihedral : 6.277 102.706 5058 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.83 % Favored : 96.14 % Rotamer: Outliers : 1.18 % Allowed : 11.34 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.14), residues: 3523 helix: 2.05 (0.16), residues: 1036 sheet: 0.79 (0.19), residues: 758 loop : -1.25 (0.14), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 357 TYR 0.024 0.001 TYR B 421 PHE 0.019 0.001 PHE A 133 TRP 0.022 0.001 TRP C 353 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00364 (29677) covalent geometry : angle 0.54995 (40362) SS BOND : bond 0.00320 ( 40) SS BOND : angle 1.42668 ( 80) hydrogen bonds : bond 0.05424 ( 1147) hydrogen bonds : angle 4.64076 ( 3186) link_ALPHA1-3 : bond 0.00772 ( 1) link_ALPHA1-3 : angle 1.35057 ( 3) link_ALPHA1-6 : bond 0.00797 ( 1) link_ALPHA1-6 : angle 1.22414 ( 3) link_BETA1-4 : bond 0.00444 ( 12) link_BETA1-4 : angle 1.44160 ( 36) link_NAG-ASN : bond 0.00465 ( 45) link_NAG-ASN : angle 3.04294 ( 135) *********************** 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 197 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 160 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 515 PHE cc_start: 0.7527 (m-80) cc_final: 0.7149 (m-10) REVERT: B 160 TYR cc_start: 0.8422 (p90) cc_final: 0.7815 (p90) REVERT: B 423 TYR cc_start: 0.7268 (t80) cc_final: 0.6881 (t80) REVERT: B 449 TYR cc_start: 0.8838 (OUTLIER) cc_final: 0.8181 (t80) REVERT: C 528 LYS cc_start: 0.8016 (pttm) cc_final: 0.7627 (ttpp) REVERT: C 904 TYR cc_start: 0.8620 (m-80) cc_final: 0.8308 (m-10) REVERT: D 231 GLU cc_start: 0.7624 (mm-30) cc_final: 0.7308 (pt0) REVERT: D 323 MET cc_start: 0.6302 (mmt) cc_final: 0.5580 (mmt) REVERT: D 360 MET cc_start: 0.0941 (ttp) cc_final: 0.0245 (ppp) REVERT: D 366 MET cc_start: 0.3630 (tpp) cc_final: 0.2690 (mmm) REVERT: D 376 MET cc_start: 0.8314 (tpp) cc_final: 0.7554 (mtp) REVERT: D 557 MET cc_start: 0.8459 (tpt) cc_final: 0.8063 (mmt) REVERT: D 579 MET cc_start: -0.0120 (mtt) cc_final: -0.0419 (mmm) outliers start: 37 outliers final: 29 residues processed: 187 average time/residue: 0.1823 time to fit residues: 56.8950 Evaluate side-chains 183 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 153 time to evaluate : 1.185 ------------------------------------------------------------------------------- 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 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 B residue 118 LEU Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 449 TYR 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 963 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1096 VAL 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 312 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 315 optimal weight: 20.0000 chunk 71 optimal weight: 0.5980 chunk 260 optimal weight: 1.9990 chunk 336 optimal weight: 20.0000 chunk 145 optimal weight: 5.9990 chunk 190 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 305 optimal weight: 8.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 505 HIS B 450 ASN ** C 394 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 = 0.4185 r_free = 0.4185 target = 0.142223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.081837 restraints weight = 64416.672| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 3.40 r_work: 0.2854 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 29776 Z= 0.126 Angle : 0.563 10.791 40619 Z= 0.278 Chirality : 0.045 0.398 4699 Planarity : 0.004 0.053 5130 Dihedral : 6.168 102.410 5058 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.75 % Favored : 96.22 % Rotamer: Outliers : 1.15 % Allowed : 11.66 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.14), residues: 3523 helix: 2.13 (0.16), residues: 1035 sheet: 0.77 (0.19), residues: 769 loop : -1.23 (0.14), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 403 TYR 0.015 0.001 TYR B1067 PHE 0.018 0.001 PHE B 375 TRP 0.020 0.001 TRP A 436 HIS 0.012 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00297 (29677) covalent geometry : angle 0.53349 (40362) SS BOND : bond 0.00303 ( 40) SS BOND : angle 1.32358 ( 80) hydrogen bonds : bond 0.04967 ( 1147) hydrogen bonds : angle 4.55531 ( 3186) link_ALPHA1-3 : bond 0.00742 ( 1) link_ALPHA1-3 : angle 1.36030 ( 3) link_ALPHA1-6 : bond 0.00741 ( 1) link_ALPHA1-6 : angle 1.22089 ( 3) link_BETA1-4 : bond 0.00397 ( 12) link_BETA1-4 : angle 1.36488 ( 36) link_NAG-ASN : bond 0.00479 ( 45) link_NAG-ASN : angle 2.94309 ( 135) *********************** 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 187 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 151 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 515 PHE cc_start: 0.7558 (m-80) cc_final: 0.7169 (m-10) REVERT: B 160 TYR cc_start: 0.8355 (p90) cc_final: 0.7775 (p90) REVERT: B 449 TYR cc_start: 0.8808 (OUTLIER) cc_final: 0.8110 (t80) REVERT: C 528 LYS cc_start: 0.8088 (pttm) cc_final: 0.7657 (ttpp) REVERT: C 904 TYR cc_start: 0.8759 (m-80) cc_final: 0.8524 (m-10) REVERT: D 231 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7308 (pt0) REVERT: D 323 MET cc_start: 0.6320 (mmt) cc_final: 0.5615 (mmt) REVERT: D 360 MET cc_start: 0.0962 (ttp) cc_final: 0.0224 (ppp) REVERT: D 366 MET cc_start: 0.3639 (tpp) cc_final: 0.2818 (mmm) REVERT: D 376 MET cc_start: 0.8305 (tpp) cc_final: 0.7544 (mtp) REVERT: D 557 MET cc_start: 0.8473 (tpt) cc_final: 0.8081 (mmt) REVERT: D 579 MET cc_start: -0.0119 (mtt) cc_final: -0.0440 (mmm) outliers start: 36 outliers final: 28 residues processed: 179 average time/residue: 0.1739 time to fit residues: 53.1349 Evaluate side-chains 181 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 152 time to evaluate : 1.154 ------------------------------------------------------------------------------- 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 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 878 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 449 TYR 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 963 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 916 LEU 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 145 optimal weight: 1.9990 chunk 229 optimal weight: 0.5980 chunk 119 optimal weight: 9.9990 chunk 51 optimal weight: 0.8980 chunk 225 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 161 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 242 optimal weight: 9.9990 chunk 75 optimal weight: 0.4980 chunk 123 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS B 450 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.142806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.082907 restraints weight = 64381.301| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 3.57 r_work: 0.2865 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 29776 Z= 0.109 Angle : 0.548 11.712 40619 Z= 0.268 Chirality : 0.044 0.377 4699 Planarity : 0.004 0.048 5130 Dihedral : 5.966 100.715 5058 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.63 % Favored : 96.34 % Rotamer: Outliers : 1.02 % Allowed : 11.82 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.14), residues: 3523 helix: 2.21 (0.17), residues: 1034 sheet: 0.90 (0.19), residues: 747 loop : -1.20 (0.14), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 357 TYR 0.014 0.001 TYR A1067 PHE 0.018 0.001 PHE B 375 TRP 0.021 0.001 TRP A 436 HIS 0.002 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00249 (29677) covalent geometry : angle 0.52159 (40362) SS BOND : bond 0.00271 ( 40) SS BOND : angle 1.15859 ( 80) hydrogen bonds : bond 0.04443 ( 1147) hydrogen bonds : angle 4.44722 ( 3186) link_ALPHA1-3 : bond 0.00700 ( 1) link_ALPHA1-3 : angle 1.40147 ( 3) link_ALPHA1-6 : bond 0.00776 ( 1) link_ALPHA1-6 : angle 1.27035 ( 3) link_BETA1-4 : bond 0.00419 ( 12) link_BETA1-4 : angle 1.31817 ( 36) link_NAG-ASN : bond 0.00492 ( 45) link_NAG-ASN : angle 2.79795 ( 135) ********************** 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 196 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 164 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 160 TYR cc_start: 0.8378 (p90) cc_final: 0.7786 (p90) REVERT: B 364 ASP cc_start: 0.8794 (m-30) cc_final: 0.7753 (t0) REVERT: B 449 TYR cc_start: 0.8813 (OUTLIER) cc_final: 0.8128 (t80) REVERT: B 450 ASN cc_start: 0.8317 (m-40) cc_final: 0.7681 (p0) REVERT: C 116 SER cc_start: 0.7526 (m) cc_final: 0.7239 (p) REVERT: C 528 LYS cc_start: 0.8066 (pttm) cc_final: 0.7576 (ptmm) REVERT: D 123 MET cc_start: 0.1355 (mtt) cc_final: 0.0732 (tpt) REVERT: D 231 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7408 (pt0) REVERT: D 323 MET cc_start: 0.6247 (mmt) cc_final: 0.5400 (tpt) REVERT: D 360 MET cc_start: 0.0979 (ttp) cc_final: 0.0149 (ppp) REVERT: D 366 MET cc_start: 0.3608 (tpp) cc_final: 0.2869 (mmm) REVERT: D 376 MET cc_start: 0.8250 (tpp) cc_final: 0.7483 (mtp) REVERT: D 455 MET cc_start: 0.6417 (tmm) cc_final: 0.5979 (ppp) REVERT: D 557 MET cc_start: 0.8455 (tpt) cc_final: 0.8065 (mmm) REVERT: D 579 MET cc_start: -0.0157 (mtt) cc_final: -0.0394 (mmm) outliers start: 32 outliers final: 27 residues processed: 186 average time/residue: 0.1800 time to fit residues: 56.6548 Evaluate side-chains 185 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 1.180 ------------------------------------------------------------------------------- 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 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 878 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 449 TYR 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 203 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 973 ILE 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 137 optimal weight: 8.9990 chunk 55 optimal weight: 0.6980 chunk 309 optimal weight: 20.0000 chunk 350 optimal weight: 5.9990 chunk 174 optimal weight: 0.7980 chunk 142 optimal weight: 6.9990 chunk 34 optimal weight: 20.0000 chunk 262 optimal weight: 0.9990 chunk 333 optimal weight: 7.9990 chunk 355 optimal weight: 5.9990 chunk 337 optimal weight: 9.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 339 HIS ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN C 804 GLN ** 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 = 0.4158 r_free = 0.4158 target = 0.140259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.077212 restraints weight = 64653.552| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 3.09 r_work: 0.2813 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 29776 Z= 0.224 Angle : 0.633 12.169 40619 Z= 0.314 Chirality : 0.047 0.447 4699 Planarity : 0.004 0.051 5130 Dihedral : 6.365 100.146 5058 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.54 % Favored : 95.43 % Rotamer: Outliers : 1.08 % Allowed : 11.88 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.14), residues: 3523 helix: 1.93 (0.16), residues: 1045 sheet: 0.70 (0.19), residues: 748 loop : -1.29 (0.14), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 403 TYR 0.019 0.001 TYR B1067 PHE 0.018 0.002 PHE B 375 TRP 0.017 0.001 TRP A 436 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00547 (29677) covalent geometry : angle 0.60265 (40362) SS BOND : bond 0.00320 ( 40) SS BOND : angle 1.64012 ( 80) hydrogen bonds : bond 0.06351 ( 1147) hydrogen bonds : angle 4.76359 ( 3186) link_ALPHA1-3 : bond 0.00787 ( 1) link_ALPHA1-3 : angle 1.31229 ( 3) link_ALPHA1-6 : bond 0.00773 ( 1) link_ALPHA1-6 : angle 1.30141 ( 3) link_BETA1-4 : bond 0.00457 ( 12) link_BETA1-4 : angle 1.53163 ( 36) link_NAG-ASN : bond 0.00455 ( 45) link_NAG-ASN : angle 3.08236 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12236.29 seconds wall clock time: 208 minutes 48.11 seconds (12528.11 seconds total)