Starting phenix.real_space_refine on Thu Mar 5 22:15:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r1b_14237/03_2026/7r1b_14237.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r1b_14237/03_2026/7r1b_14237.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7r1b_14237/03_2026/7r1b_14237.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r1b_14237/03_2026/7r1b_14237.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7r1b_14237/03_2026/7r1b_14237.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r1b_14237/03_2026/7r1b_14237.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.099 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 114 5.16 5 C 16269 2.51 5 N 4209 2.21 5 O 4962 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25554 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 8297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8297 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 53, 'TRANS': 1007} Chain breaks: 5 Chain: "B" Number of atoms: 8352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1068, 8352 Classifications: {'peptide': 1068} Link IDs: {'PTRANS': 54, 'TRANS': 1013} Chain breaks: 5 Chain: "C" Number of atoms: 8317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1064, 8317 Classifications: {'peptide': 1064} Link IDs: {'PTRANS': 54, 'TRANS': 1009} Chain breaks: 5 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: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 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: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 5.39, per 1000 atoms: 0.21 Number of scatterers: 25554 At special positions: 0 Unit cell: (157.388, 153.076, 198.352, 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 114 16.00 O 4962 8.00 N 4209 7.00 C 16269 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=2.05 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 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=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 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-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A 801 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A1134 " " NAG B1301 " - " ASN B 234 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 801 " " NAG B1306 " - " ASN B1074 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B1134 " " NAG C1301 " - " ASN C1134 " " NAG C1302 " - " ASN C1074 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C 331 " " NAG C1308 " - " ASN C 616 " " NAG C1309 " - " ASN C 343 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A1098 " " NAG F 1 " - " ASN B 717 " " NAG G 1 " - " ASN B1098 " " NAG H 1 " - " ASN B 331 " " NAG I 1 " - " ASN C1098 " " NAG J 1 " - " ASN C 717 " " NAG K 1 " - " ASN C 801 " Time building additional restraints: 2.05 Conformation dependent library (CDL) restraints added in 1.0 seconds 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5972 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 47 sheets defined 23.5% alpha, 29.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.943A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.046A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.128A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 4.386A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 411 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.746A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.543A pdb=" N LYS A 825 " --> pdb=" O LEU A 821 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.012A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.847A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.350A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.797A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.125A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 384 through 388 removed outlier: 4.262A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 759 through 783 removed outlier: 3.831A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.501A pdb=" N LYS B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 853 through 856 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.965A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.076A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.012A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.530A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.017A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 removed outlier: 3.573A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 372 removed outlier: 4.216A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.569A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.676A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.549A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.155A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.824A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.275A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.975A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.627A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.255A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.551A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.957A pdb=" N LEU A 141 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU A 244 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL A 143 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG A 246 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N MET A 153 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.888A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE A 106 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE A 119 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 310 through 319 removed outlier: 5.333A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 595 " --> pdb=" O SER A 316 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.366A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.971A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.971A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.610A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.215A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.785A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.785A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.682A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.544A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.416A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.068A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.889A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER B 116 " --> pdb=" O CYS B 131 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.889A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.332A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 324 through 325 removed outlier: 6.652A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.909A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.625A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.396A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.711A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.711A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.608A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD7, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.973A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.436A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.505A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.743A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 126 through 127 Processing sheet with id=AE1, first strand: chain 'C' and resid 156 through 157 removed outlier: 4.049A pdb=" N GLU C 156 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY C 142 " --> pdb=" O GLU C 156 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.565A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.573A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.743A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 453 removed outlier: 3.576A pdb=" N PHE C 453 " --> pdb=" O GLN C 493 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 660 removed outlier: 6.327A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.831A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 9.114A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.695A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.695A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.673A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1122 980 hydrogen bonds defined for protein. 2739 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.63 Time building geometry restraints manager: 2.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5462 1.33 - 1.45: 6496 1.45 - 1.58: 14031 1.58 - 1.70: 0 1.70 - 1.83: 144 Bond restraints: 26133 Sorted by residual: bond pdb=" N ILE A 233 " pdb=" CA ILE A 233 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.14e-02 7.69e+03 1.16e+01 bond pdb=" N VAL A 171 " pdb=" CA VAL A 171 " ideal model delta sigma weight residual 1.458 1.496 -0.039 1.14e-02 7.69e+03 1.14e+01 bond pdb=" N ILE A 235 " pdb=" CA ILE A 235 " ideal model delta sigma weight residual 1.464 1.501 -0.037 1.13e-02 7.83e+03 1.08e+01 bond pdb=" N VAL A 126 " pdb=" CA VAL A 126 " ideal model delta sigma weight residual 1.461 1.495 -0.035 1.08e-02 8.57e+03 1.03e+01 bond pdb=" N VAL C 911 " pdb=" CA VAL C 911 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.14e-02 7.69e+03 9.97e+00 ... (remaining 26128 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 33861 1.51 - 3.02: 1443 3.02 - 4.53: 221 4.53 - 6.03: 30 6.03 - 7.54: 6 Bond angle restraints: 35561 Sorted by residual: angle pdb=" CA ASN A 121 " pdb=" C ASN A 121 " pdb=" O ASN A 121 " ideal model delta sigma weight residual 122.64 117.78 4.86 1.25e+00 6.40e-01 1.51e+01 angle pdb=" N PRO B 600 " pdb=" CA PRO B 600 " pdb=" C PRO B 600 " ideal model delta sigma weight residual 111.41 105.62 5.79 1.50e+00 4.44e-01 1.49e+01 angle pdb=" CA GLY B 601 " pdb=" C GLY B 601 " pdb=" O GLY B 601 " ideal model delta sigma weight residual 121.41 118.05 3.36 8.80e-01 1.29e+00 1.46e+01 angle pdb=" CA THR B 33 " pdb=" C THR B 33 " pdb=" O THR B 33 " ideal model delta sigma weight residual 121.84 117.44 4.40 1.16e+00 7.43e-01 1.44e+01 angle pdb=" N THR B 470 " pdb=" CA THR B 470 " pdb=" C THR B 470 " ideal model delta sigma weight residual 111.28 107.14 4.14 1.09e+00 8.42e-01 1.44e+01 ... (remaining 35556 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 14886 17.56 - 35.12: 1030 35.12 - 52.68: 160 52.68 - 70.25: 33 70.25 - 87.81: 15 Dihedral angle restraints: 16124 sinusoidal: 6839 harmonic: 9285 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 -145.45 59.45 1 1.00e+01 1.00e-02 4.72e+01 dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 55.86 37.14 1 1.00e+01 1.00e-02 1.95e+01 dihedral pdb=" CB CYS C 15 " pdb=" SG CYS C 15 " pdb=" SG CYS C 136 " pdb=" CB CYS C 136 " ideal model delta sinusoidal sigma weight residual -86.00 -49.43 -36.57 1 1.00e+01 1.00e-02 1.89e+01 ... (remaining 16121 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 3879 0.104 - 0.208: 244 0.208 - 0.312: 19 0.312 - 0.416: 0 0.416 - 0.520: 1 Chirality restraints: 4143 Sorted by residual: chirality pdb=" C1 NAG C1305 " pdb=" ND2 ASN C 657 " pdb=" C2 NAG C1305 " pdb=" O5 NAG C1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.76e+00 chirality pdb=" CA ILE B 598 " pdb=" N ILE B 598 " pdb=" C ILE B 598 " pdb=" CB ILE B 598 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" C1 NAG B1304 " pdb=" ND2 ASN B 616 " pdb=" C2 NAG B1304 " pdb=" O5 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 4140 not shown) Planarity restraints: 4596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 127 " 0.022 2.00e-02 2.50e+03 4.45e-02 1.98e+01 pdb=" C VAL B 127 " -0.077 2.00e-02 2.50e+03 pdb=" O VAL B 127 " 0.029 2.00e-02 2.50e+03 pdb=" N ILE B 128 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 617 " -0.019 2.00e-02 2.50e+03 3.64e-02 1.32e+01 pdb=" C CYS A 617 " 0.063 2.00e-02 2.50e+03 pdb=" O CYS A 617 " -0.023 2.00e-02 2.50e+03 pdb=" N THR A 618 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 603 " -0.001 2.00e-02 2.50e+03 1.69e-02 3.56e+00 pdb=" CG ASN C 603 " -0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN C 603 " 0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN C 603 " -0.021 2.00e-02 2.50e+03 pdb=" C1 NAG C1304 " 0.018 2.00e-02 2.50e+03 ... (remaining 4593 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3042 2.76 - 3.29: 23300 3.29 - 3.83: 39265 3.83 - 4.36: 47674 4.36 - 4.90: 83776 Nonbonded interactions: 197057 Sorted by model distance: nonbonded pdb=" O ASN C 439 " pdb=" OG SER C 443 " model vdw 2.220 3.040 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.220 3.040 nonbonded pdb=" OD1 ASN A 394 " pdb=" OH TYR B 200 " model vdw 2.239 3.040 nonbonded pdb=" OG SER A 98 " pdb=" O LYS A 182 " model vdw 2.316 3.040 nonbonded pdb=" O ALA C 879 " pdb=" OG1 THR C 883 " model vdw 2.323 3.040 ... (remaining 197052 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 675 or resid 690 through 1308)) selection = (chain 'B' and (resid 14 through 620 or resid 641 through 826 or resid 856 throu \ gh 1308)) selection = (chain 'C' and (resid 14 through 620 or resid 641 through 826 or resid 856 throu \ gh 1308)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.200 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: 0.280 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 23.290 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 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 0.053 26217 Z= 0.293 Angle : 0.700 17.786 35771 Z= 0.424 Chirality : 0.054 0.520 4143 Planarity : 0.004 0.044 4562 Dihedral : 12.031 87.807 10026 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.54 % Allowed : 0.90 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.14), residues: 3157 helix: 1.85 (0.21), residues: 660 sheet: 0.38 (0.19), residues: 705 loop : -1.27 (0.13), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 214 TYR 0.017 0.001 TYR B 37 PHE 0.018 0.001 PHE C 490 TRP 0.021 0.001 TRP B 886 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00457 (26133) covalent geometry : angle 0.67532 (35561) SS BOND : bond 0.00405 ( 42) SS BOND : angle 1.40480 ( 84) hydrogen bonds : bond 0.19944 ( 936) hydrogen bonds : angle 7.63122 ( 2739) link_BETA1-4 : bond 0.00533 ( 8) link_BETA1-4 : angle 1.13720 ( 24) link_NAG-ASN : bond 0.00525 ( 34) link_NAG-ASN : angle 3.31332 ( 102) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 254 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 CYS cc_start: 0.3499 (OUTLIER) cc_final: 0.3208 (m) REVERT: A 188 ASN cc_start: 0.7950 (OUTLIER) cc_final: 0.7477 (p0) REVERT: A 378 LYS cc_start: 0.6900 (mttp) cc_final: 0.6461 (mtpp) REVERT: A 409 GLN cc_start: 0.7806 (mt0) cc_final: 0.7601 (mt0) REVERT: A 455 LEU cc_start: 0.8047 (tt) cc_final: 0.7777 (tm) REVERT: B 99 ASN cc_start: 0.8213 (m-40) cc_final: 0.7464 (t0) REVERT: B 129 LYS cc_start: 0.7383 (mptt) cc_final: 0.7086 (mmtp) REVERT: C 53 ASP cc_start: 0.6657 (t0) cc_final: 0.6363 (t0) REVERT: C 237 ARG cc_start: 0.7206 (mtm-85) cc_final: 0.6638 (mtm110) REVERT: C 529 LYS cc_start: 0.8120 (mmtt) cc_final: 0.7904 (mmpt) REVERT: C 697 MET cc_start: 0.8242 (ptm) cc_final: 0.8003 (ptp) REVERT: C 988 GLU cc_start: 0.6507 (tp30) cc_final: 0.6285 (tp30) outliers start: 15 outliers final: 3 residues processed: 267 average time/residue: 0.5626 time to fit residues: 176.5607 Evaluate side-chains 189 residues out of total 2789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 184 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain C residue 68 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 2.9990 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 394 ASN A 564 GLN A 675 GLN A 690 GLN A 764 ASN A 901 GLN A 969 ASN B 122 ASN B 146 HIS B 218 GLN B 532 ASN C 314 GLN C 394 ASN C 613 GLN C 675 GLN C 901 GLN C1002 GLN C1005 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.197919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.130207 restraints weight = 29833.498| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.55 r_work: 0.3156 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 26217 Z= 0.185 Angle : 0.659 25.974 35771 Z= 0.331 Chirality : 0.049 0.331 4143 Planarity : 0.004 0.047 4562 Dihedral : 6.335 59.167 4311 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.61 % Allowed : 6.27 % Favored : 92.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.14), residues: 3157 helix: 1.66 (0.21), residues: 671 sheet: 0.41 (0.19), residues: 731 loop : -1.36 (0.13), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 466 TYR 0.026 0.001 TYR A1067 PHE 0.021 0.002 PHE C 400 TRP 0.016 0.002 TRP B 886 HIS 0.006 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00449 (26133) covalent geometry : angle 0.61511 (35561) SS BOND : bond 0.00590 ( 42) SS BOND : angle 1.61108 ( 84) hydrogen bonds : bond 0.07312 ( 936) hydrogen bonds : angle 5.81381 ( 2739) link_BETA1-4 : bond 0.00585 ( 8) link_BETA1-4 : angle 1.15584 ( 24) link_NAG-ASN : bond 0.00531 ( 34) link_NAG-ASN : angle 4.22928 ( 102) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 196 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 HIS cc_start: 0.7357 (t-90) cc_final: 0.7095 (m90) REVERT: A 254 SER cc_start: 0.3119 (OUTLIER) cc_final: 0.2468 (p) REVERT: A 319 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7700 (mtt-85) REVERT: A 378 LYS cc_start: 0.7121 (mttp) cc_final: 0.6552 (mtpp) REVERT: A 409 GLN cc_start: 0.7945 (mt0) cc_final: 0.7656 (mt0) REVERT: A 455 LEU cc_start: 0.8090 (tt) cc_final: 0.7741 (tm) REVERT: A 508 TYR cc_start: 0.7531 (m-80) cc_final: 0.7255 (m-80) REVERT: A 745 ASP cc_start: 0.7967 (p0) cc_final: 0.7567 (p0) REVERT: B 99 ASN cc_start: 0.8257 (m-40) cc_final: 0.7579 (t0) REVERT: B 129 LYS cc_start: 0.7896 (mptt) cc_final: 0.7672 (mmtp) REVERT: B 177 MET cc_start: 0.4302 (ttm) cc_final: 0.2877 (pmt) REVERT: B 586 ASP cc_start: 0.8460 (m-30) cc_final: 0.8062 (m-30) REVERT: B 868 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7815 (mp0) REVERT: C 80 ASP cc_start: 0.6475 (m-30) cc_final: 0.6156 (p0) REVERT: C 153 MET cc_start: 0.7490 (pmm) cc_final: 0.6687 (pp-130) REVERT: C 177 MET cc_start: 0.3364 (pmt) cc_final: 0.3128 (pmm) REVERT: C 237 ARG cc_start: 0.7759 (mtm-85) cc_final: 0.6892 (mtm110) REVERT: C 529 LYS cc_start: 0.8321 (mmtt) cc_final: 0.8088 (mmpt) REVERT: C 988 GLU cc_start: 0.6815 (tp30) cc_final: 0.6377 (tp30) outliers start: 45 outliers final: 17 residues processed: 222 average time/residue: 0.5349 time to fit residues: 140.9438 Evaluate side-chains 195 residues out of total 2789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 176 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 960 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 42 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 210 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 198 optimal weight: 0.5980 chunk 155 optimal weight: 2.9990 chunk 125 optimal weight: 0.0020 chunk 247 optimal weight: 0.6980 chunk 165 optimal weight: 0.8980 chunk 179 optimal weight: 1.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN A 901 GLN A 969 ASN B 532 ASN C 99 ASN C 234 ASN C 394 ASN C 675 GLN C 901 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.199757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.130882 restraints weight = 29878.344| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.56 r_work: 0.3107 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 26217 Z= 0.120 Angle : 0.556 13.115 35771 Z= 0.282 Chirality : 0.045 0.303 4143 Planarity : 0.004 0.045 4562 Dihedral : 5.777 59.975 4307 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.61 % Allowed : 7.92 % Favored : 90.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.14), residues: 3157 helix: 1.99 (0.21), residues: 666 sheet: 0.53 (0.19), residues: 727 loop : -1.27 (0.13), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 319 TYR 0.018 0.001 TYR A1067 PHE 0.022 0.001 PHE C 400 TRP 0.012 0.001 TRP B 64 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00271 (26133) covalent geometry : angle 0.52961 (35561) SS BOND : bond 0.00401 ( 42) SS BOND : angle 1.74160 ( 84) hydrogen bonds : bond 0.05754 ( 936) hydrogen bonds : angle 5.30386 ( 2739) link_BETA1-4 : bond 0.00498 ( 8) link_BETA1-4 : angle 1.04767 ( 24) link_NAG-ASN : bond 0.00398 ( 34) link_NAG-ASN : angle 2.77119 ( 102) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 190 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7692 (tm-30) cc_final: 0.7387 (tm-30) REVERT: A 108 THR cc_start: 0.6545 (OUTLIER) cc_final: 0.5898 (m) REVERT: A 207 HIS cc_start: 0.7307 (t-90) cc_final: 0.7043 (m90) REVERT: A 319 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7648 (mtt-85) REVERT: A 378 LYS cc_start: 0.7114 (mttp) cc_final: 0.6517 (mtpp) REVERT: A 409 GLN cc_start: 0.7703 (mt0) cc_final: 0.7359 (mt0) REVERT: A 423 TYR cc_start: 0.8220 (t80) cc_final: 0.7860 (t80) REVERT: A 455 LEU cc_start: 0.8048 (tt) cc_final: 0.7666 (tm) REVERT: A 508 TYR cc_start: 0.7483 (m-80) cc_final: 0.7021 (m-80) REVERT: A 613 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8628 (mt0) REVERT: A 745 ASP cc_start: 0.7932 (p0) cc_final: 0.7474 (p0) REVERT: A 916 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8550 (tp) REVERT: B 128 ILE cc_start: 0.6690 (OUTLIER) cc_final: 0.6379 (mp) REVERT: B 177 MET cc_start: 0.4039 (ttm) cc_final: 0.1742 (pmt) REVERT: B 208 THR cc_start: 0.8087 (m) cc_final: 0.7882 (m) REVERT: B 586 ASP cc_start: 0.8236 (m-30) cc_final: 0.8006 (m-30) REVERT: B 619 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7268 (mp0) REVERT: C 80 ASP cc_start: 0.6297 (m-30) cc_final: 0.6052 (p0) REVERT: C 81 ASN cc_start: 0.7891 (p0) cc_final: 0.7686 (p0) REVERT: C 153 MET cc_start: 0.7449 (pmm) cc_final: 0.6707 (pp-130) REVERT: C 237 ARG cc_start: 0.7632 (mtm-85) cc_final: 0.6781 (mtm110) REVERT: C 529 LYS cc_start: 0.8297 (mmtt) cc_final: 0.8061 (mmpt) REVERT: C 988 GLU cc_start: 0.6672 (tp30) cc_final: 0.6228 (tp30) outliers start: 45 outliers final: 16 residues processed: 213 average time/residue: 0.5172 time to fit residues: 131.8269 Evaluate side-chains 195 residues out of total 2789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 173 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 960 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 29 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 chunk 244 optimal weight: 9.9990 chunk 232 optimal weight: 1.9990 chunk 78 optimal weight: 0.0870 chunk 307 optimal weight: 1.9990 chunk 213 optimal weight: 0.9990 chunk 218 optimal weight: 4.9990 chunk 224 optimal weight: 8.9990 chunk 254 optimal weight: 1.9990 chunk 296 optimal weight: 0.9980 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN A 969 ASN B 532 ASN C 394 ASN C 675 GLN C 919 ASN C1005 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.202365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.130905 restraints weight = 29265.750| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.73 r_work: 0.3156 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 26217 Z= 0.130 Angle : 0.551 10.655 35771 Z= 0.281 Chirality : 0.045 0.288 4143 Planarity : 0.004 0.047 4562 Dihedral : 5.516 59.362 4305 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.19 % Allowed : 8.35 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.14), residues: 3157 helix: 2.06 (0.21), residues: 660 sheet: 0.45 (0.19), residues: 747 loop : -1.29 (0.13), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 190 TYR 0.022 0.001 TYR A1067 PHE 0.019 0.001 PHE C 400 TRP 0.011 0.001 TRP B 64 HIS 0.005 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00303 (26133) covalent geometry : angle 0.53032 (35561) SS BOND : bond 0.00453 ( 42) SS BOND : angle 1.31878 ( 84) hydrogen bonds : bond 0.05966 ( 936) hydrogen bonds : angle 5.16735 ( 2739) link_BETA1-4 : bond 0.00475 ( 8) link_BETA1-4 : angle 1.04966 ( 24) link_NAG-ASN : bond 0.00390 ( 34) link_NAG-ASN : angle 2.58124 ( 102) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 184 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7730 (tm-30) cc_final: 0.7333 (tm-30) REVERT: A 188 ASN cc_start: 0.8122 (OUTLIER) cc_final: 0.7804 (p0) REVERT: A 207 HIS cc_start: 0.7406 (t-90) cc_final: 0.7003 (m90) REVERT: A 319 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7690 (mtt-85) REVERT: A 378 LYS cc_start: 0.7084 (mttp) cc_final: 0.6490 (mtpp) REVERT: A 409 GLN cc_start: 0.7710 (mt0) cc_final: 0.7409 (mt0) REVERT: A 423 TYR cc_start: 0.8360 (t80) cc_final: 0.8011 (t80) REVERT: A 455 LEU cc_start: 0.8090 (tt) cc_final: 0.7684 (tm) REVERT: A 508 TYR cc_start: 0.7373 (m-80) cc_final: 0.6899 (m-80) REVERT: A 745 ASP cc_start: 0.8118 (p0) cc_final: 0.7644 (p0) REVERT: A 916 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8485 (tp) REVERT: A 977 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8031 (mp) REVERT: B 128 ILE cc_start: 0.6756 (OUTLIER) cc_final: 0.6360 (mp) REVERT: B 177 MET cc_start: 0.3995 (ttm) cc_final: 0.1889 (pmt) REVERT: B 586 ASP cc_start: 0.8289 (m-30) cc_final: 0.8071 (m-30) REVERT: B 619 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.6640 (mp0) REVERT: C 153 MET cc_start: 0.7497 (pmm) cc_final: 0.6775 (pp-130) REVERT: C 237 ARG cc_start: 0.7810 (mtm-85) cc_final: 0.7016 (mtp-110) REVERT: C 529 LYS cc_start: 0.8332 (mmtt) cc_final: 0.8075 (mmpt) REVERT: C 697 MET cc_start: 0.8748 (ptm) cc_final: 0.8487 (ptp) REVERT: C 988 GLU cc_start: 0.6752 (tp30) cc_final: 0.6237 (tp30) outliers start: 61 outliers final: 28 residues processed: 222 average time/residue: 0.4749 time to fit residues: 127.8525 Evaluate side-chains 211 residues out of total 2789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 177 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 960 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 280 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 252 optimal weight: 2.9990 chunk 236 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 185 optimal weight: 1.9990 chunk 310 optimal weight: 2.9990 chunk 135 optimal weight: 0.5980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 564 GLN A 901 GLN A 969 ASN B 207 HIS B 532 ASN C 81 ASN C 394 ASN C 675 GLN C 901 GLN C1002 GLN C1005 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.201174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.139767 restraints weight = 29149.369| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.94 r_work: 0.3227 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 26217 Z= 0.176 Angle : 0.605 15.037 35771 Z= 0.309 Chirality : 0.047 0.290 4143 Planarity : 0.004 0.050 4562 Dihedral : 5.594 58.845 4305 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.08 % Allowed : 9.47 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.14), residues: 3157 helix: 1.81 (0.21), residues: 659 sheet: 0.47 (0.19), residues: 743 loop : -1.39 (0.13), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 190 TYR 0.024 0.001 TYR A1067 PHE 0.019 0.002 PHE C 168 TRP 0.009 0.001 TRP B 436 HIS 0.007 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00431 (26133) covalent geometry : angle 0.58363 (35561) SS BOND : bond 0.00695 ( 42) SS BOND : angle 1.83552 ( 84) hydrogen bonds : bond 0.06907 ( 936) hydrogen bonds : angle 5.26234 ( 2739) link_BETA1-4 : bond 0.00512 ( 8) link_BETA1-4 : angle 1.14719 ( 24) link_NAG-ASN : bond 0.00410 ( 34) link_NAG-ASN : angle 2.59008 ( 102) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 176 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ASN cc_start: 0.8139 (p0) cc_final: 0.7743 (p0) REVERT: A 319 ARG cc_start: 0.7842 (tpp-160) cc_final: 0.7626 (mtt-85) REVERT: A 378 LYS cc_start: 0.7388 (mttp) cc_final: 0.6711 (mtpp) REVERT: A 409 GLN cc_start: 0.7947 (mt0) cc_final: 0.7721 (mt0) REVERT: A 455 LEU cc_start: 0.8241 (tt) cc_final: 0.7844 (tm) REVERT: A 508 TYR cc_start: 0.7459 (m-80) cc_final: 0.7024 (m-80) REVERT: A 745 ASP cc_start: 0.7986 (p0) cc_final: 0.7516 (p0) REVERT: A 916 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8642 (tp) REVERT: B 117 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7229 (tt) REVERT: B 128 ILE cc_start: 0.6908 (OUTLIER) cc_final: 0.6509 (mp) REVERT: B 177 MET cc_start: 0.4082 (ttm) cc_final: 0.1939 (pmt) REVERT: B 586 ASP cc_start: 0.8159 (m-30) cc_final: 0.7923 (m-30) REVERT: B 619 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.6688 (mp0) REVERT: C 153 MET cc_start: 0.7442 (pmm) cc_final: 0.6831 (pp-130) REVERT: C 237 ARG cc_start: 0.7771 (mtm-85) cc_final: 0.7086 (mtp-110) REVERT: C 512 VAL cc_start: 0.7974 (t) cc_final: 0.7733 (m) REVERT: C 529 LYS cc_start: 0.8263 (mmtt) cc_final: 0.8054 (mmpt) REVERT: C 988 GLU cc_start: 0.6847 (tp30) cc_final: 0.6468 (tp30) outliers start: 58 outliers final: 32 residues processed: 215 average time/residue: 0.4838 time to fit residues: 125.4481 Evaluate side-chains 205 residues out of total 2789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 169 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 960 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 39 optimal weight: 6.9990 chunk 183 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 21 optimal weight: 5.9990 chunk 164 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 285 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 145 optimal weight: 20.0000 chunk 276 optimal weight: 2.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 564 GLN A 957 GLN A 969 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 ASN B 532 ASN C 81 ASN C 394 ASN C 675 GLN C 762 GLN C1002 GLN C1005 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.198347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.130901 restraints weight = 29167.025| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.88 r_work: 0.3216 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.104 26217 Z= 0.295 Angle : 0.732 16.854 35771 Z= 0.373 Chirality : 0.053 0.298 4143 Planarity : 0.005 0.062 4562 Dihedral : 6.183 59.540 4305 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.62 % Allowed : 9.97 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.14), residues: 3157 helix: 1.23 (0.21), residues: 658 sheet: 0.38 (0.19), residues: 733 loop : -1.63 (0.13), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1039 TYR 0.029 0.002 TYR B 265 PHE 0.022 0.003 PHE C 898 TRP 0.010 0.002 TRP C 104 HIS 0.009 0.002 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00747 (26133) covalent geometry : angle 0.70771 (35561) SS BOND : bond 0.00626 ( 42) SS BOND : angle 2.00953 ( 84) hydrogen bonds : bond 0.08687 ( 936) hydrogen bonds : angle 5.53169 ( 2739) link_BETA1-4 : bond 0.00536 ( 8) link_BETA1-4 : angle 1.42114 ( 24) link_NAG-ASN : bond 0.00524 ( 34) link_NAG-ASN : angle 3.05030 ( 102) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 173 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.6355 (mtpp) cc_final: 0.6014 (ttmm) REVERT: A 188 ASN cc_start: 0.8130 (p0) cc_final: 0.7677 (p0) REVERT: A 254 SER cc_start: 0.3198 (OUTLIER) cc_final: 0.2277 (p) REVERT: A 305 SER cc_start: 0.9015 (t) cc_final: 0.8689 (m) REVERT: A 378 LYS cc_start: 0.7394 (mttp) cc_final: 0.6754 (mtpp) REVERT: A 455 LEU cc_start: 0.8185 (tt) cc_final: 0.7803 (tm) REVERT: A 508 TYR cc_start: 0.7555 (m-80) cc_final: 0.7222 (m-80) REVERT: A 745 ASP cc_start: 0.8138 (p0) cc_final: 0.7665 (p0) REVERT: A 977 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8159 (mp) REVERT: B 129 LYS cc_start: 0.7902 (mptt) cc_final: 0.7593 (mptm) REVERT: B 177 MET cc_start: 0.4085 (ttm) cc_final: 0.1985 (pmt) REVERT: B 208 THR cc_start: 0.8272 (OUTLIER) cc_final: 0.8025 (m) REVERT: B 319 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7428 (mtm110) REVERT: B 586 ASP cc_start: 0.8350 (m-30) cc_final: 0.8109 (m-30) REVERT: B 619 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.7097 (mp0) REVERT: C 153 MET cc_start: 0.7473 (pmm) cc_final: 0.6815 (pp-130) REVERT: C 237 ARG cc_start: 0.8007 (mtm-85) cc_final: 0.7282 (mtp85) REVERT: C 529 LYS cc_start: 0.8327 (mmtt) cc_final: 0.8111 (mmpt) REVERT: C 558 LYS cc_start: 0.8022 (OUTLIER) cc_final: 0.7808 (mppt) REVERT: C 988 GLU cc_start: 0.7095 (tp30) cc_final: 0.6555 (tp30) outliers start: 73 outliers final: 34 residues processed: 221 average time/residue: 0.4655 time to fit residues: 124.6638 Evaluate side-chains 202 residues out of total 2789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 162 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 960 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 207 optimal weight: 0.5980 chunk 313 optimal weight: 1.9990 chunk 168 optimal weight: 0.6980 chunk 197 optimal weight: 0.5980 chunk 82 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 125 optimal weight: 0.6980 chunk 312 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 314 optimal weight: 0.5980 chunk 127 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN A 901 GLN A 969 ASN B 146 HIS B 207 HIS B 334 ASN B 532 ASN C 81 ASN C 196 ASN C 394 ASN C 675 GLN C1002 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.202046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.133612 restraints weight = 29190.769| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 3.06 r_work: 0.3242 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 26217 Z= 0.125 Angle : 0.562 13.464 35771 Z= 0.285 Chirality : 0.044 0.271 4143 Planarity : 0.004 0.047 4562 Dihedral : 5.583 58.717 4305 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.69 % Allowed : 11.37 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.14), residues: 3157 helix: 1.81 (0.21), residues: 659 sheet: 0.48 (0.19), residues: 736 loop : -1.50 (0.13), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 319 TYR 0.017 0.001 TYR A1067 PHE 0.018 0.001 PHE C 400 TRP 0.008 0.001 TRP B 436 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00282 (26133) covalent geometry : angle 0.53728 (35561) SS BOND : bond 0.00577 ( 42) SS BOND : angle 1.60412 ( 84) hydrogen bonds : bond 0.05782 ( 936) hydrogen bonds : angle 5.12105 ( 2739) link_BETA1-4 : bond 0.00488 ( 8) link_BETA1-4 : angle 1.02775 ( 24) link_NAG-ASN : bond 0.00378 ( 34) link_NAG-ASN : angle 2.77799 ( 102) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 179 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.6030 (mtpp) cc_final: 0.5786 (ttmm) REVERT: A 188 ASN cc_start: 0.8128 (OUTLIER) cc_final: 0.7713 (p0) REVERT: A 305 SER cc_start: 0.8970 (t) cc_final: 0.8649 (m) REVERT: A 378 LYS cc_start: 0.7278 (mttp) cc_final: 0.6956 (mttp) REVERT: A 455 LEU cc_start: 0.8198 (tt) cc_final: 0.7822 (tm) REVERT: A 508 TYR cc_start: 0.7418 (m-80) cc_final: 0.7010 (m-80) REVERT: A 556 ASN cc_start: 0.7695 (p0) cc_final: 0.7213 (p0) REVERT: A 745 ASP cc_start: 0.8092 (p0) cc_final: 0.7578 (p0) REVERT: B 177 MET cc_start: 0.4077 (ttm) cc_final: 0.2072 (pmt) REVERT: B 208 THR cc_start: 0.8045 (m) cc_final: 0.7840 (m) REVERT: B 229 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7156 (mp) REVERT: B 619 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.6735 (mp0) REVERT: C 153 MET cc_start: 0.7468 (pmm) cc_final: 0.6825 (pp-130) REVERT: C 237 ARG cc_start: 0.7830 (mtm-85) cc_final: 0.7058 (mtp85) REVERT: C 512 VAL cc_start: 0.7867 (t) cc_final: 0.7619 (m) REVERT: C 529 LYS cc_start: 0.8365 (mmtt) cc_final: 0.8131 (mmpt) REVERT: C 697 MET cc_start: 0.8724 (ptm) cc_final: 0.8472 (ptp) REVERT: C 988 GLU cc_start: 0.6887 (tp30) cc_final: 0.6357 (tp30) outliers start: 47 outliers final: 29 residues processed: 209 average time/residue: 0.4840 time to fit residues: 122.2320 Evaluate side-chains 198 residues out of total 2789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 166 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 960 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 8 optimal weight: 4.9990 chunk 208 optimal weight: 0.2980 chunk 91 optimal weight: 2.9990 chunk 297 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 chunk 38 optimal weight: 0.4980 chunk 182 optimal weight: 1.9990 chunk 205 optimal weight: 1.9990 chunk 190 optimal weight: 0.9980 chunk 248 optimal weight: 4.9990 chunk 88 optimal weight: 0.3980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN A 969 ASN B 334 ASN B 532 ASN C 81 ASN C 196 ASN C 234 ASN C 394 ASN C 556 ASN C 675 GLN C 901 GLN C1002 GLN C1005 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.202038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.140668 restraints weight = 29191.573| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.88 r_work: 0.3298 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 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 0.064 26217 Z= 0.122 Angle : 0.553 12.656 35771 Z= 0.281 Chirality : 0.044 0.266 4143 Planarity : 0.004 0.045 4562 Dihedral : 5.384 58.658 4305 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.01 % Allowed : 11.26 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.14), residues: 3157 helix: 2.04 (0.21), residues: 659 sheet: 0.57 (0.19), residues: 722 loop : -1.44 (0.13), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 319 TYR 0.020 0.001 TYR A1067 PHE 0.019 0.001 PHE C 400 TRP 0.014 0.001 TRP B 64 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00279 (26133) covalent geometry : angle 0.53099 (35561) SS BOND : bond 0.00414 ( 42) SS BOND : angle 1.51493 ( 84) hydrogen bonds : bond 0.05670 ( 936) hydrogen bonds : angle 4.99755 ( 2739) link_BETA1-4 : bond 0.00500 ( 8) link_BETA1-4 : angle 1.03362 ( 24) link_NAG-ASN : bond 0.00372 ( 34) link_NAG-ASN : angle 2.57684 ( 102) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 179 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7801 (tm-30) cc_final: 0.7488 (tm-30) REVERT: A 188 ASN cc_start: 0.8144 (OUTLIER) cc_final: 0.7781 (p0) REVERT: A 305 SER cc_start: 0.8928 (t) cc_final: 0.8651 (m) REVERT: A 378 LYS cc_start: 0.7437 (mttp) cc_final: 0.7085 (mttp) REVERT: A 423 TYR cc_start: 0.8438 (t80) cc_final: 0.8180 (t80) REVERT: A 455 LEU cc_start: 0.8287 (tt) cc_final: 0.7904 (tm) REVERT: A 508 TYR cc_start: 0.7422 (m-80) cc_final: 0.7060 (m-80) REVERT: A 556 ASN cc_start: 0.7738 (p0) cc_final: 0.7296 (p0) REVERT: A 745 ASP cc_start: 0.8109 (p0) cc_final: 0.7611 (p0) REVERT: B 177 MET cc_start: 0.4028 (ttm) cc_final: 0.2114 (pmt) REVERT: B 229 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.6843 (mt) REVERT: B 619 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.6623 (mp0) REVERT: C 153 MET cc_start: 0.7493 (pmm) cc_final: 0.6893 (pp-130) REVERT: C 237 ARG cc_start: 0.7910 (mtm-85) cc_final: 0.7234 (mtp85) REVERT: C 529 LYS cc_start: 0.8284 (mmtt) cc_final: 0.8073 (mmpt) REVERT: C 697 MET cc_start: 0.8785 (ptm) cc_final: 0.8529 (ptp) REVERT: C 988 GLU cc_start: 0.6922 (tp30) cc_final: 0.6450 (tp30) outliers start: 56 outliers final: 34 residues processed: 216 average time/residue: 0.4866 time to fit residues: 126.5525 Evaluate side-chains 203 residues out of total 2789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 166 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 960 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 26 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 181 optimal weight: 0.1980 chunk 214 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 207 optimal weight: 0.9980 chunk 96 optimal weight: 0.4980 chunk 309 optimal weight: 0.0970 chunk 233 optimal weight: 0.9990 chunk 311 optimal weight: 1.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN A 969 ASN B 334 ASN C 81 ASN C 394 ASN C 556 ASN C 675 GLN C1002 GLN C1005 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.202998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 101)---------------| | r_work = 0.3608 r_free = 0.3608 target = 0.134210 restraints weight = 29370.850| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 3.07 r_work: 0.3275 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 26217 Z= 0.113 Angle : 0.540 11.978 35771 Z= 0.274 Chirality : 0.044 0.255 4143 Planarity : 0.004 0.044 4562 Dihedral : 5.249 59.094 4305 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.47 % Allowed : 12.08 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.15), residues: 3157 helix: 2.15 (0.21), residues: 659 sheet: 0.58 (0.19), residues: 722 loop : -1.38 (0.13), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 319 TYR 0.018 0.001 TYR A1067 PHE 0.017 0.001 PHE C 400 TRP 0.020 0.001 TRP B 64 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00253 (26133) covalent geometry : angle 0.52071 (35561) SS BOND : bond 0.00395 ( 42) SS BOND : angle 1.44795 ( 84) hydrogen bonds : bond 0.05264 ( 936) hydrogen bonds : angle 4.92517 ( 2739) link_BETA1-4 : bond 0.00494 ( 8) link_BETA1-4 : angle 1.00456 ( 24) link_NAG-ASN : bond 0.00390 ( 34) link_NAG-ASN : angle 2.41177 ( 102) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 179 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ASN cc_start: 0.8132 (OUTLIER) cc_final: 0.7731 (p0) REVERT: A 305 SER cc_start: 0.8958 (t) cc_final: 0.8642 (m) REVERT: A 378 LYS cc_start: 0.7285 (mttp) cc_final: 0.6948 (mttp) REVERT: A 423 TYR cc_start: 0.8360 (t80) cc_final: 0.8120 (t80) REVERT: A 455 LEU cc_start: 0.8233 (tt) cc_final: 0.7862 (tm) REVERT: A 508 TYR cc_start: 0.7391 (m-80) cc_final: 0.7030 (m-80) REVERT: A 556 ASN cc_start: 0.7721 (p0) cc_final: 0.7307 (p0) REVERT: A 745 ASP cc_start: 0.8100 (p0) cc_final: 0.7569 (p0) REVERT: B 177 MET cc_start: 0.4002 (ttm) cc_final: 0.2144 (pmt) REVERT: B 229 LEU cc_start: 0.7187 (OUTLIER) cc_final: 0.6737 (mt) REVERT: B 619 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.6527 (mp0) REVERT: C 153 MET cc_start: 0.7495 (pmm) cc_final: 0.6885 (pp-130) REVERT: C 237 ARG cc_start: 0.7860 (mtm-85) cc_final: 0.7127 (mtp85) REVERT: C 529 LYS cc_start: 0.8337 (mmtt) cc_final: 0.8094 (mmpt) REVERT: C 697 MET cc_start: 0.8741 (ptm) cc_final: 0.8478 (ptp) REVERT: C 988 GLU cc_start: 0.6799 (tp30) cc_final: 0.6269 (tp30) outliers start: 41 outliers final: 34 residues processed: 209 average time/residue: 0.4714 time to fit residues: 119.3025 Evaluate side-chains 204 residues out of total 2789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 167 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 960 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 294 optimal weight: 0.9990 chunk 160 optimal weight: 0.6980 chunk 179 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 174 optimal weight: 1.9990 chunk 300 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 chunk 259 optimal weight: 20.0000 chunk 67 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 969 ASN B 66 HIS B 334 ASN B 532 ASN C 394 ASN C 556 ASN C 675 GLN C 901 GLN C1002 GLN C1005 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.202090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.133092 restraints weight = 29183.094| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 3.26 r_work: 0.3245 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 26217 Z= 0.135 Angle : 0.569 12.026 35771 Z= 0.289 Chirality : 0.045 0.260 4143 Planarity : 0.004 0.046 4562 Dihedral : 5.290 58.689 4305 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.65 % Allowed : 11.90 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.14), residues: 3157 helix: 2.09 (0.21), residues: 659 sheet: 0.57 (0.19), residues: 711 loop : -1.40 (0.13), residues: 1787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 319 TYR 0.021 0.001 TYR A1067 PHE 0.016 0.001 PHE C 400 TRP 0.018 0.001 TRP B 64 HIS 0.008 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00320 (26133) covalent geometry : angle 0.54836 (35561) SS BOND : bond 0.00397 ( 42) SS BOND : angle 1.73308 ( 84) hydrogen bonds : bond 0.05820 ( 936) hydrogen bonds : angle 4.97554 ( 2739) link_BETA1-4 : bond 0.00490 ( 8) link_BETA1-4 : angle 1.03724 ( 24) link_NAG-ASN : bond 0.00392 ( 34) link_NAG-ASN : angle 2.41152 ( 102) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 170 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ASN cc_start: 0.8068 (OUTLIER) cc_final: 0.7637 (p0) REVERT: A 305 SER cc_start: 0.8979 (t) cc_final: 0.8670 (m) REVERT: A 378 LYS cc_start: 0.7308 (mttp) cc_final: 0.6971 (mttp) REVERT: A 423 TYR cc_start: 0.8405 (t80) cc_final: 0.8087 (t80) REVERT: A 455 LEU cc_start: 0.8234 (tt) cc_final: 0.7867 (tm) REVERT: A 508 TYR cc_start: 0.7394 (m-80) cc_final: 0.6972 (m-80) REVERT: A 745 ASP cc_start: 0.8119 (p0) cc_final: 0.7593 (p0) REVERT: B 177 MET cc_start: 0.4102 (ttm) cc_final: 0.2267 (pmt) REVERT: B 229 LEU cc_start: 0.7192 (OUTLIER) cc_final: 0.6687 (mt) REVERT: B 619 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.6520 (mp0) REVERT: C 153 MET cc_start: 0.7510 (pmm) cc_final: 0.6894 (pp-130) REVERT: C 237 ARG cc_start: 0.7928 (mtm-85) cc_final: 0.7204 (mtp85) REVERT: C 529 LYS cc_start: 0.8341 (mmtt) cc_final: 0.8102 (mmpt) REVERT: C 697 MET cc_start: 0.8765 (ptm) cc_final: 0.8511 (ptp) REVERT: C 988 GLU cc_start: 0.6894 (tp30) cc_final: 0.6407 (tp30) outliers start: 46 outliers final: 36 residues processed: 204 average time/residue: 0.4699 time to fit residues: 117.1268 Evaluate side-chains 204 residues out of total 2789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 165 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 960 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 199 optimal weight: 1.9990 chunk 180 optimal weight: 0.3980 chunk 59 optimal weight: 0.5980 chunk 297 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 258 optimal weight: 7.9990 chunk 191 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 190 optimal weight: 0.3980 chunk 47 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 969 ASN A1010 GLN B 334 ASN C 394 ASN C 556 ASN C 901 GLN C1002 GLN C1005 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.202693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.133339 restraints weight = 29139.218| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 3.11 r_work: 0.3269 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 26217 Z= 0.121 Angle : 0.551 11.729 35771 Z= 0.280 Chirality : 0.044 0.256 4143 Planarity : 0.004 0.045 4562 Dihedral : 5.205 58.383 4305 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.69 % Allowed : 12.05 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.14), residues: 3157 helix: 2.14 (0.21), residues: 659 sheet: 0.55 (0.19), residues: 715 loop : -1.37 (0.13), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 319 TYR 0.019 0.001 TYR A1067 PHE 0.016 0.001 PHE C 400 TRP 0.014 0.001 TRP B 64 HIS 0.007 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00278 (26133) covalent geometry : angle 0.53279 (35561) SS BOND : bond 0.00423 ( 42) SS BOND : angle 1.49320 ( 84) hydrogen bonds : bond 0.05488 ( 936) hydrogen bonds : angle 4.92727 ( 2739) link_BETA1-4 : bond 0.00494 ( 8) link_BETA1-4 : angle 1.00354 ( 24) link_NAG-ASN : bond 0.00389 ( 34) link_NAG-ASN : angle 2.33095 ( 102) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10677.92 seconds wall clock time: 181 minutes 33.69 seconds (10893.69 seconds total)