Starting phenix.real_space_refine on Sun Jul 5 09:17:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tb4_25792/07_2026/7tb4_25792.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tb4_25792/07_2026/7tb4_25792.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tb4_25792/07_2026/7tb4_25792.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tb4_25792/07_2026/7tb4_25792.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tb4_25792/07_2026/7tb4_25792.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tb4_25792/07_2026/7tb4_25792.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7tb4_25792/07_2026/7tb4_25792.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tb4_25792/07_2026/7tb4_25792.cif" } resolution = 3.29 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= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 119 5.16 5 C 17138 2.51 5 N 4416 2.21 5 O 5224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.03s 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: 26897 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 8601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8601 Classifications: {'peptide': 1097} Link IDs: {'PTRANS': 57, 'TRANS': 1039} Chain breaks: 2 Chain: "B" Number of atoms: 8715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1114, 8715 Classifications: {'peptide': 1114} Link IDs: {'PTRANS': 56, 'TRANS': 1057} Chain breaks: 2 Chain: "C" Number of atoms: 8755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1118, 8755 Classifications: {'peptide': 1118} Link IDs: {'PTRANS': 57, 'TRANS': 1060} Chain breaks: 1 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 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 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 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 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 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 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 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 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 chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" 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 chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 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 chiralities: 10 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 5.63, per 1000 atoms: 0.21 Number of scatterers: 26897 At special positions: 0 Unit cell: (157.32, 153.045, 198.36, 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 119 16.00 O 5224 8.00 N 4416 7.00 C 17138 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " 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=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 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 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " 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=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 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 B 840 " - pdb=" SG CYS B 851 " 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=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " 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=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " 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 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " 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 N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 343 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A 122 " " NAG A1308 " - " ASN A 165 " " NAG A1309 " - " ASN A 234 " " NAG A1310 " - " ASN A 616 " " NAG A1311 " - " ASN A 603 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 709 " " NAG B1303 " - " ASN B1074 " " NAG B1304 " - " ASN B 61 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 343 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 603 " " NAG B1310 " - " ASN B 234 " " NAG C1301 " - " ASN C1074 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 657 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 603 " " NAG C1306 " - " ASN C 282 " " NAG C1307 " - " ASN C 234 " " NAG C1308 " - " ASN C 122 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN A1074 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 717 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN B1098 " " NAG L 1 " - " ASN B1134 " " NAG M 1 " - " ASN C 709 " " NAG N 1 " - " ASN C 717 " " NAG O 1 " - " ASN C1098 " " NAG P 1 " - " ASN C1134 " " NAG Q 1 " - " ASN C 331 " " NAG R 1 " - " ASN C 801 " Time building additional restraints: 2.33 Conformation dependent library (CDL) restraints added in 1.2 seconds 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6238 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 54 sheets defined 22.6% alpha, 22.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.956A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.615A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 removed outlier: 4.335A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 620 through 625 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 753 Processing helix chain 'A' and resid 756 through 783 removed outlier: 4.135A pdb=" N CYS A 760 " --> pdb=" O TYR A 756 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR A 761 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY A 769 " --> pdb=" O ARG A 765 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ALA A 771 " --> pdb=" O LEU A 767 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL A 772 " --> pdb=" O THR A 768 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.508A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 856 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.510A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.232A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.711A pdb=" N LEU A 938 " --> pdb=" O ILE A 934 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.128A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 982 removed outlier: 3.688A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.903A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.567A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 370 removed outlier: 3.689A pdb=" N ASN B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 407 removed outlier: 3.514A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.515A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 638 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.617A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 783 removed outlier: 3.596A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 836 through 841 Processing helix chain 'B' and resid 848 through 855 removed outlier: 3.749A pdb=" N ALA B 852 " --> pdb=" O ASP B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.606A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.229A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 removed outlier: 4.472A pdb=" N SER B 939 " --> pdb=" O GLN B 935 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N SER B 940 " --> pdb=" O ASP B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.941A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.946A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU B1004 " --> pdb=" O ARG B1000 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA B1016 " --> pdb=" O LEU B1012 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU B1024 " --> pdb=" O ALA B1020 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 4.024A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.032A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 619 through 628 removed outlier: 3.515A pdb=" N ALA C 623 " --> pdb=" O GLU C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 636 removed outlier: 4.273A pdb=" N TYR C 636 " --> pdb=" O THR C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 753 Processing helix chain 'C' and resid 754 through 757 removed outlier: 4.155A pdb=" N GLY C 757 " --> pdb=" O LEU C 754 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 754 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.693A pdb=" N THR C 768 " --> pdb=" O LYS C 764 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY C 769 " --> pdb=" O ARG C 765 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ALA C 771 " --> pdb=" O LEU C 767 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.951A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS C 825 " --> pdb=" O LEU C 821 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 840 Processing helix chain 'C' and resid 848 through 855 removed outlier: 3.505A pdb=" N PHE C 855 " --> pdb=" O CYS C 851 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.664A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.542A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 965 removed outlier: 4.133A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.006A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR C1006 " --> pdb=" O GLN C1002 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL C1008 " --> pdb=" O LEU C1004 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 4.242A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU C1145 " --> pdb=" O LEU C1141 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1140 through 1145' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 29 removed outlier: 3.853A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.696A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.827A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.606A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.737A pdb=" N SER A 116 " --> pdb=" O CYS A 131 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE A 128 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLU A 169 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N ASN A 165 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N GLN A 134 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ALA A 163 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.950A pdb=" N CYS A 136 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N SER A 161 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ASP A 138 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL A 159 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ASP A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.737A pdb=" N SER A 116 " --> pdb=" O CYS A 131 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N HIS A 146 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 312 removed outlier: 4.650A pdb=" N SER A 596 " --> pdb=" O LEU A 611 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 326 removed outlier: 7.772A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE A 541 " --> pdb=" O GLY A 548 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 374 through 380 removed outlier: 3.509A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG A 509 " --> pdb=" O TRP A 436 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 453 removed outlier: 3.649A pdb=" N ARG A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.103A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 575 through 577 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.212A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 712 Processing sheet with id=AB5, first strand: chain 'A' and resid 715 through 722 removed outlier: 6.128A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 715 through 722 removed outlier: 6.128A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB8, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.903A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1081 through 1082 removed outlier: 4.409A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC2, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.522A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.622A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER B 205 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR B 266 " --> pdb=" O ALA B 93 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.673A pdb=" N VAL B 289 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.208A pdb=" N ARG B 237 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 116 through 117 removed outlier: 3.679A pdb=" N SER B 116 " --> pdb=" O CYS B 131 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR B 170 " --> pdb=" O ILE B 128 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 314 removed outlier: 3.692A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR B 612 " --> pdb=" O CYS B 649 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 355 through 358 removed outlier: 3.932A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER B 514 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY B 431 " --> pdb=" O TYR B 380 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 539 through 542 Processing sheet with id=AD2, first strand: chain 'B' and resid 553 through 554 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.080A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 701 through 704 removed outlier: 3.816A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 712 through 713 removed outlier: 3.885A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 718 through 719 Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 719 removed outlier: 3.643A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD9, first strand: chain 'B' and resid 1081 through 1082 removed outlier: 4.222A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.628A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 36 through 37 removed outlier: 6.947A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.605A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 9.654A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS C 202 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 48 through 50 removed outlier: 6.490A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 53 through 55 removed outlier: 3.677A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE6, first strand: chain 'C' and resid 118 through 120 Processing sheet with id=AE7, first strand: chain 'C' and resid 133 through 135 removed outlier: 4.781A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 141 through 146 removed outlier: 3.547A pdb=" N LEU C 244 " --> pdb=" O LEU C 141 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.038A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 325 through 327 removed outlier: 3.510A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE C 541 " --> pdb=" O GLY C 548 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 355 through 358 removed outlier: 3.757A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER C 514 " --> pdb=" O TYR C 396 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL C 512 " --> pdb=" O ASP C 398 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU C 513 " --> pdb=" O CYS C 432 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 355 through 358 removed outlier: 3.757A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER C 514 " --> pdb=" O TYR C 396 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL C 512 " --> pdb=" O ASP C 398 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.149A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 712 through 722 removed outlier: 6.618A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 712 through 722 removed outlier: 6.618A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE C1052 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 734 through 735 Processing sheet with id=AF8, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AF9, first strand: chain 'C' and resid 1094 through 1097 828 hydrogen bonds defined for protein. 2265 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: 6.94 Time building geometry restraints manager: 3.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 8544 1.35 - 1.48: 7227 1.48 - 1.61: 11602 1.61 - 1.73: 0 1.73 - 1.86: 149 Bond restraints: 27522 Sorted by residual: bond pdb=" C1 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.406 1.475 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C1 NAG M 1 " pdb=" O5 NAG M 1 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.78e+00 bond pdb=" C1 NAG B1309 " pdb=" O5 NAG B1309 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.63e+00 bond pdb=" C1 NAG B1305 " pdb=" O5 NAG B1305 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.31e+00 bond pdb=" C1 NAG B1306 " pdb=" O5 NAG B1306 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.30e+00 ... (remaining 27517 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 36475 1.73 - 3.46: 854 3.46 - 5.19: 94 5.19 - 6.92: 29 6.92 - 8.65: 5 Bond angle restraints: 37457 Sorted by residual: angle pdb=" N ILE C 332 " pdb=" CA ILE C 332 " pdb=" C ILE C 332 " ideal model delta sigma weight residual 107.18 113.37 -6.19 1.73e+00 3.34e-01 1.28e+01 angle pdb=" C ASN C 717 " pdb=" CA ASN C 717 " pdb=" CB ASN C 717 " ideal model delta sigma weight residual 113.33 105.68 7.65 2.26e+00 1.96e-01 1.15e+01 angle pdb=" N THR C 333 " pdb=" CA THR C 333 " pdb=" C THR C 333 " ideal model delta sigma weight residual 110.91 114.81 -3.90 1.17e+00 7.31e-01 1.11e+01 angle pdb=" C ASN C 717 " pdb=" N PHE C 718 " pdb=" CA PHE C 718 " ideal model delta sigma weight residual 121.62 127.43 -5.81 1.83e+00 2.99e-01 1.01e+01 angle pdb=" N ASN C 370 " pdb=" CA ASN C 370 " pdb=" C ASN C 370 " ideal model delta sigma weight residual 112.57 109.06 3.51 1.13e+00 7.83e-01 9.64e+00 ... (remaining 37452 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 14328 17.96 - 35.92: 1314 35.92 - 53.89: 239 53.89 - 71.85: 37 71.85 - 89.81: 21 Dihedral angle restraints: 15939 sinusoidal: 6234 harmonic: 9705 Sorted by residual: dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual 93.00 8.81 84.19 1 1.00e+01 1.00e-02 8.63e+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 -17.46 -68.54 1 1.00e+01 1.00e-02 6.09e+01 dihedral pdb=" CB CYS B 840 " pdb=" SG CYS B 840 " pdb=" SG CYS B 851 " pdb=" CB CYS B 851 " ideal model delta sinusoidal sigma weight residual 93.00 159.19 -66.19 1 1.00e+01 1.00e-02 5.73e+01 ... (remaining 15936 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 3828 0.073 - 0.146: 550 0.146 - 0.219: 16 0.219 - 0.292: 1 0.292 - 0.365: 3 Chirality restraints: 4398 Sorted by residual: chirality pdb=" C1 NAG C1306 " pdb=" ND2 ASN C 282 " pdb=" C2 NAG C1306 " pdb=" O5 NAG C1306 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" C1 NAG B1307 " pdb=" ND2 ASN B 616 " pdb=" C2 NAG B1307 " pdb=" O5 NAG B1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.18e+00 chirality pdb=" C1 NAG A1311 " pdb=" ND2 ASN A 603 " pdb=" C2 NAG A1311 " pdb=" O5 NAG A1311 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.78e+00 ... (remaining 4395 not shown) Planarity restraints: 4815 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 603 " -0.001 2.00e-02 2.50e+03 4.23e-02 2.23e+01 pdb=" CG ASN A 603 " -0.049 2.00e-02 2.50e+03 pdb=" OD1 ASN A 603 " 0.051 2.00e-02 2.50e+03 pdb=" ND2 ASN A 603 " -0.045 2.00e-02 2.50e+03 pdb=" C1 NAG A1311 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 298 " 0.018 2.00e-02 2.50e+03 3.54e-02 1.25e+01 pdb=" C GLU B 298 " -0.061 2.00e-02 2.50e+03 pdb=" O GLU B 298 " 0.023 2.00e-02 2.50e+03 pdb=" N THR B 299 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 224 " -0.039 5.00e-02 4.00e+02 5.97e-02 5.71e+00 pdb=" N PRO B 225 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 225 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 225 " -0.033 5.00e-02 4.00e+02 ... (remaining 4812 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1145 2.72 - 3.26: 26105 3.26 - 3.81: 40154 3.81 - 4.35: 47911 4.35 - 4.90: 85175 Nonbonded interactions: 200490 Sorted by model distance: nonbonded pdb=" OH TYR C 756 " pdb=" OD1 ASP C 994 " model vdw 2.173 3.040 nonbonded pdb=" O GLY A 72 " pdb=" OG1 THR A 76 " model vdw 2.207 3.040 nonbonded pdb=" OG SER A 349 " pdb=" O ASN A 450 " model vdw 2.211 3.040 nonbonded pdb=" O CYS A 617 " pdb=" OG1 THR A 618 " model vdw 2.212 3.040 nonbonded pdb=" O CYS C 15 " pdb=" N ASN C 17 " model vdw 2.220 3.120 ... (remaining 200485 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 14 through 213 or resid 215 through 676 or resid 691 throu \ gh 1308)) selection = (chain 'B' and (resid 14 through 676 or resid 691 through 827 or resid 848 throu \ gh 1308)) selection = (chain 'C' and (resid 14 through 213 or resid 215 through 676 or resid 691 throu \ gh 827 or resid 848 through 1308)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } 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: 6.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 25.180 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.070 Set refine NCS operators: 0.010 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 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 0.069 27622 Z= 0.163 Angle : 0.645 10.752 37716 Z= 0.315 Chirality : 0.047 0.365 4398 Planarity : 0.004 0.060 4771 Dihedral : 13.845 89.811 9578 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.12 % Favored : 92.60 % Rotamer: Outliers : 0.03 % Allowed : 0.34 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.22 (0.14), residues: 3313 helix: 1.75 (0.22), residues: 632 sheet: -0.57 (0.21), residues: 632 loop : -1.84 (0.12), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 237 TYR 0.013 0.001 TYR C1067 PHE 0.017 0.001 PHE B 906 TRP 0.012 0.001 TRP C 436 HIS 0.003 0.000 HIS B1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 (27522) covalent geometry : angle 0.61199 / 0.31 (37457) SS BOND : bond 0.00440 / 0.30 ( 41) SS BOND : angle 1.55535 / 1.00 ( 82) hydrogen bonds : bond 0.22377 / 15.16 ( 797) hydrogen bonds : angle 7.87086 / 5.35 ( 2265) link_BETA1-4 : bond 0.00389 / 0.28 ( 15) link_BETA1-4 : angle 1.30765 / 0.93 ( 45) link_NAG-ASN : bond 0.00737 / 0.55 ( 44) link_NAG-ASN : angle 3.26819 / 2.28 ( 132) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 183 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 TYR cc_start: 0.8716 (m-80) cc_final: 0.8488 (m-80) REVERT: A 595 VAL cc_start: 0.7189 (p) cc_final: 0.6821 (p) outliers start: 1 outliers final: 0 residues processed: 184 average time/residue: 0.1895 time to fit residues: 55.1329 Evaluate side-chains 101 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.0470 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 4.9990 overall best weight: 3.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN A 360 ASN ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN B 901 GLN B1002 GLN C 81 ASN C 613 GLN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.068333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.040889 restraints weight = 119417.222| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 5.21 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 27622 Z= 0.214 Angle : 0.657 11.034 37716 Z= 0.333 Chirality : 0.046 0.252 4398 Planarity : 0.005 0.075 4771 Dihedral : 4.428 38.057 3585 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.88 % Favored : 91.85 % Rotamer: Outliers : 0.41 % Allowed : 7.23 % Favored : 92.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.19 (0.14), residues: 3313 helix: 1.83 (0.21), residues: 652 sheet: -0.53 (0.22), residues: 613 loop : -1.87 (0.12), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1019 TYR 0.018 0.001 TYR A 369 PHE 0.021 0.001 PHE B 759 TRP 0.012 0.001 TRP A 104 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.21 (27522) covalent geometry : angle 0.63580 / 0.33 (37457) SS BOND : bond 0.00434 / 0.29 ( 41) SS BOND : angle 1.49513 / 1.01 ( 82) hydrogen bonds : bond 0.05265 / 3.52 ( 797) hydrogen bonds : angle 5.85663 / 3.99 ( 2265) link_BETA1-4 : bond 0.00196 / 0.14 ( 15) link_BETA1-4 : angle 1.18107 / 0.84 ( 45) link_NAG-ASN : bond 0.00449 / 0.33 ( 44) link_NAG-ASN : angle 2.62591 / 1.80 ( 132) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 ARG cc_start: 0.8868 (tpt-90) cc_final: 0.7669 (mmm160) REVERT: A 740 MET cc_start: 0.9111 (tpp) cc_final: 0.8845 (mtp) REVERT: A 759 PHE cc_start: 0.8657 (m-80) cc_final: 0.8333 (m-80) REVERT: B 773 GLU cc_start: 0.8876 (tp30) cc_final: 0.8537 (tm-30) REVERT: C 173 GLN cc_start: 0.8821 (tp40) cc_final: 0.8517 (tm-30) outliers start: 12 outliers final: 5 residues processed: 108 average time/residue: 0.1703 time to fit residues: 30.8016 Evaluate side-chains 85 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 80 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain C residue 826 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 321 optimal weight: 0.0970 chunk 129 optimal weight: 2.9990 chunk 305 optimal weight: 4.9990 chunk 314 optimal weight: 4.9990 chunk 110 optimal weight: 0.0670 chunk 116 optimal weight: 7.9990 chunk 304 optimal weight: 0.8980 chunk 117 optimal weight: 9.9990 chunk 230 optimal weight: 9.9990 chunk 234 optimal weight: 20.0000 chunk 217 optimal weight: 0.4980 overall best weight: 0.9118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1064 HIS ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN ** C 762 GLN ** 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 = 0.3657 r_free = 0.3657 target = 0.069281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.042008 restraints weight = 118821.416| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 5.25 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 27622 Z= 0.107 Angle : 0.571 10.400 37716 Z= 0.288 Chirality : 0.044 0.248 4398 Planarity : 0.004 0.067 4771 Dihedral : 4.201 35.433 3585 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.58 % Favored : 93.18 % Rotamer: Outliers : 0.59 % Allowed : 9.92 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.99 (0.14), residues: 3313 helix: 2.12 (0.22), residues: 644 sheet: -0.35 (0.22), residues: 619 loop : -1.80 (0.13), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 158 TYR 0.017 0.001 TYR C1067 PHE 0.017 0.001 PHE A 79 TRP 0.013 0.001 TRP C 436 HIS 0.004 0.001 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (27522) covalent geometry : angle 0.55101 / 0.28 (37457) SS BOND : bond 0.00382 / 0.25 ( 41) SS BOND : angle 1.18992 / 0.81 ( 82) hydrogen bonds : bond 0.04118 / 2.76 ( 797) hydrogen bonds : angle 5.31002 / 3.61 ( 2265) link_BETA1-4 : bond 0.00340 / 0.22 ( 15) link_BETA1-4 : angle 1.13615 / 0.84 ( 45) link_NAG-ASN : bond 0.00476 / 0.34 ( 44) link_NAG-ASN : angle 2.39080 / 1.63 ( 132) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 ARG cc_start: 0.8889 (tpt-90) cc_final: 0.7509 (mmm160) REVERT: A 759 PHE cc_start: 0.8733 (m-80) cc_final: 0.8385 (m-80) REVERT: B 53 ASP cc_start: 0.8239 (t0) cc_final: 0.7997 (t0) REVERT: B 394 ASN cc_start: 0.9187 (m110) cc_final: 0.8636 (t0) REVERT: B 780 GLU cc_start: 0.8381 (mt-10) cc_final: 0.7956 (mt-10) REVERT: C 717 ASN cc_start: 0.8644 (OUTLIER) cc_final: 0.8385 (m-40) REVERT: C 900 MET cc_start: 0.8667 (mtt) cc_final: 0.8267 (mtt) outliers start: 17 outliers final: 4 residues processed: 111 average time/residue: 0.1752 time to fit residues: 32.3742 Evaluate side-chains 92 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain C residue 717 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 135 optimal weight: 8.9990 chunk 244 optimal weight: 20.0000 chunk 125 optimal weight: 30.0000 chunk 216 optimal weight: 0.9980 chunk 196 optimal weight: 0.3980 chunk 39 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 162 optimal weight: 0.8980 chunk 179 optimal weight: 9.9990 chunk 219 optimal weight: 2.9990 chunk 120 optimal weight: 9.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN C 762 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.068108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.040795 restraints weight = 119467.202| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 5.22 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 27622 Z= 0.162 Angle : 0.586 9.941 37716 Z= 0.294 Chirality : 0.044 0.242 4398 Planarity : 0.004 0.074 4771 Dihedral : 4.212 35.197 3585 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.64 % Favored : 92.12 % Rotamer: Outliers : 1.14 % Allowed : 11.78 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.97 (0.15), residues: 3313 helix: 2.18 (0.22), residues: 649 sheet: -0.40 (0.21), residues: 617 loop : -1.79 (0.13), residues: 2047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 408 TYR 0.016 0.001 TYR C1067 PHE 0.015 0.001 PHE C 201 TRP 0.011 0.001 TRP C 436 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (27522) covalent geometry : angle 0.56618 / 0.29 (37457) SS BOND : bond 0.00370 / 0.25 ( 41) SS BOND : angle 1.35223 / 0.91 ( 82) hydrogen bonds : bond 0.04366 / 2.92 ( 797) hydrogen bonds : angle 5.18810 / 3.52 ( 2265) link_BETA1-4 : bond 0.00192 / 0.14 ( 15) link_BETA1-4 : angle 1.15863 / 0.83 ( 45) link_NAG-ASN : bond 0.00420 / 0.30 ( 44) link_NAG-ASN : angle 2.38455 / 1.65 ( 132) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 90 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 759 PHE cc_start: 0.8717 (m-80) cc_final: 0.8350 (m-80) REVERT: B 53 ASP cc_start: 0.8485 (t0) cc_final: 0.8195 (t0) REVERT: B 376 THR cc_start: 0.9544 (OUTLIER) cc_final: 0.9340 (p) REVERT: B 394 ASN cc_start: 0.9150 (m110) cc_final: 0.8637 (t0) REVERT: B 780 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7969 (mt-10) REVERT: C 173 GLN cc_start: 0.8848 (tp40) cc_final: 0.8575 (tp-100) REVERT: C 762 GLN cc_start: 0.9265 (OUTLIER) cc_final: 0.8939 (mm-40) REVERT: C 900 MET cc_start: 0.8761 (mtt) cc_final: 0.8404 (mtt) outliers start: 33 outliers final: 11 residues processed: 117 average time/residue: 0.1481 time to fit residues: 29.2444 Evaluate side-chains 96 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 762 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 196 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 168 optimal weight: 3.9990 chunk 170 optimal weight: 7.9990 chunk 212 optimal weight: 0.8980 chunk 171 optimal weight: 1.9990 chunk 257 optimal weight: 30.0000 chunk 59 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 334 ASN ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN C 81 ASN C 762 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.068434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.041223 restraints weight = 118524.240| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 5.21 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27622 Z= 0.116 Angle : 0.562 9.990 37716 Z= 0.282 Chirality : 0.044 0.242 4398 Planarity : 0.004 0.063 4771 Dihedral : 4.170 36.309 3585 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.09 % Favored : 92.67 % Rotamer: Outliers : 1.07 % Allowed : 12.85 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.91 (0.15), residues: 3313 helix: 2.24 (0.22), residues: 649 sheet: -0.34 (0.21), residues: 624 loop : -1.76 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 408 TYR 0.018 0.001 TYR C1067 PHE 0.019 0.001 PHE B 759 TRP 0.011 0.001 TRP C 436 HIS 0.003 0.000 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (27522) covalent geometry : angle 0.54183 / 0.28 (37457) SS BOND : bond 0.00354 / 0.23 ( 41) SS BOND : angle 1.28010 / 0.84 ( 82) hydrogen bonds : bond 0.03966 / 2.65 ( 797) hydrogen bonds : angle 5.02673 / 3.41 ( 2265) link_BETA1-4 : bond 0.00283 / 0.19 ( 15) link_BETA1-4 : angle 1.13477 / 0.83 ( 45) link_NAG-ASN : bond 0.00422 / 0.30 ( 44) link_NAG-ASN : angle 2.33713 / 1.61 ( 132) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 86 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 759 PHE cc_start: 0.8721 (m-80) cc_final: 0.8337 (m-80) REVERT: B 53 ASP cc_start: 0.8620 (t0) cc_final: 0.8301 (t70) REVERT: B 376 THR cc_start: 0.9535 (OUTLIER) cc_final: 0.9326 (p) REVERT: B 394 ASN cc_start: 0.9155 (m110) cc_final: 0.8611 (t0) REVERT: B 780 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7947 (mt-10) REVERT: C 173 GLN cc_start: 0.8870 (tp40) cc_final: 0.8653 (tp40) REVERT: C 762 GLN cc_start: 0.9442 (OUTLIER) cc_final: 0.9173 (mm-40) REVERT: C 900 MET cc_start: 0.8737 (mtt) cc_final: 0.8363 (mtt) outliers start: 31 outliers final: 15 residues processed: 113 average time/residue: 0.1584 time to fit residues: 31.3505 Evaluate side-chains 97 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 823 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 295 optimal weight: 4.9990 chunk 268 optimal weight: 10.0000 chunk 307 optimal weight: 0.9990 chunk 253 optimal weight: 6.9990 chunk 135 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 322 optimal weight: 3.9990 chunk 301 optimal weight: 3.9990 chunk 193 optimal weight: 4.9990 chunk 298 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN C 901 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.067034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.039638 restraints weight = 120422.430| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 5.25 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 27622 Z= 0.221 Angle : 0.633 12.175 37716 Z= 0.317 Chirality : 0.045 0.269 4398 Planarity : 0.004 0.061 4771 Dihedral : 4.372 42.111 3585 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.91 % Favored : 91.85 % Rotamer: Outliers : 1.24 % Allowed : 13.47 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.04 (0.14), residues: 3313 helix: 1.96 (0.21), residues: 667 sheet: -0.41 (0.21), residues: 627 loop : -1.81 (0.13), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 408 TYR 0.017 0.001 TYR C1067 PHE 0.027 0.001 PHE C 201 TRP 0.010 0.001 TRP C 436 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.22 (27522) covalent geometry : angle 0.60960 / 0.31 (37457) SS BOND : bond 0.00487 / 0.29 ( 41) SS BOND : angle 1.95449 / 1.34 ( 82) hydrogen bonds : bond 0.04809 / 3.21 ( 797) hydrogen bonds : angle 5.13920 / 3.50 ( 2265) link_BETA1-4 : bond 0.00130 / 0.09 ( 15) link_BETA1-4 : angle 1.24940 / 0.88 ( 45) link_NAG-ASN : bond 0.00473 / 0.33 ( 44) link_NAG-ASN : angle 2.45909 / 1.74 ( 132) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 75 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 759 PHE cc_start: 0.8724 (m-80) cc_final: 0.8317 (m-80) REVERT: B 53 ASP cc_start: 0.8765 (t0) cc_final: 0.8451 (t70) REVERT: B 376 THR cc_start: 0.9523 (OUTLIER) cc_final: 0.9276 (p) REVERT: B 394 ASN cc_start: 0.9123 (m110) cc_final: 0.8645 (t0) REVERT: B 780 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7843 (mt-10) REVERT: C 173 GLN cc_start: 0.8861 (tp40) cc_final: 0.8651 (tp40) REVERT: C 900 MET cc_start: 0.8825 (mtt) cc_final: 0.8496 (mtt) outliers start: 36 outliers final: 20 residues processed: 106 average time/residue: 0.1482 time to fit residues: 27.5561 Evaluate side-chains 95 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 823 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 258 optimal weight: 6.9990 chunk 203 optimal weight: 9.9990 chunk 111 optimal weight: 6.9990 chunk 167 optimal weight: 0.3980 chunk 314 optimal weight: 0.6980 chunk 318 optimal weight: 0.7980 chunk 166 optimal weight: 1.9990 chunk 303 optimal weight: 8.9990 chunk 292 optimal weight: 5.9990 chunk 263 optimal weight: 20.0000 chunk 277 optimal weight: 9.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN C 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.067482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.040328 restraints weight = 119669.361| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 5.17 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27622 Z= 0.141 Angle : 0.588 12.015 37716 Z= 0.294 Chirality : 0.045 0.251 4398 Planarity : 0.004 0.062 4771 Dihedral : 4.268 38.382 3585 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.97 % Favored : 92.82 % Rotamer: Outliers : 1.31 % Allowed : 14.23 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.94 (0.15), residues: 3313 helix: 2.17 (0.21), residues: 655 sheet: -0.32 (0.21), residues: 627 loop : -1.79 (0.13), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 408 TYR 0.019 0.001 TYR C1067 PHE 0.022 0.001 PHE C 201 TRP 0.011 0.001 TRP C 436 HIS 0.003 0.001 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (27522) covalent geometry : angle 0.56753 / 0.29 (37457) SS BOND : bond 0.00432 / 0.28 ( 41) SS BOND : angle 1.52982 / 1.06 ( 82) hydrogen bonds : bond 0.04162 / 2.76 ( 797) hydrogen bonds : angle 4.95829 / 3.37 ( 2265) link_BETA1-4 : bond 0.00256 / 0.18 ( 15) link_BETA1-4 : angle 1.14112 / 0.84 ( 45) link_NAG-ASN : bond 0.00393 / 0.29 ( 44) link_NAG-ASN : angle 2.32910 / 1.63 ( 132) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 74 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 53 ASP cc_start: 0.8853 (t0) cc_final: 0.8554 (t70) REVERT: B 394 ASN cc_start: 0.9159 (m110) cc_final: 0.8907 (m-40) REVERT: B 780 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7942 (mt-10) REVERT: C 660 TYR cc_start: 0.8652 (OUTLIER) cc_final: 0.7445 (p90) REVERT: C 900 MET cc_start: 0.8813 (mtt) cc_final: 0.8460 (mtt) outliers start: 38 outliers final: 25 residues processed: 109 average time/residue: 0.1601 time to fit residues: 30.2079 Evaluate side-chains 100 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 74 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 133 optimal weight: 3.9990 chunk 117 optimal weight: 7.9990 chunk 181 optimal weight: 7.9990 chunk 274 optimal weight: 0.3980 chunk 81 optimal weight: 9.9990 chunk 42 optimal weight: 8.9990 chunk 278 optimal weight: 6.9990 chunk 175 optimal weight: 0.9990 chunk 271 optimal weight: 0.9990 chunk 303 optimal weight: 7.9990 chunk 187 optimal weight: 3.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN C 81 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.067248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.040102 restraints weight = 120362.279| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 5.19 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27622 Z= 0.150 Angle : 0.589 11.605 37716 Z= 0.292 Chirality : 0.045 0.298 4398 Planarity : 0.004 0.060 4771 Dihedral : 4.230 37.762 3585 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.43 % Favored : 92.36 % Rotamer: Outliers : 1.17 % Allowed : 14.54 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.94 (0.15), residues: 3313 helix: 2.12 (0.21), residues: 661 sheet: -0.31 (0.21), residues: 627 loop : -1.78 (0.13), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 408 TYR 0.018 0.001 TYR C1067 PHE 0.022 0.001 PHE C 201 TRP 0.010 0.001 TRP C 436 HIS 0.003 0.001 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (27522) covalent geometry : angle 0.56637 / 0.29 (37457) SS BOND : bond 0.00399 / 0.26 ( 41) SS BOND : angle 1.41848 / 1.00 ( 82) hydrogen bonds : bond 0.04174 / 2.77 ( 797) hydrogen bonds : angle 4.89132 / 3.32 ( 2265) link_BETA1-4 : bond 0.00194 / 0.13 ( 15) link_BETA1-4 : angle 1.17937 / 0.85 ( 45) link_NAG-ASN : bond 0.00414 / 0.30 ( 44) link_NAG-ASN : angle 2.50075 / 1.78 ( 132) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 78 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 759 PHE cc_start: 0.8637 (m-80) cc_final: 0.8339 (m-80) REVERT: B 53 ASP cc_start: 0.8884 (t0) cc_final: 0.8655 (t70) REVERT: B 376 THR cc_start: 0.9473 (OUTLIER) cc_final: 0.9203 (p) REVERT: B 394 ASN cc_start: 0.9125 (m110) cc_final: 0.8873 (m-40) REVERT: B 780 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7938 (mt-10) REVERT: C 660 TYR cc_start: 0.8694 (OUTLIER) cc_final: 0.7511 (p90) REVERT: C 900 MET cc_start: 0.8827 (mtt) cc_final: 0.8470 (mtt) outliers start: 34 outliers final: 27 residues processed: 108 average time/residue: 0.1425 time to fit residues: 27.1158 Evaluate side-chains 106 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 77 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 45 optimal weight: 30.0000 chunk 77 optimal weight: 0.9980 chunk 164 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 271 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 276 optimal weight: 5.9990 chunk 274 optimal weight: 0.7980 chunk 325 optimal weight: 4.9990 chunk 84 optimal weight: 0.5980 chunk 188 optimal weight: 6.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.067296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.039935 restraints weight = 119481.303| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 5.24 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27622 Z= 0.147 Angle : 0.586 11.782 37716 Z= 0.293 Chirality : 0.045 0.311 4398 Planarity : 0.004 0.060 4771 Dihedral : 4.216 36.895 3585 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.30 % Favored : 92.45 % Rotamer: Outliers : 1.27 % Allowed : 14.74 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.91 (0.15), residues: 3313 helix: 2.14 (0.21), residues: 661 sheet: -0.24 (0.21), residues: 619 loop : -1.78 (0.13), residues: 2033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1091 TYR 0.018 0.001 TYR C1067 PHE 0.021 0.001 PHE C 201 TRP 0.010 0.001 TRP C 436 HIS 0.003 0.001 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (27522) covalent geometry : angle 0.56614 / 0.29 (37457) SS BOND : bond 0.00399 / 0.26 ( 41) SS BOND : angle 1.39219 / 0.99 ( 82) hydrogen bonds : bond 0.04114 / 2.73 ( 797) hydrogen bonds : angle 4.84613 / 3.29 ( 2265) link_BETA1-4 : bond 0.00211 / 0.14 ( 15) link_BETA1-4 : angle 1.13397 / 0.83 ( 45) link_NAG-ASN : bond 0.00380 / 0.28 ( 44) link_NAG-ASN : angle 2.38403 / 1.67 ( 132) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 78 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 759 PHE cc_start: 0.8640 (m-80) cc_final: 0.8352 (m-80) REVERT: B 53 ASP cc_start: 0.8893 (t0) cc_final: 0.8657 (t70) REVERT: B 376 THR cc_start: 0.9474 (OUTLIER) cc_final: 0.9184 (p) REVERT: B 394 ASN cc_start: 0.9100 (m110) cc_final: 0.8857 (m-40) REVERT: B 780 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7937 (mt-10) REVERT: B 869 MET cc_start: 0.8788 (mtm) cc_final: 0.8523 (pmm) REVERT: C 660 TYR cc_start: 0.8691 (OUTLIER) cc_final: 0.7391 (p90) REVERT: C 900 MET cc_start: 0.8799 (mtt) cc_final: 0.8441 (mtt) outliers start: 37 outliers final: 28 residues processed: 112 average time/residue: 0.1395 time to fit residues: 26.8507 Evaluate side-chains 107 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 77 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 329 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 108 optimal weight: 0.4980 chunk 308 optimal weight: 0.7980 chunk 60 optimal weight: 0.0270 chunk 35 optimal weight: 0.9990 chunk 174 optimal weight: 4.9990 chunk 43 optimal weight: 20.0000 chunk 270 optimal weight: 0.9980 chunk 157 optimal weight: 0.9980 chunk 272 optimal weight: 9.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.068177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.041199 restraints weight = 119283.990| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 5.20 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 27622 Z= 0.098 Angle : 0.563 12.475 37716 Z= 0.279 Chirality : 0.045 0.298 4398 Planarity : 0.004 0.062 4771 Dihedral : 4.053 34.991 3585 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.55 % Favored : 93.21 % Rotamer: Outliers : 1.00 % Allowed : 15.05 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.77 (0.15), residues: 3313 helix: 2.28 (0.21), residues: 655 sheet: -0.12 (0.22), residues: 607 loop : -1.69 (0.13), residues: 2051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 408 TYR 0.018 0.001 TYR C1067 PHE 0.021 0.001 PHE C 201 TRP 0.012 0.001 TRP B 104 HIS 0.003 0.000 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 (27522) covalent geometry : angle 0.54504 / 0.27 (37457) SS BOND : bond 0.00371 / 0.24 ( 41) SS BOND : angle 1.18425 / 0.84 ( 82) hydrogen bonds : bond 0.03461 / 2.29 ( 797) hydrogen bonds : angle 4.65588 / 3.16 ( 2265) link_BETA1-4 : bond 0.00358 / 0.23 ( 15) link_BETA1-4 : angle 1.11802 / 0.83 ( 45) link_NAG-ASN : bond 0.00424 / 0.31 ( 44) link_NAG-ASN : angle 2.24478 / 1.57 ( 132) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 87 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 759 PHE cc_start: 0.8624 (m-80) cc_final: 0.8326 (m-80) REVERT: B 53 ASP cc_start: 0.8895 (t0) cc_final: 0.8627 (t70) REVERT: B 376 THR cc_start: 0.9499 (OUTLIER) cc_final: 0.9207 (p) REVERT: B 394 ASN cc_start: 0.9017 (m110) cc_final: 0.8789 (m-40) REVERT: B 780 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7743 (mt-10) REVERT: B 869 MET cc_start: 0.8736 (mtm) cc_final: 0.8501 (pmm) REVERT: C 104 TRP cc_start: 0.8361 (m-90) cc_final: 0.7882 (m-90) REVERT: C 660 TYR cc_start: 0.8596 (OUTLIER) cc_final: 0.7380 (p90) outliers start: 29 outliers final: 23 residues processed: 112 average time/residue: 0.1469 time to fit residues: 28.5404 Evaluate side-chains 108 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 83 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 11 optimal weight: 9.9990 chunk 271 optimal weight: 8.9990 chunk 156 optimal weight: 7.9990 chunk 258 optimal weight: 6.9990 chunk 132 optimal weight: 0.6980 chunk 204 optimal weight: 0.0010 chunk 121 optimal weight: 0.9980 chunk 329 optimal weight: 0.9990 chunk 226 optimal weight: 20.0000 chunk 8 optimal weight: 7.9990 chunk 139 optimal weight: 3.9990 overall best weight: 1.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.067871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.040696 restraints weight = 118274.937| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 5.19 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 27622 Z= 0.116 Angle : 0.574 14.438 37716 Z= 0.284 Chirality : 0.045 0.290 4398 Planarity : 0.004 0.061 4771 Dihedral : 4.049 34.702 3585 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.91 % Favored : 92.85 % Rotamer: Outliers : 1.03 % Allowed : 15.26 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.77 (0.15), residues: 3313 helix: 2.27 (0.21), residues: 653 sheet: -0.08 (0.22), residues: 614 loop : -1.70 (0.13), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 408 TYR 0.015 0.001 TYR C1067 PHE 0.020 0.001 PHE C 201 TRP 0.011 0.001 TRP C 436 HIS 0.003 0.000 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (27522) covalent geometry : angle 0.55612 / 0.28 (37457) SS BOND : bond 0.00432 / 0.31 ( 41) SS BOND : angle 1.55730 / 0.93 ( 82) hydrogen bonds : bond 0.03648 / 2.43 ( 797) hydrogen bonds : angle 4.64836 / 3.15 ( 2265) link_BETA1-4 : bond 0.00263 / 0.16 ( 15) link_BETA1-4 : angle 1.12983 / 0.83 ( 45) link_NAG-ASN : bond 0.00398 / 0.29 ( 44) link_NAG-ASN : angle 2.12993 / 1.47 ( 132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5086.10 seconds wall clock time: 104 minutes 7.33 seconds (6247.33 seconds total)