Starting phenix.real_space_refine on Sat Jun 21 22:35:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dll_27505/06_2025/8dll_27505.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dll_27505/06_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_27505/06_2025/8dll_27505.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dll_27505/06_2025/8dll_27505.map" model { file = "/net/cci-nas-00/data/ceres_data/8dll_27505/06_2025/8dll_27505.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dll_27505/06_2025/8dll_27505.cif" } resolution = 2.56 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 15.58, per 1000 atoms: 0.62 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: 6.35 Conformation dependent library (CDL) restraints added in 3.4 seconds 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: 4.47 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: 14.64 Time building geometry restraints manager: 7.30 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: 0.00 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: 3.800 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: 0.020 Extract box with map and model: 0.970 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 65.160 Find NCS groups from input model: 1.850 Set up NCS constraints: 0.450 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:59.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 132.480 ------------------------------------------------------------------------------- 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 : 3.13 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (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 TRP 0.022 0.002 TRP C 886 HIS 0.014 0.001 HIS A1048 PHE 0.047 0.002 PHE B 18 TYR 0.016 0.002 TYR A1138 ARG 0.011 0.001 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00799 ( 42) link_NAG-ASN : angle 3.22302 ( 126) link_BETA1-4 : bond 0.00656 ( 18) link_BETA1-4 : angle 1.43645 ( 54) hydrogen bonds : bond 0.19210 ( 973) hydrogen bonds : angle 8.73244 ( 2853) SS BOND : bond 0.00196 ( 42) SS BOND : angle 1.03085 ( 84) covalent geometry : bond 0.00498 (25665) covalent geometry : angle 0.78268 (34938) *********************** 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 : 4.203 Fit side-chains revert: symmetry clash 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: 0.6434 (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: 1.6256 time to fit residues: 348.6526 Evaluate side-chains 88 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 2.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 260 optimal weight: 4.9990 chunk 234 optimal weight: 8.9990 chunk 129 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 125 optimal weight: 6.9990 chunk 242 optimal weight: 20.0000 chunk 93 optimal weight: 2.9990 chunk 147 optimal weight: 30.0000 chunk 180 optimal weight: 4.9990 chunk 280 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN C 544 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 = 0.4256 r_free = 0.4256 target = 0.118108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.073180 restraints weight = 72218.580| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 3.89 r_work: 0.3147 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 25767 Z= 0.284 Angle : 0.640 9.794 35202 Z= 0.327 Chirality : 0.047 0.340 4131 Planarity : 0.005 0.065 4449 Dihedral : 6.611 59.487 4584 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.77 % Allowed : 6.26 % Favored : 92.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.15), residues: 3054 helix: 1.61 (0.20), residues: 668 sheet: -0.06 (0.19), residues: 648 loop : -0.75 (0.14), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 64 HIS 0.004 0.001 HIS C1083 PHE 0.020 0.002 PHE A 906 TYR 0.025 0.002 TYR A 170 ARG 0.006 0.001 ARG A 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00586 ( 42) link_NAG-ASN : angle 2.54609 ( 126) link_BETA1-4 : bond 0.00337 ( 18) link_BETA1-4 : angle 1.35620 ( 54) hydrogen bonds : bond 0.04795 ( 973) hydrogen bonds : angle 6.47652 ( 2853) SS BOND : bond 0.00269 ( 42) SS BOND : angle 0.89363 ( 84) covalent geometry : bond 0.00643 (25665) covalent geometry : angle 0.62061 (34938) *********************** 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 118 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 2.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 VAL cc_start: 0.8681 (t) cc_final: 0.8220 (m) REVERT: A 135 PHE cc_start: 0.6312 (m-80) cc_final: 0.5839 (m-80) REVERT: A 1010 GLN cc_start: 0.9150 (OUTLIER) cc_final: 0.8532 (mp10) REVERT: B 400 PHE cc_start: 0.8082 (p90) cc_final: 0.7745 (p90) REVERT: C 386 LYS cc_start: 0.8508 (mmtt) cc_final: 0.8199 (mmtp) REVERT: C 565 PHE cc_start: 0.7760 (OUTLIER) cc_final: 0.7258 (p90) outliers start: 21 outliers final: 7 residues processed: 112 average time/residue: 1.3370 time to fit residues: 177.2493 Evaluate side-chains 86 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 2.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 984 LEU 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 301 optimal weight: 0.8980 chunk 277 optimal weight: 0.7980 chunk 201 optimal weight: 0.6980 chunk 220 optimal weight: 3.9990 chunk 191 optimal weight: 0.8980 chunk 177 optimal weight: 0.7980 chunk 154 optimal weight: 6.9990 chunk 239 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 266 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 613 GLN B 856 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.119256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.074985 restraints weight = 71894.979| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 3.65 r_work: 0.3207 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25767 Z= 0.118 Angle : 0.525 10.081 35202 Z= 0.269 Chirality : 0.044 0.308 4131 Planarity : 0.004 0.062 4449 Dihedral : 5.851 59.370 4584 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.77 % Allowed : 7.92 % Favored : 91.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.15), residues: 3054 helix: 1.86 (0.21), residues: 678 sheet: -0.06 (0.19), residues: 637 loop : -0.57 (0.14), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 64 HIS 0.002 0.000 HIS C 66 PHE 0.029 0.001 PHE B 192 TYR 0.021 0.001 TYR C1067 ARG 0.004 0.000 ARG A 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00539 ( 42) link_NAG-ASN : angle 2.25078 ( 126) link_BETA1-4 : bond 0.00374 ( 18) link_BETA1-4 : angle 1.08380 ( 54) hydrogen bonds : bond 0.04077 ( 973) hydrogen bonds : angle 6.00826 ( 2853) SS BOND : bond 0.00189 ( 42) SS BOND : angle 0.80446 ( 84) covalent geometry : bond 0.00254 (25665) covalent geometry : angle 0.50651 (34938) *********************** 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 114 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 2.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 VAL cc_start: 0.8502 (t) cc_final: 0.8055 (m) REVERT: A 135 PHE cc_start: 0.6259 (m-80) cc_final: 0.5775 (m-80) REVERT: A 169 GLU cc_start: 0.8596 (tp30) cc_final: 0.7972 (mm-30) REVERT: B 400 PHE cc_start: 0.8057 (p90) cc_final: 0.7783 (p90) REVERT: B 432 CYS cc_start: 0.4469 (OUTLIER) cc_final: 0.3784 (p) REVERT: C 386 LYS cc_start: 0.8507 (mmtt) cc_final: 0.8238 (mmtp) REVERT: C 565 PHE cc_start: 0.7633 (OUTLIER) cc_final: 0.7143 (p90) REVERT: C 957 GLN cc_start: 0.8420 (tm-30) cc_final: 0.8091 (tm-30) REVERT: C 990 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7541 (pm20) outliers start: 21 outliers final: 6 residues processed: 106 average time/residue: 1.4027 time to fit residues: 178.3672 Evaluate side-chains 87 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 2.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 990 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 85 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 246 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 281 optimal weight: 0.8980 chunk 180 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 243 optimal weight: 5.9990 chunk 287 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN B 69 HIS ** B 394 ASN ** 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 = 0.4272 r_free = 0.4272 target = 0.118969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 108)---------------| | r_work = 0.3564 r_free = 0.3564 target = 0.073995 restraints weight = 72598.970| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 3.94 r_work: 0.3190 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25767 Z= 0.147 Angle : 0.515 8.931 35202 Z= 0.263 Chirality : 0.044 0.309 4131 Planarity : 0.004 0.063 4449 Dihedral : 5.434 58.825 4584 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.18 % Allowed : 8.69 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.15), residues: 3054 helix: 1.93 (0.21), residues: 679 sheet: -0.02 (0.20), residues: 601 loop : -0.53 (0.14), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 104 HIS 0.002 0.001 HIS C1088 PHE 0.016 0.001 PHE B 192 TYR 0.021 0.001 TYR C1067 ARG 0.003 0.000 ARG B 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00490 ( 42) link_NAG-ASN : angle 2.13678 ( 126) link_BETA1-4 : bond 0.00296 ( 18) link_BETA1-4 : angle 1.11569 ( 54) hydrogen bonds : bond 0.03931 ( 973) hydrogen bonds : angle 5.76892 ( 2853) SS BOND : bond 0.00220 ( 42) SS BOND : angle 0.78747 ( 84) covalent geometry : bond 0.00328 (25665) covalent geometry : angle 0.49731 (34938) *********************** 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: 32 poor density : 82 time to evaluate : 2.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 VAL cc_start: 0.8563 (t) cc_final: 0.8084 (m) REVERT: A 135 PHE cc_start: 0.6349 (m-80) cc_final: 0.5827 (m-80) REVERT: A 169 GLU cc_start: 0.8613 (tp30) cc_final: 0.7857 (mm-30) REVERT: A 1010 GLN cc_start: 0.9102 (OUTLIER) cc_final: 0.8471 (mp10) REVERT: B 400 PHE cc_start: 0.8061 (p90) cc_final: 0.7835 (p90) REVERT: B 432 CYS cc_start: 0.4652 (OUTLIER) cc_final: 0.3941 (p) REVERT: B 529 LYS cc_start: 0.7876 (mmpt) cc_final: 0.7567 (mttp) REVERT: B 531 THR cc_start: 0.8564 (OUTLIER) cc_final: 0.8279 (t) REVERT: C 565 PHE cc_start: 0.7758 (OUTLIER) cc_final: 0.7263 (p90) REVERT: C 957 GLN cc_start: 0.8434 (tm-30) cc_final: 0.8084 (tm-30) REVERT: C 990 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7500 (pm20) outliers start: 32 outliers final: 9 residues processed: 104 average time/residue: 1.7526 time to fit residues: 220.4626 Evaluate side-chains 92 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 5.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE 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 1010 GLN 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 565 PHE Chi-restraints excluded: chain C residue 990 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 107 optimal weight: 10.0000 chunk 298 optimal weight: 3.9990 chunk 245 optimal weight: 20.0000 chunk 18 optimal weight: 0.6980 chunk 219 optimal weight: 0.7980 chunk 261 optimal weight: 0.8980 chunk 306 optimal weight: 0.7980 chunk 285 optimal weight: 0.3980 chunk 184 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 155 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 394 ASN C 394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.119439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.075133 restraints weight = 72635.107| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 3.80 r_work: 0.3211 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 25767 Z= 0.105 Angle : 0.484 8.571 35202 Z= 0.248 Chirality : 0.044 0.293 4131 Planarity : 0.004 0.062 4449 Dihedral : 4.983 56.529 4584 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.03 % Allowed : 9.39 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.15), residues: 3054 helix: 2.09 (0.21), residues: 679 sheet: -0.01 (0.20), residues: 617 loop : -0.45 (0.15), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 104 HIS 0.001 0.000 HIS C 66 PHE 0.015 0.001 PHE B 192 TYR 0.020 0.001 TYR C1067 ARG 0.003 0.000 ARG B 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00474 ( 42) link_NAG-ASN : angle 2.00608 ( 126) link_BETA1-4 : bond 0.00346 ( 18) link_BETA1-4 : angle 1.00658 ( 54) hydrogen bonds : bond 0.03643 ( 973) hydrogen bonds : angle 5.53104 ( 2853) SS BOND : bond 0.00226 ( 42) SS BOND : angle 0.78204 ( 84) covalent geometry : bond 0.00229 (25665) covalent geometry : angle 0.46764 (34938) *********************** 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 118 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 90 time to evaluate : 2.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 VAL cc_start: 0.8322 (t) cc_final: 0.7847 (m) REVERT: A 135 PHE cc_start: 0.6373 (m-80) cc_final: 0.5875 (m-80) REVERT: A 169 GLU cc_start: 0.8520 (tp30) cc_final: 0.7856 (mm-30) REVERT: A 1010 GLN cc_start: 0.9112 (OUTLIER) cc_final: 0.8483 (mp10) REVERT: B 432 CYS cc_start: 0.4686 (OUTLIER) cc_final: 0.3929 (p) REVERT: B 529 LYS cc_start: 0.7866 (mmpt) cc_final: 0.7584 (mttp) REVERT: B 762 GLN cc_start: 0.8996 (mt0) cc_final: 0.8795 (mp10) REVERT: C 565 PHE cc_start: 0.7645 (OUTLIER) cc_final: 0.7174 (p90) REVERT: C 957 GLN cc_start: 0.8426 (tm-30) cc_final: 0.8065 (tm-30) outliers start: 28 outliers final: 10 residues processed: 110 average time/residue: 1.1160 time to fit residues: 149.7895 Evaluate side-chains 96 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 2.732 ------------------------------------------------------------------------------- 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 558 LYS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain C residue 47 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 990 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 21 optimal weight: 10.0000 chunk 253 optimal weight: 8.9990 chunk 235 optimal weight: 8.9990 chunk 7 optimal weight: 7.9990 chunk 227 optimal weight: 9.9990 chunk 104 optimal weight: 0.0870 chunk 126 optimal weight: 6.9990 chunk 108 optimal weight: 0.8980 chunk 117 optimal weight: 20.0000 chunk 268 optimal weight: 4.9990 chunk 171 optimal weight: 4.9990 overall best weight: 3.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 824 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** 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 = 0.4236 r_free = 0.4236 target = 0.116534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.071229 restraints weight = 72228.101| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 4.12 r_work: 0.3123 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 25767 Z= 0.326 Angle : 0.627 11.657 35202 Z= 0.318 Chirality : 0.048 0.321 4131 Planarity : 0.004 0.065 4449 Dihedral : 5.521 59.708 4584 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.40 % Allowed : 9.76 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.15), residues: 3054 helix: 1.77 (0.20), residues: 682 sheet: -0.25 (0.20), residues: 641 loop : -0.55 (0.15), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 104 HIS 0.005 0.001 HIS C1048 PHE 0.014 0.002 PHE B 135 TYR 0.022 0.002 TYR A1067 ARG 0.004 0.001 ARG B 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00601 ( 42) link_NAG-ASN : angle 2.16795 ( 126) link_BETA1-4 : bond 0.00330 ( 18) link_BETA1-4 : angle 1.36978 ( 54) hydrogen bonds : bond 0.04480 ( 973) hydrogen bonds : angle 5.83660 ( 2853) SS BOND : bond 0.00434 ( 42) SS BOND : angle 1.56819 ( 84) covalent geometry : bond 0.00746 (25665) covalent geometry : angle 0.60806 (34938) *********************** 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 120 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 82 time to evaluate : 2.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 VAL cc_start: 0.8606 (t) cc_final: 0.8105 (m) REVERT: A 135 PHE cc_start: 0.6294 (m-80) cc_final: 0.5880 (m-80) REVERT: A 1010 GLN cc_start: 0.9187 (OUTLIER) cc_final: 0.8576 (mp10) REVERT: B 224 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7212 (pm20) REVERT: B 432 CYS cc_start: 0.4736 (OUTLIER) cc_final: 0.4028 (p) REVERT: B 529 LYS cc_start: 0.7887 (mmpt) cc_final: 0.7541 (mttp) REVERT: B 531 THR cc_start: 0.8804 (OUTLIER) cc_final: 0.8521 (t) REVERT: C 565 PHE cc_start: 0.7921 (OUTLIER) cc_final: 0.7422 (p90) REVERT: C 957 GLN cc_start: 0.8494 (tm-30) cc_final: 0.8088 (tm-30) REVERT: C 990 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7640 (pm20) REVERT: C 1050 MET cc_start: 0.9471 (ptm) cc_final: 0.9265 (ptm) outliers start: 38 outliers final: 19 residues processed: 112 average time/residue: 1.1309 time to fit residues: 153.9543 Evaluate side-chains 100 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 75 time to evaluate : 2.616 ------------------------------------------------------------------------------- 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 651 ILE Chi-restraints excluded: chain A residue 701 VAL 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 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 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 990 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 242 optimal weight: 7.9990 chunk 189 optimal weight: 1.9990 chunk 246 optimal weight: 30.0000 chunk 30 optimal weight: 5.9990 chunk 113 optimal weight: 0.0870 chunk 91 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 179 optimal weight: 0.8980 chunk 150 optimal weight: 0.9980 chunk 184 optimal weight: 0.9980 chunk 163 optimal weight: 0.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.118706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.074314 restraints weight = 72464.928| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 3.73 r_work: 0.3191 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25767 Z= 0.117 Angle : 0.512 9.441 35202 Z= 0.261 Chirality : 0.044 0.288 4131 Planarity : 0.004 0.064 4449 Dihedral : 5.118 59.356 4584 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.33 % Allowed : 10.24 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.15), residues: 3054 helix: 2.00 (0.21), residues: 685 sheet: -0.20 (0.20), residues: 636 loop : -0.45 (0.15), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 104 HIS 0.002 0.000 HIS B1048 PHE 0.015 0.001 PHE A 565 TYR 0.021 0.001 TYR C1067 ARG 0.003 0.000 ARG A 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00468 ( 42) link_NAG-ASN : angle 1.93678 ( 126) link_BETA1-4 : bond 0.00352 ( 18) link_BETA1-4 : angle 1.00113 ( 54) hydrogen bonds : bond 0.03775 ( 973) hydrogen bonds : angle 5.56611 ( 2853) SS BOND : bond 0.00233 ( 42) SS BOND : angle 0.97944 ( 84) covalent geometry : bond 0.00258 (25665) covalent geometry : angle 0.49681 (34938) *********************** 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 122 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 86 time to evaluate : 2.680 Fit side-chains revert: symmetry clash REVERT: A 90 VAL cc_start: 0.8484 (t) cc_final: 0.7969 (m) REVERT: A 135 PHE cc_start: 0.6294 (m-80) cc_final: 0.5851 (m-80) REVERT: A 169 GLU cc_start: 0.8588 (tp30) cc_final: 0.7768 (mm-30) REVERT: A 1010 GLN cc_start: 0.9143 (OUTLIER) cc_final: 0.8450 (mp10) REVERT: B 224 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7118 (pm20) REVERT: B 432 CYS cc_start: 0.4723 (OUTLIER) cc_final: 0.4043 (p) REVERT: B 529 LYS cc_start: 0.7935 (mmpt) cc_final: 0.7520 (mttp) REVERT: B 531 THR cc_start: 0.8707 (OUTLIER) cc_final: 0.8440 (t) REVERT: C 277 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8539 (mp) REVERT: C 565 PHE cc_start: 0.7762 (OUTLIER) cc_final: 0.7279 (p90) REVERT: C 858 LEU cc_start: 0.9126 (pp) cc_final: 0.8576 (mt) REVERT: C 957 GLN cc_start: 0.8399 (tm-30) cc_final: 0.8005 (tm-30) REVERT: C 990 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7486 (pm20) outliers start: 36 outliers final: 19 residues processed: 112 average time/residue: 1.0727 time to fit residues: 146.2635 Evaluate side-chains 106 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 80 time to evaluate : 2.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 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 656 VAL 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 335 LEU Chi-restraints excluded: chain B residue 336 CYS 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 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 277 LEU 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 990 GLU Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 150 optimal weight: 0.7980 chunk 152 optimal weight: 6.9990 chunk 225 optimal weight: 5.9990 chunk 168 optimal weight: 1.9990 chunk 303 optimal weight: 0.9980 chunk 269 optimal weight: 0.9980 chunk 233 optimal weight: 10.0000 chunk 54 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 291 optimal weight: 1.9990 chunk 302 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1002 GLN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.117859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.074861 restraints weight = 72077.224| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 3.47 r_work: 0.3173 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 25767 Z= 0.151 Angle : 0.516 8.182 35202 Z= 0.263 Chirality : 0.044 0.298 4131 Planarity : 0.004 0.064 4449 Dihedral : 4.987 59.692 4584 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.18 % Allowed : 10.72 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.15), residues: 3054 helix: 2.08 (0.20), residues: 684 sheet: -0.15 (0.20), residues: 642 loop : -0.45 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 104 HIS 0.002 0.001 HIS C1088 PHE 0.018 0.001 PHE B 338 TYR 0.020 0.001 TYR C1067 ARG 0.002 0.000 ARG C1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00467 ( 42) link_NAG-ASN : angle 1.92592 ( 126) link_BETA1-4 : bond 0.00285 ( 18) link_BETA1-4 : angle 1.09819 ( 54) hydrogen bonds : bond 0.03809 ( 973) hydrogen bonds : angle 5.49221 ( 2853) SS BOND : bond 0.00237 ( 42) SS BOND : angle 0.88358 ( 84) covalent geometry : bond 0.00342 (25665) covalent geometry : angle 0.50137 (34938) *********************** 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 114 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 82 time to evaluate : 2.774 Fit side-chains revert: symmetry clash REVERT: A 90 VAL cc_start: 0.8414 (t) cc_final: 0.7890 (m) REVERT: A 135 PHE cc_start: 0.6242 (m-80) cc_final: 0.5844 (m-80) REVERT: A 169 GLU cc_start: 0.8591 (tp30) cc_final: 0.7805 (mm-30) REVERT: A 1010 GLN cc_start: 0.9159 (OUTLIER) cc_final: 0.8470 (mp10) REVERT: B 224 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7094 (pm20) REVERT: B 432 CYS cc_start: 0.4883 (OUTLIER) cc_final: 0.4266 (p) REVERT: B 529 LYS cc_start: 0.7854 (mmpt) cc_final: 0.7440 (mttp) REVERT: B 531 THR cc_start: 0.8601 (OUTLIER) cc_final: 0.8353 (t) REVERT: C 565 PHE cc_start: 0.7793 (OUTLIER) cc_final: 0.7286 (p90) REVERT: C 957 GLN cc_start: 0.8412 (tm-30) cc_final: 0.8004 (tm-30) REVERT: C 990 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7504 (pm20) REVERT: C 1050 MET cc_start: 0.9319 (ptm) cc_final: 0.9046 (ptm) outliers start: 32 outliers final: 22 residues processed: 109 average time/residue: 1.1156 time to fit residues: 149.4039 Evaluate side-chains 105 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 77 time to evaluate : 2.648 ------------------------------------------------------------------------------- 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 656 VAL Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 740 MET 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 432 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 934 ILE 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 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 990 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 239 optimal weight: 9.9990 chunk 37 optimal weight: 8.9990 chunk 61 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 299 optimal weight: 3.9990 chunk 42 optimal weight: 8.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN C 394 ASN C 564 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.117172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.072135 restraints weight = 73027.300| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 3.64 r_work: 0.3146 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 25767 Z= 0.197 Angle : 0.551 11.111 35202 Z= 0.280 Chirality : 0.045 0.293 4131 Planarity : 0.004 0.064 4449 Dihedral : 5.129 53.741 4584 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.40 % Allowed : 10.83 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.15), residues: 3054 helix: 1.98 (0.20), residues: 690 sheet: -0.24 (0.19), residues: 683 loop : -0.53 (0.15), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 104 HIS 0.004 0.001 HIS C1088 PHE 0.014 0.001 PHE C 898 TYR 0.020 0.001 TYR A1067 ARG 0.003 0.000 ARG B 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00499 ( 42) link_NAG-ASN : angle 1.96614 ( 126) link_BETA1-4 : bond 0.00375 ( 18) link_BETA1-4 : angle 1.14164 ( 54) hydrogen bonds : bond 0.04037 ( 973) hydrogen bonds : angle 5.59258 ( 2853) SS BOND : bond 0.00248 ( 42) SS BOND : angle 0.88875 ( 84) covalent geometry : bond 0.00444 (25665) covalent geometry : angle 0.53701 (34938) *********************** 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 121 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 83 time to evaluate : 2.857 Fit side-chains revert: symmetry clash REVERT: A 90 VAL cc_start: 0.8488 (t) cc_final: 0.7961 (m) REVERT: A 135 PHE cc_start: 0.6223 (m-80) cc_final: 0.5834 (m-80) REVERT: A 1010 GLN cc_start: 0.9188 (OUTLIER) cc_final: 0.8535 (mp10) REVERT: B 224 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7207 (pm20) REVERT: B 432 CYS cc_start: 0.5064 (OUTLIER) cc_final: 0.4448 (p) REVERT: B 529 LYS cc_start: 0.7915 (mmpt) cc_final: 0.7507 (mttp) REVERT: B 533 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7273 (tt) REVERT: C 565 PHE cc_start: 0.7735 (OUTLIER) cc_final: 0.7215 (p90) REVERT: C 957 GLN cc_start: 0.8448 (tm-30) cc_final: 0.8034 (tm-30) REVERT: C 990 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7534 (pm20) outliers start: 38 outliers final: 24 residues processed: 116 average time/residue: 1.7481 time to fit residues: 244.3138 Evaluate side-chains 110 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 80 time to evaluate : 3.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 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 588 THR Chi-restraints excluded: chain A residue 656 VAL 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 985 ASP 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 390 LEU Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 934 ILE 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 336 CYS Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 390 LEU 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 990 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 153 optimal weight: 6.9990 chunk 262 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 202 optimal weight: 0.6980 chunk 28 optimal weight: 6.9990 chunk 275 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 281 optimal weight: 0.9990 chunk 223 optimal weight: 7.9990 chunk 187 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.117373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.073306 restraints weight = 72410.530| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 3.62 r_work: 0.3165 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 25767 Z= 0.159 Angle : 0.530 9.479 35202 Z= 0.269 Chirality : 0.045 0.293 4131 Planarity : 0.004 0.065 4449 Dihedral : 5.005 53.261 4584 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.10 % Allowed : 11.20 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.15), residues: 3054 helix: 2.07 (0.21), residues: 684 sheet: -0.27 (0.19), residues: 677 loop : -0.50 (0.15), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP C 104 HIS 0.002 0.001 HIS C1083 PHE 0.021 0.001 PHE B 338 TYR 0.020 0.001 TYR C1067 ARG 0.003 0.000 ARG B 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00462 ( 42) link_NAG-ASN : angle 1.91481 ( 126) link_BETA1-4 : bond 0.00270 ( 18) link_BETA1-4 : angle 1.05669 ( 54) hydrogen bonds : bond 0.03854 ( 973) hydrogen bonds : angle 5.51177 ( 2853) SS BOND : bond 0.00236 ( 42) SS BOND : angle 0.85257 ( 84) covalent geometry : bond 0.00359 (25665) covalent geometry : angle 0.51643 (34938) ********************** 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 114 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 84 time to evaluate : 2.900 Fit side-chains revert: symmetry clash REVERT: A 135 PHE cc_start: 0.6190 (m-80) cc_final: 0.5786 (m-80) REVERT: A 169 GLU cc_start: 0.8581 (tp30) cc_final: 0.7723 (mm-30) REVERT: A 1010 GLN cc_start: 0.9180 (OUTLIER) cc_final: 0.8527 (mp10) REVERT: B 224 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7263 (pm20) REVERT: B 432 CYS cc_start: 0.5041 (OUTLIER) cc_final: 0.4385 (p) REVERT: B 529 LYS cc_start: 0.8046 (mmpt) cc_final: 0.7613 (mttp) REVERT: B 985 ASP cc_start: 0.8689 (p0) cc_final: 0.8368 (p0) REVERT: B 1002 GLN cc_start: 0.9054 (tt0) cc_final: 0.8629 (tp-100) REVERT: C 565 PHE cc_start: 0.7899 (OUTLIER) cc_final: 0.7352 (p90) REVERT: C 957 GLN cc_start: 0.8441 (tm-30) cc_final: 0.8025 (tm-30) REVERT: C 990 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7474 (pm20) REVERT: C 1002 GLN cc_start: 0.9217 (tp-100) cc_final: 0.9014 (tp40) outliers start: 30 outliers final: 22 residues processed: 110 average time/residue: 1.1883 time to fit residues: 159.0274 Evaluate side-chains 107 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 80 time to evaluate : 2.591 ------------------------------------------------------------------------------- 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 588 THR Chi-restraints excluded: chain A residue 656 VAL 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 432 CYS Chi-restraints excluded: chain B residue 934 ILE 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 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 990 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 143 optimal weight: 10.0000 chunk 105 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 275 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 247 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 189 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 134 optimal weight: 7.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 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 = 0.4246 r_free = 0.4246 target = 0.117333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.071920 restraints weight = 72674.375| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 3.95 r_work: 0.3158 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 25767 Z= 0.162 Angle : 0.534 9.817 35202 Z= 0.271 Chirality : 0.045 0.291 4131 Planarity : 0.004 0.065 4449 Dihedral : 4.928 53.429 4584 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.07 % Allowed : 11.42 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.15), residues: 3054 helix: 2.07 (0.20), residues: 685 sheet: -0.26 (0.19), residues: 675 loop : -0.51 (0.15), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP C 104 HIS 0.002 0.001 HIS C1088 PHE 0.017 0.001 PHE B 392 TYR 0.020 0.001 TYR C1067 ARG 0.004 0.000 ARG B 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00463 ( 42) link_NAG-ASN : angle 1.90063 ( 126) link_BETA1-4 : bond 0.00280 ( 18) link_BETA1-4 : angle 1.06519 ( 54) hydrogen bonds : bond 0.03848 ( 973) hydrogen bonds : angle 5.48847 ( 2853) SS BOND : bond 0.00237 ( 42) SS BOND : angle 0.84806 ( 84) covalent geometry : bond 0.00366 (25665) covalent geometry : angle 0.52058 (34938) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 31879.15 seconds wall clock time: 560 minutes 45.41 seconds (33645.41 seconds total)