Starting phenix.real_space_refine on Mon Aug 25 04:38:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dll_27505/08_2025/8dll_27505.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dll_27505/08_2025/8dll_27505.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dll_27505/08_2025/8dll_27505.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dll_27505/08_2025/8dll_27505.map" model { file = "/net/cci-nas-00/data/ceres_data/8dll_27505/08_2025/8dll_27505.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dll_27505/08_2025/8dll_27505.cif" } resolution = 2.56 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= -0.001 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 111 5.16 5 C 15987 2.51 5 N 4095 2.21 5 O 4902 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25095 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8085 Classifications: {'peptide': 1034} Link IDs: {'PTRANS': 56, 'TRANS': 977} Chain breaks: 7 Chain: "B" Number of atoms: 8085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8085 Classifications: {'peptide': 1034} Link IDs: {'PTRANS': 56, 'TRANS': 977} Chain breaks: 7 Chain: "C" Number of atoms: 8085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8085 Classifications: {'peptide': 1034} Link IDs: {'PTRANS': 56, 'TRANS': 977} Chain breaks: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 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 dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" 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 dihedrals: 24 Unresolved non-hydrogen chiralities: 8 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 dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 6.32, per 1000 atoms: 0.25 Number of scatterers: 25095 At special positions: 0 Unit cell: (140, 145, 198, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 111 16.00 O 4902 8.00 N 4095 7.00 C 15987 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, 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 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 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=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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 S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 709 " " NAG D 1 " - " ASN A 17 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1074 " " NAG H 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN B 17 " " NAG K 1 " - " ASN B 717 " " NAG L 1 " - " ASN B 801 " " NAG M 1 " - " ASN B1074 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN B1134 " " NAG P 1 " - " ASN C 17 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C 801 " " NAG S 1 " - " ASN C1074 " " NAG T 1 " - " ASN C1098 " " NAG U 1 " - " ASN C1134 " Time building additional restraints: 2.11 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 476.8 nanoseconds 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5802 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 45 sheets defined 25.6% alpha, 31.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 341 Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.162A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.518A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.612A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.959A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.548A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 887 through 891 removed outlier: 3.895A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.069A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.090A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 removed outlier: 3.514A pdb=" N LEU A1145 " --> pdb=" O LEU A1141 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER A1147 " --> pdb=" O PRO A1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.700A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 386 through 389 Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.851A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.737A pdb=" N ASP B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.892A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.552A 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 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 918 removed outlier: 3.933A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.809A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 removed outlier: 3.630A pdb=" N LEU B1145 " --> pdb=" O LEU B1141 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1141 through 1146' Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.728A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.739A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.506A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.502A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.811A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.767A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.530A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.058A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.323A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 removed outlier: 3.620A pdb=" N LEU C1145 " --> pdb=" O LEU C1141 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1141 through 1147' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.593A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N THR A 208 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.593A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.077A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.907A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE A 106 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 9.711A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.872A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.077A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.519A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG A 158 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 318 removed outlier: 5.110A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.590A pdb=" N ARG A 328 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.742A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.271A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.583A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.128A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.530A 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 728 removed outlier: 6.706A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.706A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.057A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 789 removed outlier: 5.662A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.891A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.727A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.540A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.543A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.554A pdb=" N LEU B 241 " --> pdb=" O GLY B 103 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE B 106 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 9.442A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 10.087A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 9.531A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY B 142 " --> pdb=" O GLU B 156 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU B 156 " --> pdb=" O GLY B 142 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.907A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.014A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TRP B 436 " --> pdb=" O ARG B 509 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.952A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 538 through 543 removed outlier: 5.200A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.921A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 701 through 703 removed outlier: 6.233A pdb=" N VAL B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.662A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.662A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.110A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.534A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.632A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 83 through 85 removed outlier: 4.391A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 9.952A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 10.130A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 10.403A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ARG C 158 " --> pdb=" O PHE C 140 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.159A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 327 through 328 removed outlier: 3.811A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.880A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.284A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.107A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.561A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.561A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.139A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1122 1034 hydrogen bonds defined for protein. 2853 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: 6.42 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7016 1.33 - 1.46: 6308 1.46 - 1.58: 12203 1.58 - 1.71: 0 1.71 - 1.83: 138 Bond restraints: 25665 Sorted by residual: bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 7.99e+00 bond pdb=" CG LEU A 916 " pdb=" CD1 LEU A 916 " ideal model delta sigma weight residual 1.521 1.432 0.089 3.30e-02 9.18e+02 7.29e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.65e+00 bond pdb=" C PRO C 986 " pdb=" N PRO C 987 " ideal model delta sigma weight residual 1.335 1.368 -0.032 1.36e-02 5.41e+03 5.61e+00 bond pdb=" CG LEU B 916 " pdb=" CD1 LEU B 916 " ideal model delta sigma weight residual 1.521 1.446 0.075 3.30e-02 9.18e+02 5.18e+00 ... (remaining 25660 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 33866 2.04 - 4.09: 958 4.09 - 6.13: 91 6.13 - 8.17: 18 8.17 - 10.21: 5 Bond angle restraints: 34938 Sorted by residual: angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 116.57 -5.87 1.22e+00 6.72e-01 2.32e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 116.41 -5.71 1.22e+00 6.72e-01 2.19e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 116.03 -5.33 1.22e+00 6.72e-01 1.91e+01 angle pdb=" CA PRO A 986 " pdb=" C PRO A 986 " pdb=" N PRO A 987 " ideal model delta sigma weight residual 117.93 122.65 -4.72 1.20e+00 6.94e-01 1.55e+01 angle pdb=" CA PRO C 986 " pdb=" C PRO C 986 " pdb=" N PRO C 987 " ideal model delta sigma weight residual 117.93 122.43 -4.50 1.20e+00 6.94e-01 1.41e+01 ... (remaining 34933 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 14804 17.75 - 35.50: 1005 35.50 - 53.25: 167 53.25 - 70.99: 64 70.99 - 88.74: 25 Dihedral angle restraints: 16065 sinusoidal: 7044 harmonic: 9021 Sorted by residual: dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -20.88 -65.12 1 1.00e+01 1.00e-02 5.56e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -40.47 -45.53 1 1.00e+01 1.00e-02 2.87e+01 dihedral pdb=" CA PHE C 392 " pdb=" C PHE C 392 " pdb=" N THR C 393 " pdb=" CA THR C 393 " ideal model delta harmonic sigma weight residual 180.00 157.97 22.03 0 5.00e+00 4.00e-02 1.94e+01 ... (remaining 16062 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 3605 0.090 - 0.179: 511 0.179 - 0.269: 12 0.269 - 0.358: 2 0.358 - 0.448: 1 Chirality restraints: 4131 Sorted by residual: chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN C 17 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.01e+00 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN B 17 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 17 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.51e+00 ... (remaining 4128 not shown) Planarity restraints: 4491 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 18 " -0.021 2.00e-02 2.50e+03 2.11e-02 7.81e+00 pdb=" CG PHE B 18 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE B 18 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE B 18 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE B 18 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 18 " -0.015 2.00e-02 2.50e+03 pdb=" CZ PHE B 18 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 294 " -0.044 5.00e-02 4.00e+02 6.67e-02 7.11e+00 pdb=" N PRO C 295 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO C 295 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 295 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET B1029 " 0.013 2.00e-02 2.50e+03 2.56e-02 6.54e+00 pdb=" C MET B1029 " -0.044 2.00e-02 2.50e+03 pdb=" O MET B1029 " 0.017 2.00e-02 2.50e+03 pdb=" N SER B1030 " 0.015 2.00e-02 2.50e+03 ... (remaining 4488 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 6253 2.80 - 3.33: 21452 3.33 - 3.85: 42368 3.85 - 4.38: 47999 4.38 - 4.90: 83438 Nonbonded interactions: 201510 Sorted by model distance: nonbonded pdb=" OG1 THR B 109 " pdb=" OD1 ASP B 111 " model vdw 2.279 3.040 nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.296 3.040 nonbonded pdb=" OE1 GLN C 115 " pdb=" OG1 THR C 167 " model vdw 2.300 3.040 nonbonded pdb=" OG1 THR A 618 " pdb=" OE1 GLU A 619 " model vdw 2.305 3.040 nonbonded pdb=" OD2 ASP B 420 " pdb=" OH TYR C 369 " model vdw 2.314 3.040 ... (remaining 201505 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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' selection = chain 'S' selection = chain 'T' selection = chain 'U' } 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: 4.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 25.780 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 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 : 0.005 0.089 25767 Z= 0.236 Angle : 0.807 14.862 35202 Z= 0.419 Chirality : 0.056 0.448 4131 Planarity : 0.006 0.067 4449 Dihedral : 12.786 88.742 10137 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.15), residues: 3054 helix: 1.52 (0.20), residues: 650 sheet: -0.04 (0.20), residues: 608 loop : -0.73 (0.14), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 273 TYR 0.016 0.002 TYR A1138 PHE 0.047 0.002 PHE B 18 TRP 0.022 0.002 TRP C 886 HIS 0.014 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00498 (25665) covalent geometry : angle 0.78268 (34938) SS BOND : bond 0.00196 ( 42) SS BOND : angle 1.03085 ( 84) hydrogen bonds : bond 0.19210 ( 973) hydrogen bonds : angle 8.73244 ( 2853) link_BETA1-4 : bond 0.00656 ( 18) link_BETA1-4 : angle 1.43645 ( 54) link_NAG-ASN : bond 0.00799 ( 42) link_NAG-ASN : angle 3.22302 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 VAL cc_start: 0.8899 (t) cc_final: 0.8617 (m) REVERT: A 104 TRP cc_start: 0.7818 (m-90) cc_final: 0.7501 (m-90) REVERT: A 135 PHE cc_start: 0.6142 (m-80) cc_final: 0.5698 (m-80) REVERT: A 239 GLN cc_start: 0.8273 (mm110) cc_final: 0.8045 (mm-40) REVERT: B 32 PHE cc_start: 0.8476 (m-10) cc_final: 0.8236 (m-10) REVERT: B 240 THR cc_start: 0.7074 (m) cc_final: 0.6448 (p) REVERT: B 400 PHE cc_start: 0.7966 (p90) cc_final: 0.7597 (p90) REVERT: C 386 LYS cc_start: 0.8743 (mmtt) cc_final: 0.8442 (mmtp) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.6658 time to fit residues: 141.7582 Evaluate side-chains 86 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.0670 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 0.2980 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 3.9990 overall best weight: 1.2322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 196 ASN A 901 GLN A1002 GLN B 188 ASN B 370 ASN B 856 ASN C 370 ASN C 824 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.120201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.075742 restraints weight = 72596.685| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 3.77 r_work: 0.3211 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25767 Z= 0.148 Angle : 0.561 10.292 35202 Z= 0.289 Chirality : 0.045 0.323 4131 Planarity : 0.004 0.071 4449 Dihedral : 6.438 58.031 4584 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.70 % Allowed : 5.30 % Favored : 94.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.15), residues: 3054 helix: 1.86 (0.21), residues: 665 sheet: 0.06 (0.19), residues: 630 loop : -0.62 (0.14), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 357 TYR 0.024 0.001 TYR A 170 PHE 0.016 0.001 PHE A 238 TRP 0.028 0.002 TRP A 64 HIS 0.002 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00327 (25665) covalent geometry : angle 0.53953 (34938) SS BOND : bond 0.00186 ( 42) SS BOND : angle 0.96612 ( 84) hydrogen bonds : bond 0.04493 ( 973) hydrogen bonds : angle 6.49193 ( 2853) link_BETA1-4 : bond 0.00338 ( 18) link_BETA1-4 : angle 1.18663 ( 54) link_NAG-ASN : bond 0.00557 ( 42) link_NAG-ASN : angle 2.47475 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 VAL cc_start: 0.8574 (t) cc_final: 0.8181 (m) REVERT: A 104 TRP cc_start: 0.7930 (m-90) cc_final: 0.7530 (m-90) REVERT: A 135 PHE cc_start: 0.6286 (m-80) cc_final: 0.5786 (m-80) REVERT: A 169 GLU cc_start: 0.8550 (tm-30) cc_final: 0.8035 (mm-30) REVERT: B 400 PHE cc_start: 0.8104 (p90) cc_final: 0.7746 (p90) REVERT: B 994 ASP cc_start: 0.8704 (t70) cc_final: 0.8227 (t0) REVERT: C 386 LYS cc_start: 0.8375 (mmtt) cc_final: 0.8105 (mmtp) REVERT: C 565 PHE cc_start: 0.7517 (OUTLIER) cc_final: 0.7059 (p90) outliers start: 19 outliers final: 3 residues processed: 110 average time/residue: 0.6415 time to fit residues: 83.3774 Evaluate side-chains 87 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 83 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 565 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 148 optimal weight: 20.0000 chunk 87 optimal weight: 2.9990 chunk 219 optimal weight: 2.9990 chunk 119 optimal weight: 9.9990 chunk 205 optimal weight: 0.9980 chunk 178 optimal weight: 2.9990 chunk 143 optimal weight: 20.0000 chunk 209 optimal weight: 8.9990 chunk 287 optimal weight: 0.7980 chunk 192 optimal weight: 3.9990 chunk 294 optimal weight: 0.7980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.119066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.073998 restraints weight = 72581.959| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 3.80 r_work: 0.3182 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 25767 Z= 0.179 Angle : 0.549 9.815 35202 Z= 0.280 Chirality : 0.045 0.321 4131 Planarity : 0.004 0.062 4449 Dihedral : 5.754 56.432 4584 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.81 % Allowed : 7.62 % Favored : 91.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.15), residues: 3054 helix: 1.90 (0.21), residues: 673 sheet: 0.03 (0.19), residues: 649 loop : -0.56 (0.15), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 995 TYR 0.021 0.001 TYR A1067 PHE 0.019 0.001 PHE A 906 TRP 0.023 0.002 TRP C 104 HIS 0.003 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00403 (25665) covalent geometry : angle 0.53000 (34938) SS BOND : bond 0.00283 ( 42) SS BOND : angle 0.84868 ( 84) hydrogen bonds : bond 0.04231 ( 973) hydrogen bonds : angle 5.98155 ( 2853) link_BETA1-4 : bond 0.00306 ( 18) link_BETA1-4 : angle 1.19196 ( 54) link_NAG-ASN : bond 0.00516 ( 42) link_NAG-ASN : angle 2.28334 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 VAL cc_start: 0.8629 (t) cc_final: 0.8190 (m) REVERT: A 104 TRP cc_start: 0.7925 (m-90) cc_final: 0.7530 (m-90) REVERT: A 135 PHE cc_start: 0.6320 (m-80) cc_final: 0.5816 (m-80) REVERT: A 1010 GLN cc_start: 0.9190 (OUTLIER) cc_final: 0.8537 (mp10) REVERT: B 400 PHE cc_start: 0.8054 (p90) cc_final: 0.7807 (p90) REVERT: B 432 CYS cc_start: 0.4448 (OUTLIER) cc_final: 0.3744 (p) REVERT: B 762 GLN cc_start: 0.8971 (mt0) cc_final: 0.8659 (mp10) REVERT: B 780 GLU cc_start: 0.9169 (mt-10) cc_final: 0.8968 (mm-30) REVERT: C 386 LYS cc_start: 0.8580 (mmtt) cc_final: 0.8293 (mmtp) REVERT: C 532 ASN cc_start: 0.8771 (t0) cc_final: 0.8567 (t0) REVERT: C 565 PHE cc_start: 0.7699 (OUTLIER) cc_final: 0.7169 (p90) outliers start: 22 outliers final: 4 residues processed: 102 average time/residue: 0.6170 time to fit residues: 74.8912 Evaluate side-chains 88 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 565 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 251 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 226 optimal weight: 5.9990 chunk 117 optimal weight: 20.0000 chunk 298 optimal weight: 3.9990 chunk 267 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 284 optimal weight: 0.5980 chunk 57 optimal weight: 8.9990 chunk 171 optimal weight: 0.8980 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 824 ASN B 69 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.117479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.072882 restraints weight = 72048.616| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 3.72 r_work: 0.3150 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 25767 Z= 0.252 Angle : 0.579 9.662 35202 Z= 0.294 Chirality : 0.046 0.319 4131 Planarity : 0.004 0.063 4449 Dihedral : 5.710 56.427 4584 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.99 % Allowed : 8.80 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.15), residues: 3054 helix: 1.79 (0.20), residues: 678 sheet: -0.06 (0.19), residues: 655 loop : -0.60 (0.15), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 237 TYR 0.022 0.001 TYR A1067 PHE 0.014 0.001 PHE A 168 TRP 0.016 0.002 TRP A 64 HIS 0.003 0.001 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00570 (25665) covalent geometry : angle 0.56147 (34938) SS BOND : bond 0.00232 ( 42) SS BOND : angle 0.90405 ( 84) hydrogen bonds : bond 0.04373 ( 973) hydrogen bonds : angle 5.95118 ( 2853) link_BETA1-4 : bond 0.00269 ( 18) link_BETA1-4 : angle 1.23659 ( 54) link_NAG-ASN : bond 0.00560 ( 42) link_NAG-ASN : angle 2.23214 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 87 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 VAL cc_start: 0.8425 (t) cc_final: 0.7943 (m) REVERT: A 135 PHE cc_start: 0.6321 (m-80) cc_final: 0.5877 (m-80) REVERT: A 169 GLU cc_start: 0.8717 (tp30) cc_final: 0.8048 (mm-30) REVERT: A 1010 GLN cc_start: 0.9160 (OUTLIER) cc_final: 0.8546 (mp10) REVERT: B 400 PHE cc_start: 0.8052 (p90) cc_final: 0.7818 (p90) REVERT: B 432 CYS cc_start: 0.5214 (OUTLIER) cc_final: 0.4446 (p) REVERT: B 529 LYS cc_start: 0.7945 (mmpt) cc_final: 0.7575 (mttp) REVERT: C 565 PHE cc_start: 0.7703 (OUTLIER) cc_final: 0.7216 (p90) REVERT: C 957 GLN cc_start: 0.8420 (tm-30) cc_final: 0.8062 (tm-30) REVERT: C 990 GLU cc_start: 0.7906 (pm20) cc_final: 0.7509 (pm20) outliers start: 27 outliers final: 10 residues processed: 106 average time/residue: 0.5965 time to fit residues: 75.7452 Evaluate side-chains 94 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 584 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 1 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 256 optimal weight: 4.9990 chunk 199 optimal weight: 0.2980 chunk 253 optimal weight: 6.9990 chunk 285 optimal weight: 0.7980 chunk 226 optimal weight: 0.9980 chunk 274 optimal weight: 0.8980 chunk 156 optimal weight: 7.9990 chunk 194 optimal weight: 2.9990 chunk 52 optimal weight: 9.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN C 394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.119039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.074416 restraints weight = 71609.574| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 3.77 r_work: 0.3200 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 25767 Z= 0.111 Angle : 0.504 11.044 35202 Z= 0.257 Chirality : 0.044 0.297 4131 Planarity : 0.004 0.062 4449 Dihedral : 5.254 53.676 4584 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.18 % Allowed : 9.28 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.15), residues: 3054 helix: 2.00 (0.21), residues: 679 sheet: -0.06 (0.20), residues: 607 loop : -0.49 (0.15), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 983 TYR 0.020 0.001 TYR C1067 PHE 0.015 0.001 PHE A 565 TRP 0.016 0.001 TRP C 104 HIS 0.002 0.000 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00242 (25665) covalent geometry : angle 0.48804 (34938) SS BOND : bond 0.00199 ( 42) SS BOND : angle 0.80886 ( 84) hydrogen bonds : bond 0.03817 ( 973) hydrogen bonds : angle 5.67569 ( 2853) link_BETA1-4 : bond 0.00343 ( 18) link_BETA1-4 : angle 1.02184 ( 54) link_NAG-ASN : bond 0.00488 ( 42) link_NAG-ASN : angle 2.04012 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 91 time to evaluate : 0.869 Fit side-chains revert: symmetry clash REVERT: A 90 VAL cc_start: 0.8569 (t) cc_final: 0.8075 (m) REVERT: A 135 PHE cc_start: 0.6379 (m-80) cc_final: 0.5864 (m-80) REVERT: A 169 GLU cc_start: 0.8567 (tp30) cc_final: 0.7815 (mm-30) REVERT: A 1010 GLN cc_start: 0.9151 (OUTLIER) cc_final: 0.8470 (mp10) REVERT: B 224 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7187 (pm20) REVERT: B 432 CYS cc_start: 0.4637 (OUTLIER) cc_final: 0.3920 (p) REVERT: B 529 LYS cc_start: 0.7858 (mmpt) cc_final: 0.7614 (mttp) REVERT: B 531 THR cc_start: 0.8781 (OUTLIER) cc_final: 0.8546 (t) REVERT: B 990 GLU cc_start: 0.8711 (pp20) cc_final: 0.8507 (pm20) REVERT: C 565 PHE cc_start: 0.7812 (OUTLIER) cc_final: 0.7328 (p90) REVERT: C 957 GLN cc_start: 0.8378 (tm-30) cc_final: 0.8000 (tm-30) REVERT: C 990 GLU cc_start: 0.7930 (pm20) cc_final: 0.7507 (pm20) REVERT: C 1050 MET cc_start: 0.9207 (ptm) cc_final: 0.8993 (ptm) outliers start: 32 outliers final: 12 residues processed: 111 average time/residue: 0.5587 time to fit residues: 74.4322 Evaluate side-chains 102 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 988 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 85 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 chunk 177 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 253 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 211 optimal weight: 8.9990 chunk 141 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 270 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.118604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.074254 restraints weight = 72171.498| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 3.66 r_work: 0.3185 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25767 Z= 0.137 Angle : 0.510 8.421 35202 Z= 0.258 Chirality : 0.044 0.300 4131 Planarity : 0.004 0.063 4449 Dihedral : 5.024 53.627 4584 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.29 % Allowed : 10.06 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.15), residues: 3054 helix: 2.08 (0.21), residues: 679 sheet: -0.11 (0.20), residues: 635 loop : -0.44 (0.15), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 983 TYR 0.033 0.001 TYR C 200 PHE 0.020 0.001 PHE B 338 TRP 0.022 0.001 TRP C 104 HIS 0.002 0.001 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00305 (25665) covalent geometry : angle 0.49474 (34938) SS BOND : bond 0.00217 ( 42) SS BOND : angle 0.81177 ( 84) hydrogen bonds : bond 0.03819 ( 973) hydrogen bonds : angle 5.57567 ( 2853) link_BETA1-4 : bond 0.00291 ( 18) link_BETA1-4 : angle 1.07080 ( 54) link_NAG-ASN : bond 0.00467 ( 42) link_NAG-ASN : angle 1.99082 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 87 time to evaluate : 1.029 Fit side-chains revert: symmetry clash REVERT: A 90 VAL cc_start: 0.8429 (t) cc_final: 0.7923 (m) REVERT: A 135 PHE cc_start: 0.6260 (m-80) cc_final: 0.5814 (m-80) REVERT: A 169 GLU cc_start: 0.8582 (tp30) cc_final: 0.7804 (mm-30) REVERT: A 1010 GLN cc_start: 0.9166 (OUTLIER) cc_final: 0.8488 (mp10) REVERT: B 224 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.7082 (pm20) REVERT: B 432 CYS cc_start: 0.4424 (OUTLIER) cc_final: 0.3784 (p) REVERT: B 529 LYS cc_start: 0.7978 (mmpt) cc_final: 0.7606 (mttp) REVERT: B 531 THR cc_start: 0.8807 (OUTLIER) cc_final: 0.8559 (t) REVERT: B 988 GLU cc_start: 0.9292 (mp0) cc_final: 0.8984 (mp0) REVERT: C 565 PHE cc_start: 0.7792 (OUTLIER) cc_final: 0.7353 (p90) REVERT: C 957 GLN cc_start: 0.8401 (tm-30) cc_final: 0.8017 (tm-30) REVERT: C 990 GLU cc_start: 0.7984 (pm20) cc_final: 0.7542 (pm20) REVERT: C 1050 MET cc_start: 0.9325 (ptm) cc_final: 0.9114 (ptm) outliers start: 35 outliers final: 18 residues processed: 115 average time/residue: 0.5645 time to fit residues: 78.3446 Evaluate side-chains 104 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 186 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 273 optimal weight: 0.7980 chunk 149 optimal weight: 10.0000 chunk 128 optimal weight: 4.9990 chunk 290 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 216 optimal weight: 2.9990 chunk 144 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1002 GLN B 394 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN C1002 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.117200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.072896 restraints weight = 72574.039| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 3.68 r_work: 0.3153 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 25767 Z= 0.226 Angle : 0.559 11.825 35202 Z= 0.284 Chirality : 0.045 0.305 4131 Planarity : 0.004 0.064 4449 Dihedral : 5.160 53.859 4584 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.36 % Allowed : 10.24 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.15), residues: 3054 helix: 2.00 (0.20), residues: 679 sheet: -0.09 (0.20), residues: 637 loop : -0.50 (0.15), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 102 TYR 0.031 0.001 TYR C 200 PHE 0.022 0.001 PHE C 392 TRP 0.025 0.001 TRP C 104 HIS 0.003 0.001 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00513 (25665) covalent geometry : angle 0.54109 (34938) SS BOND : bond 0.00387 ( 42) SS BOND : angle 1.55032 ( 84) hydrogen bonds : bond 0.04098 ( 973) hydrogen bonds : angle 5.65449 ( 2853) link_BETA1-4 : bond 0.00273 ( 18) link_BETA1-4 : angle 1.16054 ( 54) link_NAG-ASN : bond 0.00522 ( 42) link_NAG-ASN : angle 2.01386 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 83 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 VAL cc_start: 0.8597 (t) cc_final: 0.8085 (m) REVERT: A 135 PHE cc_start: 0.6258 (m-80) cc_final: 0.5830 (m-80) REVERT: A 1010 GLN cc_start: 0.9183 (OUTLIER) cc_final: 0.8533 (mp10) REVERT: B 224 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7250 (pm20) REVERT: B 432 CYS cc_start: 0.5030 (OUTLIER) cc_final: 0.4415 (p) REVERT: B 529 LYS cc_start: 0.7890 (mmpt) cc_final: 0.7543 (mttp) REVERT: B 531 THR cc_start: 0.8797 (OUTLIER) cc_final: 0.8561 (t) REVERT: C 565 PHE cc_start: 0.7876 (OUTLIER) cc_final: 0.7382 (p90) REVERT: C 957 GLN cc_start: 0.8416 (tm-30) cc_final: 0.8014 (tm-30) REVERT: C 990 GLU cc_start: 0.8000 (pm20) cc_final: 0.7570 (pm20) REVERT: C 1050 MET cc_start: 0.9423 (ptm) cc_final: 0.9183 (ptm) outliers start: 37 outliers final: 23 residues processed: 110 average time/residue: 0.5771 time to fit residues: 76.3726 Evaluate side-chains 108 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 80 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 988 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 43 optimal weight: 0.0970 chunk 207 optimal weight: 0.0030 chunk 249 optimal weight: 7.9990 chunk 89 optimal weight: 0.9980 chunk 138 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 283 optimal weight: 0.5980 chunk 214 optimal weight: 0.0870 chunk 75 optimal weight: 0.8980 chunk 201 optimal weight: 1.9990 overall best weight: 0.3366 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 580 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.119013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.075120 restraints weight = 72356.418| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 3.64 r_work: 0.3202 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 25767 Z= 0.096 Angle : 0.499 8.567 35202 Z= 0.254 Chirality : 0.044 0.288 4131 Planarity : 0.004 0.063 4449 Dihedral : 4.846 53.800 4584 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.14 % Allowed : 10.64 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.15), residues: 3054 helix: 2.17 (0.21), residues: 679 sheet: -0.14 (0.20), residues: 630 loop : -0.42 (0.15), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 328 TYR 0.020 0.001 TYR C1067 PHE 0.014 0.001 PHE C 392 TRP 0.029 0.001 TRP C 104 HIS 0.002 0.000 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00204 (25665) covalent geometry : angle 0.48379 (34938) SS BOND : bond 0.00219 ( 42) SS BOND : angle 1.07205 ( 84) hydrogen bonds : bond 0.03654 ( 973) hydrogen bonds : angle 5.44712 ( 2853) link_BETA1-4 : bond 0.00329 ( 18) link_BETA1-4 : angle 0.99857 ( 54) link_NAG-ASN : bond 0.00455 ( 42) link_NAG-ASN : angle 1.88505 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 85 time to evaluate : 1.018 Fit side-chains revert: symmetry clash REVERT: A 90 VAL cc_start: 0.8562 (t) cc_final: 0.8044 (m) REVERT: A 135 PHE cc_start: 0.6284 (m-80) cc_final: 0.5869 (m-80) REVERT: A 169 GLU cc_start: 0.8542 (tp30) cc_final: 0.7744 (mm-30) REVERT: A 1010 GLN cc_start: 0.9165 (OUTLIER) cc_final: 0.8483 (mp10) REVERT: B 224 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7274 (pm20) REVERT: B 432 CYS cc_start: 0.5142 (OUTLIER) cc_final: 0.4498 (p) REVERT: B 529 LYS cc_start: 0.7961 (mmpt) cc_final: 0.7587 (mttp) REVERT: B 531 THR cc_start: 0.8666 (OUTLIER) cc_final: 0.8388 (t) REVERT: B 762 GLN cc_start: 0.9017 (mt0) cc_final: 0.8766 (mp10) REVERT: B 988 GLU cc_start: 0.9288 (mp0) cc_final: 0.8963 (mp0) REVERT: C 565 PHE cc_start: 0.7806 (OUTLIER) cc_final: 0.7349 (p90) REVERT: C 957 GLN cc_start: 0.8380 (tm-30) cc_final: 0.7982 (tm-30) REVERT: C 990 GLU cc_start: 0.7983 (pm20) cc_final: 0.7514 (pm20) outliers start: 31 outliers final: 20 residues processed: 109 average time/residue: 0.5873 time to fit residues: 76.8109 Evaluate side-chains 104 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 79 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 235 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 93 optimal weight: 0.7980 chunk 292 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 203 optimal weight: 0.4980 chunk 265 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 277 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 394 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C1002 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.118777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.073798 restraints weight = 72772.777| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 3.84 r_work: 0.3194 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 25767 Z= 0.113 Angle : 0.498 10.099 35202 Z= 0.253 Chirality : 0.044 0.291 4131 Planarity : 0.004 0.063 4449 Dihedral : 4.655 53.655 4584 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.22 % Allowed : 10.76 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.15), residues: 3054 helix: 2.29 (0.20), residues: 672 sheet: -0.14 (0.20), residues: 618 loop : -0.41 (0.15), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 983 TYR 0.020 0.001 TYR C1067 PHE 0.021 0.001 PHE B 338 TRP 0.038 0.001 TRP C 104 HIS 0.001 0.000 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00249 (25665) covalent geometry : angle 0.48319 (34938) SS BOND : bond 0.00224 ( 42) SS BOND : angle 0.94827 ( 84) hydrogen bonds : bond 0.03634 ( 973) hydrogen bonds : angle 5.35913 ( 2853) link_BETA1-4 : bond 0.00294 ( 18) link_BETA1-4 : angle 1.03386 ( 54) link_NAG-ASN : bond 0.00441 ( 42) link_NAG-ASN : angle 1.86502 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 85 time to evaluate : 1.002 Fit side-chains revert: symmetry clash REVERT: A 90 VAL cc_start: 0.8505 (t) cc_final: 0.7985 (m) REVERT: A 135 PHE cc_start: 0.6266 (m-80) cc_final: 0.5851 (m-80) REVERT: A 169 GLU cc_start: 0.8577 (tp30) cc_final: 0.7806 (mm-30) REVERT: A 1010 GLN cc_start: 0.9181 (OUTLIER) cc_final: 0.8458 (mp10) REVERT: B 224 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7128 (pm20) REVERT: B 432 CYS cc_start: 0.4697 (OUTLIER) cc_final: 0.4026 (p) REVERT: B 529 LYS cc_start: 0.7945 (mmpt) cc_final: 0.7577 (mttp) REVERT: B 531 THR cc_start: 0.8624 (OUTLIER) cc_final: 0.8380 (t) REVERT: B 762 GLN cc_start: 0.9036 (mt0) cc_final: 0.8707 (mp10) REVERT: B 988 GLU cc_start: 0.9288 (mp0) cc_final: 0.8965 (mp0) REVERT: B 995 ARG cc_start: 0.9112 (ttm-80) cc_final: 0.8761 (ttm-80) REVERT: C 565 PHE cc_start: 0.7766 (OUTLIER) cc_final: 0.7300 (p90) REVERT: C 957 GLN cc_start: 0.8395 (tm-30) cc_final: 0.7995 (tm-30) REVERT: C 990 GLU cc_start: 0.7985 (pm20) cc_final: 0.7492 (pm20) outliers start: 33 outliers final: 24 residues processed: 115 average time/residue: 0.5806 time to fit residues: 80.0913 Evaluate side-chains 110 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 81 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 91 optimal weight: 3.9990 chunk 253 optimal weight: 0.9990 chunk 232 optimal weight: 0.1980 chunk 103 optimal weight: 20.0000 chunk 137 optimal weight: 20.0000 chunk 230 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 159 optimal weight: 0.7980 chunk 181 optimal weight: 0.5980 chunk 200 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.118941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.075466 restraints weight = 72538.433| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 3.55 r_work: 0.3208 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 25767 Z= 0.105 Angle : 0.496 8.645 35202 Z= 0.252 Chirality : 0.044 0.288 4131 Planarity : 0.004 0.063 4449 Dihedral : 4.549 53.349 4584 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.14 % Allowed : 10.90 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.15), residues: 3054 helix: 2.32 (0.21), residues: 672 sheet: -0.14 (0.20), residues: 619 loop : -0.38 (0.15), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 983 TYR 0.020 0.001 TYR C1067 PHE 0.026 0.001 PHE B 392 TRP 0.037 0.001 TRP C 104 HIS 0.002 0.000 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00231 (25665) covalent geometry : angle 0.48156 (34938) SS BOND : bond 0.00225 ( 42) SS BOND : angle 0.91537 ( 84) hydrogen bonds : bond 0.03563 ( 973) hydrogen bonds : angle 5.30621 ( 2853) link_BETA1-4 : bond 0.00329 ( 18) link_BETA1-4 : angle 1.00466 ( 54) link_NAG-ASN : bond 0.00443 ( 42) link_NAG-ASN : angle 1.83821 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 84 time to evaluate : 1.145 Fit side-chains revert: symmetry clash REVERT: A 90 VAL cc_start: 0.8523 (t) cc_final: 0.7966 (m) REVERT: A 135 PHE cc_start: 0.6282 (m-80) cc_final: 0.5858 (m-80) REVERT: A 169 GLU cc_start: 0.8519 (tp30) cc_final: 0.7731 (mm-30) REVERT: A 1010 GLN cc_start: 0.9181 (OUTLIER) cc_final: 0.8466 (mp10) REVERT: B 224 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7103 (pm20) REVERT: B 432 CYS cc_start: 0.4628 (OUTLIER) cc_final: 0.4035 (p) REVERT: B 529 LYS cc_start: 0.7963 (mmpt) cc_final: 0.7602 (mttp) REVERT: B 531 THR cc_start: 0.8672 (OUTLIER) cc_final: 0.8426 (t) REVERT: B 762 GLN cc_start: 0.9041 (mt0) cc_final: 0.8719 (mp10) REVERT: B 988 GLU cc_start: 0.9213 (mp0) cc_final: 0.8892 (mp0) REVERT: B 995 ARG cc_start: 0.9095 (ttm-80) cc_final: 0.8785 (ttm-80) REVERT: C 565 PHE cc_start: 0.7821 (OUTLIER) cc_final: 0.7360 (p90) REVERT: C 957 GLN cc_start: 0.8392 (tm-30) cc_final: 0.8000 (tm-30) REVERT: C 990 GLU cc_start: 0.7998 (pm20) cc_final: 0.7493 (pm20) outliers start: 31 outliers final: 23 residues processed: 111 average time/residue: 0.5895 time to fit residues: 78.5551 Evaluate side-chains 109 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 81 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 27 optimal weight: 1.9990 chunk 299 optimal weight: 0.2980 chunk 262 optimal weight: 0.9990 chunk 114 optimal weight: 4.9990 chunk 29 optimal weight: 20.0000 chunk 268 optimal weight: 0.9990 chunk 215 optimal weight: 0.0570 chunk 115 optimal weight: 6.9990 chunk 227 optimal weight: 6.9990 chunk 219 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 overall best weight: 0.8704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN B 394 ASN ** B 506 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 = 0.4271 r_free = 0.4271 target = 0.118813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.074027 restraints weight = 72545.550| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 3.85 r_work: 0.3194 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25767 Z= 0.115 Angle : 0.496 8.557 35202 Z= 0.252 Chirality : 0.044 0.289 4131 Planarity : 0.004 0.063 4449 Dihedral : 4.499 53.585 4584 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.29 % Allowed : 10.79 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.15), residues: 3054 helix: 2.30 (0.20), residues: 678 sheet: -0.15 (0.20), residues: 624 loop : -0.37 (0.15), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 237 TYR 0.020 0.001 TYR C1067 PHE 0.021 0.001 PHE B 338 TRP 0.038 0.001 TRP C 104 HIS 0.003 0.000 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00256 (25665) covalent geometry : angle 0.48208 (34938) SS BOND : bond 0.00224 ( 42) SS BOND : angle 0.88654 ( 84) hydrogen bonds : bond 0.03578 ( 973) hydrogen bonds : angle 5.27731 ( 2853) link_BETA1-4 : bond 0.00308 ( 18) link_BETA1-4 : angle 1.02893 ( 54) link_NAG-ASN : bond 0.00439 ( 42) link_NAG-ASN : angle 1.83461 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13492.94 seconds wall clock time: 230 minutes 1.83 seconds (13801.83 seconds total)