Starting phenix.real_space_refine on Mon Jul 6 06:08:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8jyn_36727/07_2026/8jyn_36727.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jyn_36727/07_2026/8jyn_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 { model { file = "/net/cci-nas-00/data/ceres_data/8jyn_36727/07_2026/8jyn_36727.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jyn_36727/07_2026/8jyn_36727.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8jyn_36727/07_2026/8jyn_36727.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8jyn_36727/07_2026/8jyn_36727.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jyn_36727/07_2026/8jyn_36727.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jyn_36727/07_2026/8jyn_36727.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 9 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: 5.93, per 1000 atoms: 0.20 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: 2.63 Conformation dependent library (CDL) restraints added in 1.4 seconds 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6726 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 47 sheets defined 31.6% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 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: 7.06 Time building geometry restraints manager: 3.48 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: 17375 23.27 - 46.55: 870 46.55 - 69.82: 104 69.82 - 93.10: 37 93.10 - 116.37: 14 Dihedral angle restraints: 18400 sinusoidal: 7962 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 18397 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: 3.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 27.970 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 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 : 13.727 116.371 11554 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 are 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/Z covalent geometry : bond 0.00322 / 0.15 (29677) covalent geometry : angle 0.53515 / 0.26 (40362) SS BOND : bond 0.00315 / 0.21 ( 40) SS BOND : angle 1.19406 / 0.81 ( 80) hydrogen bonds : bond 0.21536 / 14.01 ( 1147) hydrogen bonds : angle 7.21272 / 4.96 ( 3186) link_ALPHA1-3 : bond 0.00354 / 0.19 ( 1) link_ALPHA1-3 : angle 1.52854 / 0.85 ( 3) link_ALPHA1-6 : bond 0.00421 / 0.22 ( 1) link_ALPHA1-6 : angle 1.58765 / 0.88 ( 3) link_BETA1-4 : bond 0.00324 / 0.19 ( 12) link_BETA1-4 : angle 1.73553 / 0.99 ( 36) link_NAG-ASN : bond 0.00641 / 0.41 ( 45) link_NAG-ASN : angle 3.55174 / 2.51 ( 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 : 1.076 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: 0.1941 time to fit residues: 84.9869 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 : 1.043 ------------------------------------------------------------------------------- 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... 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 = 0.4189 r_free = 0.4189 target = 0.142641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.080630 restraints weight = 64439.366| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 3.57 r_work: 0.2830 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 29776 Z= 0.229 Angle : 0.677 11.302 40619 Z= 0.340 Chirality : 0.050 0.478 4699 Planarity : 0.005 0.046 5130 Dihedral : 8.806 107.950 5020 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.34 % Favored : 95.63 % Rotamer: Outliers : 0.64 % Allowed : 5.92 % Favored : 93.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.14), residues: 3523 helix: 1.79 (0.16), residues: 1028 sheet: 0.81 (0.19), residues: 726 loop : -1.28 (0.14), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 177 TYR 0.021 0.002 TYR B1067 PHE 0.036 0.002 PHE B 906 TRP 0.026 0.002 TRP C 353 HIS 0.006 0.001 HIS D 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.23 (29677) covalent geometry : angle 0.64219 / 0.33 (40362) SS BOND : bond 0.00340 / 0.21 ( 40) SS BOND : angle 1.68329 / 1.19 ( 80) hydrogen bonds : bond 0.06664 / 4.30 ( 1147) hydrogen bonds : angle 5.33725 / 3.67 ( 3186) link_ALPHA1-3 : bond 0.00804 / 0.42 ( 1) link_ALPHA1-3 : angle 2.38248 / 1.15 ( 3) link_ALPHA1-6 : bond 0.00060 / 0.03 ( 1) link_ALPHA1-6 : angle 2.03618 / 1.02 ( 3) link_BETA1-4 : bond 0.00500 / 0.28 ( 12) link_BETA1-4 : angle 1.93971 / 1.22 ( 36) link_NAG-ASN : bond 0.00586 / 0.40 ( 45) link_NAG-ASN : angle 3.43967 / 2.47 ( 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 217 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 197 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 PHE cc_start: 0.6647 (t80) cc_final: 0.6293 (t80) REVERT: A 353 TRP cc_start: 0.4959 (p-90) cc_final: 0.2712 (p-90) REVERT: A 515 PHE cc_start: 0.7109 (m-80) cc_final: 0.6681 (m-10) REVERT: B 160 TYR cc_start: 0.8258 (p90) cc_final: 0.7808 (p90) REVERT: B 175 PHE cc_start: 0.7790 (m-80) cc_final: 0.7493 (m-10) REVERT: B 398 ASP cc_start: 0.7121 (m-30) cc_final: 0.6650 (p0) REVERT: B 449 TYR cc_start: 0.8482 (m-80) cc_final: 0.8269 (t80) REVERT: C 235 ILE cc_start: 0.6069 (mm) cc_final: 0.5829 (mm) REVERT: C 357 ARG cc_start: 0.7168 (ttm170) cc_final: 0.6930 (ttm110) REVERT: C 528 LYS cc_start: 0.8200 (pttm) cc_final: 0.7552 (ttpp) REVERT: D 231 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7228 (pt0) REVERT: D 329 GLU cc_start: 0.7093 (mm-30) cc_final: 0.6841 (mm-30) REVERT: D 455 MET cc_start: 0.6347 (tmm) cc_final: 0.5776 (ptm) outliers start: 20 outliers final: 13 residues processed: 209 average time/residue: 0.1776 time to fit residues: 61.8982 Evaluate side-chains 184 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 171 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain D residue 280 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 31 optimal weight: 5.9990 chunk 146 optimal weight: 10.0000 chunk 176 optimal weight: 0.9980 chunk 254 optimal weight: 1.9990 chunk 147 optimal weight: 0.0970 chunk 267 optimal weight: 0.4980 chunk 56 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 244 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS B 613 GLN B1088 HIS C1088 HIS D 524 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.144685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.085511 restraints weight = 64752.325| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 3.81 r_work: 0.2884 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 29776 Z= 0.107 Angle : 0.567 10.950 40619 Z= 0.277 Chirality : 0.045 0.406 4699 Planarity : 0.004 0.046 5130 Dihedral : 7.745 106.755 5020 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.95 % Favored : 97.02 % Rotamer: Outliers : 0.64 % Allowed : 8.12 % Favored : 91.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.14), residues: 3523 helix: 2.04 (0.16), residues: 1028 sheet: 1.00 (0.19), residues: 746 loop : -1.21 (0.14), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 357 TYR 0.014 0.001 TYR B 495 PHE 0.020 0.001 PHE B 106 TRP 0.022 0.001 TRP C 353 HIS 0.003 0.000 HIS D 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.11 (29677) covalent geometry : angle 0.53472 / 0.27 (40362) SS BOND : bond 0.00287 / 0.18 ( 40) SS BOND : angle 1.21167 / 0.82 ( 80) hydrogen bonds : bond 0.04818 / 3.11 ( 1147) hydrogen bonds : angle 4.81908 / 3.32 ( 3186) link_ALPHA1-3 : bond 0.01094 / 0.58 ( 1) link_ALPHA1-3 : angle 1.39716 / 0.71 ( 3) link_ALPHA1-6 : bond 0.00637 / 0.34 ( 1) link_ALPHA1-6 : angle 1.75638 / 0.86 ( 3) link_BETA1-4 : bond 0.00504 / 0.31 ( 12) link_BETA1-4 : angle 1.61376 / 1.04 ( 36) link_NAG-ASN : bond 0.00669 / 0.47 ( 45) link_NAG-ASN : angle 3.07787 / 2.23 ( 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 199 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 179 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 TRP cc_start: 0.4979 (p-90) cc_final: 0.2666 (p-90) REVERT: A 515 PHE cc_start: 0.7146 (m-80) cc_final: 0.6683 (m-10) REVERT: B 158 ARG cc_start: 0.6142 (mtt180) cc_final: 0.5783 (mtt90) REVERT: B 160 TYR cc_start: 0.8206 (p90) cc_final: 0.7735 (p90) REVERT: C 357 ARG cc_start: 0.7217 (ttm170) cc_final: 0.6987 (ttm110) REVERT: C 528 LYS cc_start: 0.8180 (pttm) cc_final: 0.7604 (ttpp) REVERT: D 231 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7267 (pt0) REVERT: D 332 MET cc_start: 0.4063 (ppp) cc_final: 0.3854 (ppp) REVERT: D 383 MET cc_start: 0.6447 (mtm) cc_final: 0.6201 (mtm) REVERT: D 579 MET cc_start: 0.2224 (mtt) cc_final: 0.1433 (mmt) outliers start: 20 outliers final: 12 residues processed: 192 average time/residue: 0.1777 time to fit residues: 57.1461 Evaluate side-chains 178 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 166 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 940 SER 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 553 THR Chi-restraints excluded: chain B residue 811 LYS 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 973 ILE 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: 2.9990 chunk 272 optimal weight: 0.9980 chunk 230 optimal weight: 9.9990 chunk 337 optimal weight: 30.0000 chunk 168 optimal weight: 2.9990 chunk 299 optimal weight: 30.0000 chunk 157 optimal weight: 5.9990 chunk 122 optimal weight: 0.4980 chunk 52 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 164 ASN A 207 HIS C 544 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.143214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.083523 restraints weight = 64407.651| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 3.74 r_work: 0.2840 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 29776 Z= 0.149 Angle : 0.587 14.010 40619 Z= 0.288 Chirality : 0.046 0.409 4699 Planarity : 0.004 0.046 5130 Dihedral : 7.323 105.346 5020 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.69 % Favored : 96.28 % Rotamer: Outliers : 0.96 % Allowed : 9.01 % Favored : 90.03 % 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 are not related in a simple way. whole: 0.33 (0.14), residues: 3523 helix: 1.96 (0.16), residues: 1034 sheet: 0.92 (0.19), residues: 744 loop : -1.24 (0.14), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1091 TYR 0.018 0.001 TYR B1067 PHE 0.018 0.001 PHE A 157 TRP 0.024 0.001 TRP C 353 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (29677) covalent geometry : angle 0.55136 / 0.28 (40362) SS BOND : bond 0.00266 / 0.17 ( 40) SS BOND : angle 1.31356 / 0.90 ( 80) hydrogen bonds : bond 0.05352 / 3.47 ( 1147) hydrogen bonds : angle 4.75944 / 3.28 ( 3186) link_ALPHA1-3 : bond 0.00991 / 0.52 ( 1) link_ALPHA1-3 : angle 1.52581 / 0.77 ( 3) link_ALPHA1-6 : bond 0.00741 / 0.39 ( 1) link_ALPHA1-6 : angle 1.60258 / 0.79 ( 3) link_BETA1-4 : bond 0.00409 / 0.28 ( 12) link_BETA1-4 : angle 1.66348 / 1.05 ( 36) link_NAG-ASN : bond 0.00517 / 0.36 ( 45) link_NAG-ASN : angle 3.32369 / 2.37 ( 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: 30 poor density : 167 time to evaluate : 0.982 Fit side-chains revert: symmetry clash REVERT: A 515 PHE cc_start: 0.7240 (m-80) cc_final: 0.6941 (m-10) REVERT: B 106 PHE cc_start: 0.8134 (m-10) cc_final: 0.7919 (m-10) REVERT: B 160 TYR cc_start: 0.8249 (p90) cc_final: 0.7804 (p90) REVERT: C 528 LYS cc_start: 0.8209 (pttm) cc_final: 0.7614 (ttpp) REVERT: C 904 TYR cc_start: 0.8639 (m-80) cc_final: 0.8290 (m-10) REVERT: D 231 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7266 (pt0) REVERT: D 249 MET cc_start: 0.3164 (mmm) cc_final: 0.2845 (mmt) REVERT: D 323 MET cc_start: 0.6097 (mmt) cc_final: 0.5070 (tpp) REVERT: D 332 MET cc_start: 0.4205 (ppp) cc_final: 0.3998 (ppp) REVERT: D 376 MET cc_start: 0.8002 (tpp) cc_final: 0.7423 (mtp) REVERT: D 455 MET cc_start: 0.6358 (tmm) cc_final: 0.5759 (ptm) REVERT: D 579 MET cc_start: 0.1230 (mtt) cc_final: 0.0202 (mmm) outliers start: 30 outliers final: 19 residues processed: 188 average time/residue: 0.1671 time to fit residues: 53.5230 Evaluate side-chains 175 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 0.697 ------------------------------------------------------------------------------- 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 1041 ASP Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 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 C residue 976 VAL 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: 5.9990 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: 0.7980 chunk 194 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 58 optimal weight: 0.2980 chunk 234 optimal weight: 1.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS C 394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.142591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.081595 restraints weight = 64425.915| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 3.54 r_work: 0.2844 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 29776 Z= 0.155 Angle : 0.582 10.990 40619 Z= 0.288 Chirality : 0.046 0.412 4699 Planarity : 0.004 0.046 5130 Dihedral : 6.884 104.543 5020 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.60 % Favored : 96.37 % 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 are not related in a simple way. whole: 0.27 (0.14), residues: 3523 helix: 1.94 (0.16), residues: 1034 sheet: 0.80 (0.19), residues: 747 loop : -1.24 (0.14), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 357 TYR 0.016 0.001 TYR B1067 PHE 0.013 0.001 PHE B 375 TRP 0.022 0.001 TRP C 353 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.15 (29677) covalent geometry : angle 0.55116 / 0.28 (40362) SS BOND : bond 0.00255 / 0.16 ( 40) SS BOND : angle 1.39483 / 0.97 ( 80) hydrogen bonds : bond 0.05474 / 3.54 ( 1147) hydrogen bonds : angle 4.70393 / 3.25 ( 3186) link_ALPHA1-3 : bond 0.01300 / 0.68 ( 1) link_ALPHA1-3 : angle 1.59618 / 0.82 ( 3) link_ALPHA1-6 : bond 0.00750 / 0.39 ( 1) link_ALPHA1-6 : angle 1.32921 / 0.66 ( 3) link_BETA1-4 : bond 0.00485 / 0.31 ( 12) link_BETA1-4 : angle 1.58742 / 1.00 ( 36) link_NAG-ASN : bond 0.00488 / 0.32 ( 45) link_NAG-ASN : angle 3.05726 / 2.19 ( 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 205 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 167 time to evaluate : 0.768 Fit side-chains revert: symmetry clash REVERT: A 515 PHE cc_start: 0.7446 (m-80) cc_final: 0.7082 (m-10) REVERT: B 160 TYR cc_start: 0.8313 (p90) cc_final: 0.7813 (p90) REVERT: C 528 LYS cc_start: 0.8201 (pttm) cc_final: 0.7638 (ttpp) REVERT: C 904 TYR cc_start: 0.8819 (m-80) cc_final: 0.8526 (m-10) REVERT: D 231 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7281 (pt0) REVERT: D 323 MET cc_start: 0.6006 (mmt) cc_final: 0.4696 (tpp) REVERT: D 376 MET cc_start: 0.8235 (tpp) cc_final: 0.7488 (mtp) REVERT: D 557 MET cc_start: 0.8404 (tpt) cc_final: 0.8000 (mmt) REVERT: D 579 MET cc_start: 0.0616 (mtt) cc_final: -0.0249 (mmm) outliers start: 38 outliers final: 26 residues processed: 196 average time/residue: 0.1413 time to fit residues: 47.3492 Evaluate side-chains 180 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 0.970 ------------------------------------------------------------------------------- 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 940 SER 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 401 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 916 LEU 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 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: 5.9990 chunk 61 optimal weight: 0.9980 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: 4.9990 chunk 187 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 chunk 101 optimal weight: 7.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS C 394 ASN D 345 HIS ** D 373 HIS ** 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 = 0.4168 r_free = 0.4168 target = 0.141066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.078463 restraints weight = 64132.779| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 3.21 r_work: 0.2819 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 29776 Z= 0.196 Angle : 0.626 11.258 40619 Z= 0.311 Chirality : 0.047 0.454 4699 Planarity : 0.004 0.048 5130 Dihedral : 6.754 104.401 5020 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.46 % Favored : 95.52 % Rotamer: Outliers : 1.56 % Allowed : 10.19 % Favored : 88.25 % 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 are not related in a simple way. whole: 0.15 (0.14), residues: 3523 helix: 1.80 (0.16), residues: 1043 sheet: 0.69 (0.19), residues: 748 loop : -1.30 (0.14), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 403 TYR 0.017 0.001 TYR B1067 PHE 0.015 0.002 PHE A 392 TRP 0.018 0.001 TRP D 275 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.20 (29677) covalent geometry : angle 0.59399 / 0.30 (40362) SS BOND : bond 0.00285 / 0.18 ( 40) SS BOND : angle 1.63124 / 1.14 ( 80) hydrogen bonds : bond 0.06135 / 3.97 ( 1147) hydrogen bonds : angle 4.79033 / 3.30 ( 3186) link_ALPHA1-3 : bond 0.00719 / 0.38 ( 1) link_ALPHA1-3 : angle 1.13127 / 0.59 ( 3) link_ALPHA1-6 : bond 0.01033 / 0.54 ( 1) link_ALPHA1-6 : angle 1.30027 / 0.68 ( 3) link_BETA1-4 : bond 0.00394 / 0.27 ( 12) link_BETA1-4 : angle 1.60500 / 0.98 ( 36) link_NAG-ASN : bond 0.00476 / 0.32 ( 45) link_NAG-ASN : angle 3.20460 / 2.29 ( 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 215 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 166 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 PHE cc_start: 0.7384 (t80) cc_final: 0.6969 (t80) REVERT: A 515 PHE cc_start: 0.7566 (m-80) cc_final: 0.7241 (m-10) REVERT: B 160 TYR cc_start: 0.8400 (p90) cc_final: 0.7832 (p90) REVERT: B 339 HIS cc_start: 0.8943 (OUTLIER) cc_final: 0.8740 (m90) REVERT: C 528 LYS cc_start: 0.8179 (pttm) cc_final: 0.7663 (ttpp) REVERT: C 904 TYR cc_start: 0.8773 (m-80) cc_final: 0.8488 (m-10) REVERT: D 231 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7344 (pt0) REVERT: D 323 MET cc_start: 0.6418 (mmt) cc_final: 0.4856 (tpp) REVERT: D 366 MET cc_start: 0.4118 (tpp) cc_final: 0.3700 (mmm) REVERT: D 376 MET cc_start: 0.8330 (tpp) cc_final: 0.7491 (mtp) REVERT: D 557 MET cc_start: 0.8436 (tpt) cc_final: 0.8018 (mmt) REVERT: D 579 MET cc_start: 0.0586 (mtt) cc_final: -0.0270 (mmm) outliers start: 49 outliers final: 31 residues processed: 201 average time/residue: 0.1667 time to fit residues: 56.3670 Evaluate side-chains 182 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 150 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 940 SER Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 339 HIS Chi-restraints excluded: chain B residue 353 TRP 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 242 LEU Chi-restraints excluded: chain C residue 270 LEU 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 C residue 973 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 213 optimal weight: 7.9990 chunk 329 optimal weight: 6.9990 chunk 310 optimal weight: 6.9990 chunk 355 optimal weight: 5.9990 chunk 309 optimal weight: 0.0770 chunk 118 optimal weight: 6.9990 chunk 296 optimal weight: 0.8980 chunk 319 optimal weight: 6.9990 chunk 128 optimal weight: 7.9990 chunk 194 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 overall best weight: 2.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 804 GLN C 992 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 = 0.4169 r_free = 0.4169 target = 0.141122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.078457 restraints weight = 64464.958| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 3.17 r_work: 0.2831 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 29776 Z= 0.178 Angle : 0.603 10.958 40619 Z= 0.299 Chirality : 0.046 0.441 4699 Planarity : 0.004 0.046 5130 Dihedral : 6.534 104.231 5020 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.83 % Favored : 96.14 % Rotamer: Outliers : 1.50 % Allowed : 11.24 % Favored : 87.26 % 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 are not related in a simple way. whole: 0.16 (0.14), residues: 3523 helix: 1.88 (0.16), residues: 1037 sheet: 0.72 (0.19), residues: 745 loop : -1.34 (0.14), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 357 TYR 0.017 0.001 TYR B1067 PHE 0.014 0.001 PHE A 133 TRP 0.017 0.001 TRP A 436 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.18 (29677) covalent geometry : angle 0.57081 / 0.29 (40362) SS BOND : bond 0.00280 / 0.17 ( 40) SS BOND : angle 1.56627 / 1.10 ( 80) hydrogen bonds : bond 0.05699 / 3.68 ( 1147) hydrogen bonds : angle 4.71575 / 3.25 ( 3186) link_ALPHA1-3 : bond 0.00795 / 0.42 ( 1) link_ALPHA1-3 : angle 1.33595 / 0.71 ( 3) link_ALPHA1-6 : bond 0.00827 / 0.44 ( 1) link_ALPHA1-6 : angle 1.32892 / 0.71 ( 3) link_BETA1-4 : bond 0.00436 / 0.30 ( 12) link_BETA1-4 : angle 1.49886 / 0.93 ( 36) link_NAG-ASN : bond 0.00458 / 0.30 ( 45) link_NAG-ASN : angle 3.15956 / 2.27 ( 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 210 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 163 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 515 PHE cc_start: 0.7648 (m-80) cc_final: 0.7299 (m-10) REVERT: B 160 TYR cc_start: 0.8401 (p90) cc_final: 0.7825 (p90) REVERT: B 339 HIS cc_start: 0.8961 (OUTLIER) cc_final: 0.8741 (m90) REVERT: B 449 TYR cc_start: 0.8843 (OUTLIER) cc_final: 0.8300 (t80) REVERT: C 528 LYS cc_start: 0.8152 (pttm) cc_final: 0.7689 (ttpp) REVERT: C 904 TYR cc_start: 0.8769 (m-80) cc_final: 0.8512 (m-10) REVERT: D 231 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7338 (pt0) REVERT: D 323 MET cc_start: 0.6430 (mmt) cc_final: 0.5717 (mmt) REVERT: D 360 MET cc_start: 0.0939 (ttp) cc_final: 0.0258 (ppp) REVERT: D 366 MET cc_start: 0.3907 (tpp) cc_final: 0.3164 (mmm) REVERT: D 376 MET cc_start: 0.8298 (tpp) cc_final: 0.7491 (mtp) REVERT: D 557 MET cc_start: 0.8495 (tpt) cc_final: 0.8080 (mmt) REVERT: D 579 MET cc_start: 0.0333 (mtt) cc_final: -0.0351 (mmm) outliers start: 47 outliers final: 32 residues processed: 197 average time/residue: 0.1737 time to fit residues: 57.3880 Evaluate side-chains 186 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 152 time to evaluate : 1.002 ------------------------------------------------------------------------------- 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 165 ASN Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 339 HIS Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 401 VAL 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 916 LEU 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 976 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1116 THR 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: 1.9990 chunk 67 optimal weight: 0.7980 chunk 145 optimal weight: 0.9990 chunk 47 optimal weight: 9.9990 chunk 303 optimal weight: 0.0270 chunk 325 optimal weight: 10.0000 chunk 280 optimal weight: 2.9990 chunk 190 optimal weight: 0.6980 chunk 169 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 311 optimal weight: 5.9990 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS C 394 ASN ** 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 = 0.4192 r_free = 0.4192 target = 0.142785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.082388 restraints weight = 64744.684| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 3.58 r_work: 0.2866 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 29776 Z= 0.102 Angle : 0.557 10.734 40619 Z= 0.273 Chirality : 0.044 0.394 4699 Planarity : 0.004 0.046 5130 Dihedral : 6.189 103.298 5020 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.55 % Favored : 96.42 % Rotamer: Outliers : 1.15 % Allowed : 11.69 % 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 are not related in a simple way. whole: 0.36 (0.14), residues: 3523 helix: 2.13 (0.17), residues: 1027 sheet: 0.78 (0.19), residues: 762 loop : -1.25 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 357 TYR 0.028 0.001 TYR B 421 PHE 0.014 0.001 PHE A 133 TRP 0.020 0.001 TRP A 436 HIS 0.002 0.000 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (29677) covalent geometry : angle 0.52797 / 0.27 (40362) SS BOND : bond 0.00331 / 0.23 ( 40) SS BOND : angle 1.19919 / 0.84 ( 80) hydrogen bonds : bond 0.04471 / 2.89 ( 1147) hydrogen bonds : angle 4.51904 / 3.11 ( 3186) link_ALPHA1-3 : bond 0.00731 / 0.38 ( 1) link_ALPHA1-3 : angle 1.37910 / 0.74 ( 3) link_ALPHA1-6 : bond 0.00784 / 0.41 ( 1) link_ALPHA1-6 : angle 1.27460 / 0.69 ( 3) link_BETA1-4 : bond 0.00402 / 0.26 ( 12) link_BETA1-4 : angle 1.33681 / 0.83 ( 36) link_NAG-ASN : bond 0.00515 / 0.34 ( 45) link_NAG-ASN : angle 2.95306 / 2.12 ( 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 198 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 162 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 515 PHE cc_start: 0.7591 (m-80) cc_final: 0.7246 (m-10) REVERT: B 160 TYR cc_start: 0.8352 (p90) cc_final: 0.7764 (p90) REVERT: B 339 HIS cc_start: 0.8922 (OUTLIER) cc_final: 0.8715 (m90) REVERT: B 364 ASP cc_start: 0.8824 (m-30) cc_final: 0.7794 (t0) REVERT: B 421 TYR cc_start: 0.8983 (m-10) cc_final: 0.8691 (m-10) REVERT: B 449 TYR cc_start: 0.8835 (OUTLIER) cc_final: 0.8252 (t80) REVERT: C 528 LYS cc_start: 0.8112 (pttm) cc_final: 0.7684 (ttpp) REVERT: D 231 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7308 (pt0) REVERT: D 249 MET cc_start: 0.3030 (mmp) cc_final: 0.2763 (mmt) REVERT: D 323 MET cc_start: 0.6384 (mmt) cc_final: 0.5694 (mmt) REVERT: D 360 MET cc_start: 0.0955 (ttp) cc_final: 0.0216 (ppp) REVERT: D 366 MET cc_start: 0.4141 (tpp) cc_final: 0.3546 (mmm) REVERT: D 376 MET cc_start: 0.8293 (tpp) cc_final: 0.7536 (mtp) REVERT: D 557 MET cc_start: 0.8498 (tpt) cc_final: 0.8097 (mmt) REVERT: D 579 MET cc_start: 0.0188 (mtt) cc_final: -0.0470 (mmm) outliers start: 36 outliers final: 25 residues processed: 188 average time/residue: 0.1704 time to fit residues: 54.3597 Evaluate side-chains 180 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 339 HIS 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 916 LEU 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 916 LEU Chi-restraints excluded: chain C residue 973 ILE 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: 7.9990 chunk 90 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 315 optimal weight: 8.9990 chunk 71 optimal weight: 0.9980 chunk 260 optimal weight: 1.9990 chunk 336 optimal weight: 30.0000 chunk 145 optimal weight: 0.9990 chunk 190 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 305 optimal weight: 6.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** 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 = 0.4168 r_free = 0.4168 target = 0.140999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.078465 restraints weight = 64445.540| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 3.25 r_work: 0.2823 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 29776 Z= 0.175 Angle : 0.597 10.823 40619 Z= 0.296 Chirality : 0.046 0.426 4699 Planarity : 0.004 0.047 5130 Dihedral : 6.336 102.353 5020 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.09 % Favored : 95.88 % Rotamer: Outliers : 1.24 % Allowed : 11.85 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.14), residues: 3523 helix: 1.99 (0.17), residues: 1038 sheet: 0.67 (0.19), residues: 771 loop : -1.31 (0.14), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 498 TYR 0.030 0.001 TYR B 421 PHE 0.015 0.001 PHE A 133 TRP 0.020 0.001 TRP A 436 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.17 (29677) covalent geometry : angle 0.56668 / 0.29 (40362) SS BOND : bond 0.00300 / 0.20 ( 40) SS BOND : angle 1.51790 / 1.08 ( 80) hydrogen bonds : bond 0.05754 / 3.73 ( 1147) hydrogen bonds : angle 4.67430 / 3.22 ( 3186) link_ALPHA1-3 : bond 0.00757 / 0.40 ( 1) link_ALPHA1-3 : angle 1.33791 / 0.73 ( 3) link_ALPHA1-6 : bond 0.00704 / 0.37 ( 1) link_ALPHA1-6 : angle 1.25598 / 0.69 ( 3) link_BETA1-4 : bond 0.00410 / 0.27 ( 12) link_BETA1-4 : angle 1.45177 / 0.90 ( 36) link_NAG-ASN : bond 0.00462 / 0.31 ( 45) link_NAG-ASN : angle 3.05785 / 2.20 ( 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 194 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 155 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 515 PHE cc_start: 0.7665 (m-80) cc_final: 0.7337 (m-10) REVERT: B 160 TYR cc_start: 0.8458 (p90) cc_final: 0.7833 (p90) REVERT: B 339 HIS cc_start: 0.8941 (OUTLIER) cc_final: 0.8732 (m90) REVERT: B 421 TYR cc_start: 0.8946 (m-10) cc_final: 0.8641 (m-10) REVERT: B 449 TYR cc_start: 0.8864 (OUTLIER) cc_final: 0.8227 (t80) REVERT: C 528 LYS cc_start: 0.8018 (pttm) cc_final: 0.7656 (ttpp) REVERT: C 904 TYR cc_start: 0.8770 (m-80) cc_final: 0.8464 (m-10) REVERT: D 231 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7389 (pt0) REVERT: D 249 MET cc_start: 0.3262 (mmp) cc_final: 0.3045 (mmt) REVERT: D 323 MET cc_start: 0.6397 (mmt) cc_final: 0.5543 (tpt) REVERT: D 360 MET cc_start: 0.0907 (ttp) cc_final: 0.0177 (ppp) REVERT: D 366 MET cc_start: 0.3980 (tpp) cc_final: 0.3314 (mmm) REVERT: D 376 MET cc_start: 0.8299 (tpp) cc_final: 0.7535 (mtp) REVERT: D 557 MET cc_start: 0.8476 (tpt) cc_final: 0.8072 (mmm) REVERT: D 579 MET cc_start: -0.0021 (mtt) cc_final: -0.0608 (mmm) outliers start: 39 outliers final: 28 residues processed: 182 average time/residue: 0.1682 time to fit residues: 51.8171 Evaluate side-chains 180 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 150 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 339 HIS 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 560 LEU Chi-restraints excluded: chain B residue 576 VAL 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 208 THR 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 C residue 973 ILE Chi-restraints excluded: chain C residue 1096 VAL 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: 2.9990 chunk 119 optimal weight: 20.0000 chunk 51 optimal weight: 5.9990 chunk 225 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 161 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 242 optimal weight: 10.0000 chunk 75 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** 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 = 0.4179 r_free = 0.4179 target = 0.141776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.079592 restraints weight = 64137.718| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 3.17 r_work: 0.2853 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29776 Z= 0.128 Angle : 0.571 10.668 40619 Z= 0.281 Chirality : 0.045 0.402 4699 Planarity : 0.004 0.048 5130 Dihedral : 6.192 101.810 5020 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.69 % Favored : 96.28 % Rotamer: Outliers : 1.08 % Allowed : 12.20 % Favored : 86.72 % 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 are not related in a simple way. whole: 0.32 (0.14), residues: 3523 helix: 2.12 (0.17), residues: 1029 sheet: 0.74 (0.19), residues: 766 loop : -1.28 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 357 TYR 0.027 0.001 TYR C 160 PHE 0.022 0.001 PHE C 133 TRP 0.022 0.001 TRP A 436 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (29677) covalent geometry : angle 0.54215 / 0.27 (40362) SS BOND : bond 0.00290 / 0.19 ( 40) SS BOND : angle 1.32600 / 0.93 ( 80) hydrogen bonds : bond 0.04979 / 3.22 ( 1147) hydrogen bonds : angle 4.56659 / 3.14 ( 3186) link_ALPHA1-3 : bond 0.00685 / 0.36 ( 1) link_ALPHA1-3 : angle 1.35172 / 0.74 ( 3) link_ALPHA1-6 : bond 0.00746 / 0.39 ( 1) link_ALPHA1-6 : angle 1.32565 / 0.72 ( 3) link_BETA1-4 : bond 0.00398 / 0.26 ( 12) link_BETA1-4 : angle 1.36624 / 0.85 ( 36) link_NAG-ASN : bond 0.00475 / 0.32 ( 45) link_NAG-ASN : angle 2.93418 / 2.11 ( 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 192 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 158 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 515 PHE cc_start: 0.7700 (m-80) cc_final: 0.7360 (m-10) REVERT: B 160 TYR cc_start: 0.8396 (p90) cc_final: 0.7800 (p90) REVERT: B 339 HIS cc_start: 0.8930 (OUTLIER) cc_final: 0.8726 (m90) REVERT: B 364 ASP cc_start: 0.8775 (m-30) cc_final: 0.7732 (t0) REVERT: B 421 TYR cc_start: 0.8956 (m-10) cc_final: 0.8647 (m-10) REVERT: B 449 TYR cc_start: 0.8831 (OUTLIER) cc_final: 0.8199 (t80) REVERT: C 116 SER cc_start: 0.7587 (m) cc_final: 0.7322 (p) REVERT: C 200 TYR cc_start: 0.8577 (m-80) cc_final: 0.8188 (m-80) REVERT: C 271 GLN cc_start: 0.8414 (tp-100) cc_final: 0.8161 (tp40) REVERT: C 528 LYS cc_start: 0.7929 (pttm) cc_final: 0.7548 (ptmm) REVERT: D 231 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7393 (pt0) REVERT: D 249 MET cc_start: 0.3363 (mmp) cc_final: 0.3158 (mmt) REVERT: D 323 MET cc_start: 0.6452 (mmt) cc_final: 0.5640 (tpt) REVERT: D 360 MET cc_start: 0.0897 (ttp) cc_final: 0.0167 (ppp) REVERT: D 366 MET cc_start: 0.4102 (tpp) cc_final: 0.3418 (mmm) REVERT: D 376 MET cc_start: 0.8242 (tpp) cc_final: 0.7433 (mtp) REVERT: D 557 MET cc_start: 0.8470 (tpt) cc_final: 0.8082 (mmm) REVERT: D 579 MET cc_start: 0.0022 (mtt) cc_final: -0.0443 (mmm) outliers start: 34 outliers final: 29 residues processed: 184 average time/residue: 0.1507 time to fit residues: 47.7201 Evaluate side-chains 183 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 152 time to evaluate : 0.904 ------------------------------------------------------------------------------- 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 318 PHE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 339 HIS Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 401 VAL 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 560 LEU Chi-restraints excluded: chain B residue 576 VAL 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 208 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 512 VAL 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 C residue 1096 VAL 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: 10.0000 chunk 55 optimal weight: 0.9980 chunk 309 optimal weight: 6.9990 chunk 350 optimal weight: 8.9990 chunk 174 optimal weight: 0.2980 chunk 142 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 262 optimal weight: 0.8980 chunk 333 optimal weight: 8.9990 chunk 355 optimal weight: 7.9990 chunk 337 optimal weight: 5.9990 overall best weight: 3.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** 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 = 0.4151 r_free = 0.4151 target = 0.139683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.076838 restraints weight = 64689.176| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 3.17 r_work: 0.2798 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 29776 Z= 0.236 Angle : 0.653 10.991 40619 Z= 0.326 Chirality : 0.048 0.475 4699 Planarity : 0.004 0.048 5130 Dihedral : 6.591 101.077 5020 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.77 % Favored : 95.20 % Rotamer: Outliers : 1.24 % Allowed : 12.26 % Favored : 86.50 % 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 are not related in a simple way. whole: 0.06 (0.14), residues: 3523 helix: 1.85 (0.16), residues: 1038 sheet: 0.55 (0.19), residues: 747 loop : -1.38 (0.14), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1000 TYR 0.026 0.002 TYR B 421 PHE 0.022 0.002 PHE A 133 TRP 0.018 0.001 TRP A 436 HIS 0.006 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.24 (29677) covalent geometry : angle 0.62160 / 0.32 (40362) SS BOND : bond 0.00351 / 0.23 ( 40) SS BOND : angle 1.74605 / 1.24 ( 80) hydrogen bonds : bond 0.06620 / 4.29 ( 1147) hydrogen bonds : angle 4.84219 / 3.33 ( 3186) link_ALPHA1-3 : bond 0.00738 / 0.39 ( 1) link_ALPHA1-3 : angle 1.29402 / 0.71 ( 3) link_ALPHA1-6 : bond 0.00726 / 0.38 ( 1) link_ALPHA1-6 : angle 1.37518 / 0.76 ( 3) link_BETA1-4 : bond 0.00456 / 0.31 ( 12) link_BETA1-4 : angle 1.58528 / 0.97 ( 36) link_NAG-ASN : bond 0.00460 / 0.32 ( 45) link_NAG-ASN : angle 3.18401 / 2.30 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12238.17 seconds wall clock time: 208 minutes 29.60 seconds (12509.60 seconds total)