Starting phenix.real_space_refine on Sun Jun 22 10:29:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r1b_14237/06_2025/7r1b_14237.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r1b_14237/06_2025/7r1b_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7r1b_14237/06_2025/7r1b_14237.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r1b_14237/06_2025/7r1b_14237.map" model { file = "/net/cci-nas-00/data/ceres_data/7r1b_14237/06_2025/7r1b_14237.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r1b_14237/06_2025/7r1b_14237.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 16.32, per 1000 atoms: 0.64 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: 6.48 Conformation dependent library (CDL) restraints added in 3.4 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: 4.30 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: 11.99 Time building geometry restraints manager: 7.65 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 1146 or resid 1301 thr \ ough 1308)) selection = (chain 'B' and (resid 14 through 620 or resid 641 through 826 or resid 856 throu \ gh 1146 or resid 1301 through 1308)) selection = (chain 'C' and (resid 14 through 620 or resid 641 through 826 or resid 856 throu \ gh 1146 or resid 1301 through 1308)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } 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: 5.490 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: 1.120 Check model and map are aligned: 0.200 Set scattering table: 0.240 Process input model: 62.950 Find NCS groups from input model: 1.690 Set up NCS constraints: 0.120 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:13.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.620 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (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 TRP 0.021 0.001 TRP B 886 HIS 0.004 0.001 HIS A 207 PHE 0.018 0.001 PHE C 490 TYR 0.017 0.001 TYR B 37 ARG 0.004 0.000 ARG B 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00525 ( 34) link_NAG-ASN : angle 3.31332 ( 102) link_BETA1-4 : bond 0.00533 ( 8) link_BETA1-4 : angle 1.13720 ( 24) hydrogen bonds : bond 0.19944 ( 936) hydrogen bonds : angle 7.63122 ( 2739) SS BOND : bond 0.00405 ( 42) SS BOND : angle 1.40480 ( 84) covalent geometry : bond 0.00457 (26133) covalent geometry : angle 0.67532 (35561) *********************** 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 : 2.716 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: 0.6383 (t70) 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: 1.1674 time to fit residues: 369.3801 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 : 3.060 ------------------------------------------------------------------------------- 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 268 optimal weight: 2.9990 chunk 241 optimal weight: 0.9990 chunk 133 optimal weight: 0.5980 chunk 82 optimal weight: 0.9980 chunk 162 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 249 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 151 optimal weight: 0.9980 chunk 185 optimal weight: 1.9990 chunk 288 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 969 ASN B 122 ASN B 146 HIS B 218 GLN B 532 ASN C 314 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 675 GLN C1002 GLN C1005 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.199166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.131192 restraints weight = 29678.523| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.51 r_work: 0.3164 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 26217 Z= 0.151 Angle : 0.625 27.789 35771 Z= 0.313 Chirality : 0.047 0.344 4143 Planarity : 0.004 0.047 4562 Dihedral : 6.253 59.980 4311 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.25 % Allowed : 6.31 % Favored : 92.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.14), residues: 3157 helix: 1.84 (0.21), residues: 672 sheet: 0.47 (0.19), residues: 732 loop : -1.30 (0.13), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 886 HIS 0.006 0.001 HIS C 207 PHE 0.022 0.002 PHE C 400 TYR 0.023 0.001 TYR A1067 ARG 0.004 0.000 ARG A 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00509 ( 34) link_NAG-ASN : angle 4.20838 ( 102) link_BETA1-4 : bond 0.00517 ( 8) link_BETA1-4 : angle 1.08661 ( 24) hydrogen bonds : bond 0.06594 ( 936) hydrogen bonds : angle 5.75086 ( 2739) SS BOND : bond 0.00510 ( 42) SS BOND : angle 1.46394 ( 84) covalent geometry : bond 0.00350 (26133) covalent geometry : angle 0.58011 (35561) *********************** 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 230 residues out of total 2789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 195 time to evaluate : 3.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 HIS cc_start: 0.7396 (t-90) cc_final: 0.7133 (m90) REVERT: A 254 SER cc_start: 0.3125 (OUTLIER) cc_final: 0.2467 (p) REVERT: A 319 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7712 (mtt-85) REVERT: A 378 LYS cc_start: 0.7146 (mttp) cc_final: 0.6594 (mtpp) REVERT: A 409 GLN cc_start: 0.7885 (mt0) cc_final: 0.7664 (mt0) REVERT: A 455 LEU cc_start: 0.8092 (tt) cc_final: 0.7752 (tm) REVERT: A 508 TYR cc_start: 0.7513 (m-80) cc_final: 0.7242 (m-80) REVERT: A 745 ASP cc_start: 0.7969 (p0) cc_final: 0.7588 (p0) REVERT: B 129 LYS cc_start: 0.7907 (mptt) cc_final: 0.7705 (mmtp) REVERT: B 177 MET cc_start: 0.4287 (ttm) cc_final: 0.1856 (pmt) REVERT: C 80 ASP cc_start: 0.6446 (m-30) cc_final: 0.6143 (p0) REVERT: C 153 MET cc_start: 0.7485 (pmm) cc_final: 0.6684 (pp-130) REVERT: C 177 MET cc_start: 0.3269 (pmt) cc_final: 0.3059 (pmm) REVERT: C 237 ARG cc_start: 0.7728 (mtm-85) cc_final: 0.6841 (mtm110) REVERT: C 529 LYS cc_start: 0.8339 (mmtt) cc_final: 0.8111 (mmpt) REVERT: C 602 THR cc_start: 0.7801 (m) cc_final: 0.7562 (m) REVERT: C 988 GLU cc_start: 0.6754 (tp30) cc_final: 0.6335 (tp30) outliers start: 35 outliers final: 13 residues processed: 214 average time/residue: 1.1053 time to fit residues: 285.0587 Evaluate side-chains 186 residues out of total 2789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 171 time to evaluate : 3.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 960 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 167 optimal weight: 0.9980 chunk 141 optimal weight: 7.9990 chunk 68 optimal weight: 0.2980 chunk 317 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 291 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 78 optimal weight: 0.4980 chunk 175 optimal weight: 3.9990 chunk 102 optimal weight: 0.0020 chunk 19 optimal weight: 0.1980 overall best weight: 0.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN B 532 ASN C 99 ASN C 234 ASN C 394 ASN C 675 GLN C1005 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.201084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.129028 restraints weight = 29769.264| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.40 r_work: 0.3178 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 26217 Z= 0.105 Angle : 0.534 12.554 35771 Z= 0.270 Chirality : 0.044 0.277 4143 Planarity : 0.004 0.043 4562 Dihedral : 5.685 59.884 4307 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.54 % Allowed : 7.74 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.14), residues: 3157 helix: 2.20 (0.21), residues: 665 sheet: 0.60 (0.19), residues: 724 loop : -1.21 (0.13), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 64 HIS 0.004 0.001 HIS C 66 PHE 0.022 0.001 PHE C 400 TYR 0.018 0.001 TYR A1067 ARG 0.005 0.000 ARG C 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00394 ( 34) link_NAG-ASN : angle 2.75591 ( 102) link_BETA1-4 : bond 0.00515 ( 8) link_BETA1-4 : angle 1.02578 ( 24) hydrogen bonds : bond 0.05197 ( 936) hydrogen bonds : angle 5.22337 ( 2739) SS BOND : bond 0.00676 ( 42) SS BOND : angle 1.60756 ( 84) covalent geometry : bond 0.00222 (26133) covalent geometry : angle 0.50821 (35561) *********************** 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 230 residues out of total 2789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 187 time to evaluate : 2.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7691 (tm-30) cc_final: 0.7329 (tm-30) REVERT: A 108 THR cc_start: 0.6449 (OUTLIER) cc_final: 0.5787 (m) REVERT: A 207 HIS cc_start: 0.7393 (t-90) cc_final: 0.7119 (m90) REVERT: A 319 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7753 (mtt-85) REVERT: A 378 LYS cc_start: 0.7238 (mttp) cc_final: 0.6638 (mtpp) REVERT: A 409 GLN cc_start: 0.7815 (mt0) cc_final: 0.7555 (mt0) REVERT: A 423 TYR cc_start: 0.8261 (t80) cc_final: 0.7879 (t80) REVERT: A 455 LEU cc_start: 0.8074 (tt) cc_final: 0.7698 (tm) REVERT: A 508 TYR cc_start: 0.7457 (m-80) cc_final: 0.7041 (m-80) REVERT: A 613 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8679 (mt0) REVERT: A 745 ASP cc_start: 0.8069 (p0) cc_final: 0.7631 (p0) REVERT: A 916 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8544 (tp) REVERT: B 177 MET cc_start: 0.3988 (ttm) cc_final: 0.1750 (pmt) REVERT: B 586 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.7891 (m-30) REVERT: C 237 ARG cc_start: 0.7752 (mtm-85) cc_final: 0.6895 (mtm110) REVERT: C 529 LYS cc_start: 0.8367 (mmtt) cc_final: 0.8127 (mmpt) REVERT: C 988 GLU cc_start: 0.6662 (tp30) cc_final: 0.6175 (tp30) outliers start: 43 outliers final: 16 residues processed: 210 average time/residue: 1.1295 time to fit residues: 290.5732 Evaluate side-chains 192 residues out of total 2789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 171 time to evaluate : 2.747 ------------------------------------------------------------------------------- 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 433 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 646 ARG 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 1043 CYS Chi-restraints excluded: chain B residue 586 ASP 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 206 optimal weight: 0.8980 chunk 310 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 286 optimal weight: 2.9990 chunk 235 optimal weight: 50.0000 chunk 80 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 ASN C 394 ASN C 675 GLN C 901 GLN C 919 ASN 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 = 0.4244 r_free = 0.4244 target = 0.197515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.126991 restraints weight = 29680.365| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.43 r_work: 0.3138 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 26217 Z= 0.191 Angle : 0.615 11.053 35771 Z= 0.314 Chirality : 0.048 0.307 4143 Planarity : 0.004 0.048 4562 Dihedral : 5.694 58.594 4305 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.37 % Allowed : 8.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.14), residues: 3157 helix: 1.84 (0.21), residues: 660 sheet: 0.41 (0.19), residues: 744 loop : -1.34 (0.13), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 64 HIS 0.008 0.001 HIS C1048 PHE 0.017 0.002 PHE C 400 TYR 0.026 0.001 TYR A1067 ARG 0.004 0.000 ARG C 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00432 ( 34) link_NAG-ASN : angle 2.71892 ( 102) link_BETA1-4 : bond 0.00529 ( 8) link_BETA1-4 : angle 1.19529 ( 24) hydrogen bonds : bond 0.07166 ( 936) hydrogen bonds : angle 5.35014 ( 2739) SS BOND : bond 0.00515 ( 42) SS BOND : angle 1.50877 ( 84) covalent geometry : bond 0.00472 (26133) covalent geometry : angle 0.59454 (35561) *********************** 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 250 residues out of total 2789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 184 time to evaluate : 2.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ASN cc_start: 0.8140 (OUTLIER) cc_final: 0.7837 (p0) REVERT: A 207 HIS cc_start: 0.7432 (t-90) cc_final: 0.7004 (m90) REVERT: A 319 ARG cc_start: 0.7978 (tpp-160) cc_final: 0.7738 (mtt-85) REVERT: A 378 LYS cc_start: 0.7195 (mttp) cc_final: 0.6598 (mtpp) REVERT: A 409 GLN cc_start: 0.7790 (mt0) cc_final: 0.7486 (mt0) REVERT: A 455 LEU cc_start: 0.8081 (tt) cc_final: 0.7689 (tm) REVERT: A 508 TYR cc_start: 0.7485 (m-80) cc_final: 0.7078 (m-80) REVERT: A 745 ASP cc_start: 0.8081 (p0) cc_final: 0.7599 (p0) REVERT: A 916 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8571 (tp) REVERT: B 117 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7147 (tt) REVERT: B 129 LYS cc_start: 0.8160 (mmmt) cc_final: 0.7875 (mmmt) REVERT: B 177 MET cc_start: 0.4087 (ttm) cc_final: 0.1776 (pmt) REVERT: B 586 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7900 (m-30) REVERT: B 619 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.6793 (mp0) REVERT: C 80 ASP cc_start: 0.6651 (p0) cc_final: 0.5611 (m-30) REVERT: C 81 ASN cc_start: 0.8099 (p0) cc_final: 0.7834 (p0) REVERT: C 153 MET cc_start: 0.7477 (pmm) cc_final: 0.6706 (pp-130) REVERT: C 177 MET cc_start: 0.3115 (pmt) cc_final: 0.2770 (pmm) REVERT: C 237 ARG cc_start: 0.7875 (mtm-85) cc_final: 0.7082 (mtp85) REVERT: C 529 LYS cc_start: 0.8340 (mmtt) cc_final: 0.8093 (mmpt) REVERT: C 988 GLU cc_start: 0.6807 (tp30) cc_final: 0.6311 (tp30) outliers start: 66 outliers final: 29 residues processed: 226 average time/residue: 1.0291 time to fit residues: 283.8864 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 : 2.579 ------------------------------------------------------------------------------- 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 188 ASN 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 646 ARG 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 B residue 117 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 586 ASP 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 292 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 chunk 200 optimal weight: 0.6980 chunk 149 optimal weight: 50.0000 chunk 303 optimal weight: 0.5980 chunk 258 optimal weight: 8.9990 chunk 273 optimal weight: 0.4980 chunk 214 optimal weight: 0.8980 chunk 286 optimal weight: 0.4980 chunk 93 optimal weight: 2.9990 chunk 265 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 ASN C 394 ASN C 675 GLN C 901 GLN C1005 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.202932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.134260 restraints weight = 29446.638| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 3.27 r_work: 0.3244 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 26217 Z= 0.120 Angle : 0.552 13.874 35771 Z= 0.280 Chirality : 0.044 0.298 4143 Planarity : 0.004 0.047 4562 Dihedral : 5.452 59.201 4305 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.90 % Allowed : 9.25 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.14), residues: 3157 helix: 2.06 (0.21), residues: 659 sheet: 0.52 (0.19), residues: 748 loop : -1.29 (0.13), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 64 HIS 0.004 0.001 HIS C1048 PHE 0.019 0.001 PHE C 400 TYR 0.019 0.001 TYR A1067 ARG 0.004 0.000 ARG C 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00381 ( 34) link_NAG-ASN : angle 2.51396 ( 102) link_BETA1-4 : bond 0.00504 ( 8) link_BETA1-4 : angle 1.04142 ( 24) hydrogen bonds : bond 0.05737 ( 936) hydrogen bonds : angle 5.12675 ( 2739) SS BOND : bond 0.00638 ( 42) SS BOND : angle 1.72595 ( 84) covalent geometry : bond 0.00271 (26133) covalent geometry : angle 0.52944 (35561) *********************** 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: 53 poor density : 181 time to evaluate : 2.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7759 (tm-30) cc_final: 0.7444 (tm-30) REVERT: A 188 ASN cc_start: 0.8196 (OUTLIER) cc_final: 0.7898 (p0) REVERT: A 207 HIS cc_start: 0.7509 (t-90) cc_final: 0.7105 (m90) REVERT: A 254 SER cc_start: 0.3101 (OUTLIER) cc_final: 0.2263 (p) REVERT: A 319 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7708 (mtt-85) REVERT: A 378 LYS cc_start: 0.7358 (mttp) cc_final: 0.6706 (mtpp) REVERT: A 409 GLN cc_start: 0.7796 (mt0) cc_final: 0.7527 (mt0) REVERT: A 423 TYR cc_start: 0.8387 (t80) cc_final: 0.8099 (t80) REVERT: A 455 LEU cc_start: 0.8132 (tt) cc_final: 0.7725 (tm) REVERT: A 508 TYR cc_start: 0.7414 (m-80) cc_final: 0.7036 (m-80) REVERT: A 745 ASP cc_start: 0.8206 (p0) cc_final: 0.7728 (p0) REVERT: A 916 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8559 (tp) REVERT: B 129 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7830 (mmmt) REVERT: B 177 MET cc_start: 0.4133 (ttm) cc_final: 0.2045 (pmt) REVERT: B 586 ASP cc_start: 0.8134 (OUTLIER) cc_final: 0.7920 (m-30) REVERT: B 619 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.6730 (mp0) REVERT: C 80 ASP cc_start: 0.6616 (p0) cc_final: 0.5533 (m-30) REVERT: C 81 ASN cc_start: 0.8047 (p0) cc_final: 0.7740 (p0) REVERT: C 153 MET cc_start: 0.7507 (pmm) cc_final: 0.6786 (pp-130) REVERT: C 177 MET cc_start: 0.3434 (pmt) cc_final: 0.3205 (pmm) REVERT: C 237 ARG cc_start: 0.7889 (mtm-85) cc_final: 0.7143 (mtp-110) REVERT: C 529 LYS cc_start: 0.8329 (mmtt) cc_final: 0.8103 (mmpt) REVERT: C 988 GLU cc_start: 0.6807 (tp30) cc_final: 0.6271 (tp30) outliers start: 53 outliers final: 27 residues processed: 212 average time/residue: 1.0556 time to fit residues: 272.2630 Evaluate side-chains 209 residues out of total 2789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 175 time to evaluate : 2.657 ------------------------------------------------------------------------------- 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 188 ASN Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 319 ARG 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 646 ARG 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 934 ILE Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 586 ASP 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 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 325 SER 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 209 optimal weight: 1.9990 chunk 235 optimal weight: 40.0000 chunk 193 optimal weight: 2.9990 chunk 0 optimal weight: 40.0000 chunk 283 optimal weight: 0.5980 chunk 278 optimal weight: 0.7980 chunk 233 optimal weight: 0.7980 chunk 200 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 212 optimal weight: 20.0000 chunk 99 optimal weight: 0.0170 overall best weight: 0.8420 ------------------------------------------------------------------------------- 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 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 ASN C 394 ASN C 675 GLN C1005 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.202381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.131500 restraints weight = 29247.764| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 3.31 r_work: 0.3138 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 26217 Z= 0.136 Angle : 0.569 15.421 35771 Z= 0.286 Chirality : 0.045 0.276 4143 Planarity : 0.004 0.048 4562 Dihedral : 5.576 59.870 4305 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.01 % Allowed : 9.75 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.14), residues: 3157 helix: 2.03 (0.21), residues: 659 sheet: 0.57 (0.19), residues: 733 loop : -1.30 (0.13), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 64 HIS 0.005 0.001 HIS C1048 PHE 0.016 0.001 PHE C 400 TYR 0.022 0.001 TYR A1067 ARG 0.003 0.000 ARG C 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00393 ( 34) link_NAG-ASN : angle 2.74544 ( 102) link_BETA1-4 : bond 0.00513 ( 8) link_BETA1-4 : angle 1.06906 ( 24) hydrogen bonds : bond 0.06039 ( 936) hydrogen bonds : angle 5.09837 ( 2739) SS BOND : bond 0.00467 ( 42) SS BOND : angle 1.56563 ( 84) covalent geometry : bond 0.00321 (26133) covalent geometry : angle 0.54590 (35561) *********************** 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 239 residues out of total 2789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 183 time to evaluate : 2.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7739 (tm-30) cc_final: 0.7381 (tm-30) REVERT: A 108 THR cc_start: 0.6525 (OUTLIER) cc_final: 0.5936 (m) REVERT: A 188 ASN cc_start: 0.8117 (OUTLIER) cc_final: 0.7801 (p0) REVERT: A 207 HIS cc_start: 0.7411 (t-90) cc_final: 0.7043 (m-70) REVERT: A 254 SER cc_start: 0.3116 (OUTLIER) cc_final: 0.2273 (p) REVERT: A 319 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7677 (mtt-85) REVERT: A 378 LYS cc_start: 0.7185 (mttp) cc_final: 0.6884 (mttp) REVERT: A 409 GLN cc_start: 0.7665 (mt0) cc_final: 0.7425 (mt0) REVERT: A 455 LEU cc_start: 0.8049 (tt) cc_final: 0.7655 (tm) REVERT: A 508 TYR cc_start: 0.7337 (m-80) cc_final: 0.6948 (m-80) REVERT: A 745 ASP cc_start: 0.8136 (p0) cc_final: 0.7629 (p0) REVERT: A 916 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8498 (tp) REVERT: A 977 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8040 (mp) REVERT: B 129 LYS cc_start: 0.8325 (mmmt) cc_final: 0.7936 (mmmt) REVERT: B 177 MET cc_start: 0.4107 (ttm) cc_final: 0.2137 (pmt) REVERT: B 586 ASP cc_start: 0.8089 (OUTLIER) cc_final: 0.7852 (m-30) REVERT: B 619 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.6610 (mp0) REVERT: C 80 ASP cc_start: 0.6642 (p0) cc_final: 0.5509 (m-30) REVERT: C 81 ASN cc_start: 0.8079 (p0) cc_final: 0.7730 (p0) REVERT: C 153 MET cc_start: 0.7492 (pmm) cc_final: 0.6756 (pp-130) REVERT: C 177 MET cc_start: 0.3186 (pmt) cc_final: 0.2907 (pmm) REVERT: C 237 ARG cc_start: 0.7788 (mtm-85) cc_final: 0.7040 (mtp-110) REVERT: C 529 LYS cc_start: 0.8360 (mmtt) cc_final: 0.8105 (mmpt) REVERT: C 988 GLU cc_start: 0.6752 (tp30) cc_final: 0.6231 (tp30) outliers start: 56 outliers final: 31 residues processed: 215 average time/residue: 1.0383 time to fit residues: 272.1428 Evaluate side-chains 211 residues out of total 2789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 172 time to evaluate : 2.694 ------------------------------------------------------------------------------- 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 108 THR 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 319 ARG 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 646 ARG 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 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 586 ASP 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 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 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 297 optimal weight: 0.8980 chunk 151 optimal weight: 0.2980 chunk 33 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 298 optimal weight: 2.9990 chunk 172 optimal weight: 0.5980 chunk 5 optimal weight: 4.9990 chunk 190 optimal weight: 1.9990 chunk 252 optimal weight: 8.9990 chunk 89 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 146 HIS ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 ASN C 196 ASN C 394 ASN C 675 GLN C 901 GLN C1005 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.201907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.131469 restraints weight = 29435.607| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 3.25 r_work: 0.3215 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1547 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= 0.146 Angle : 0.570 12.611 35771 Z= 0.289 Chirality : 0.045 0.267 4143 Planarity : 0.004 0.049 4562 Dihedral : 5.471 59.881 4303 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.72 % Allowed : 10.47 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.14), residues: 3157 helix: 1.98 (0.21), residues: 659 sheet: 0.57 (0.19), residues: 736 loop : -1.35 (0.13), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 64 HIS 0.006 0.001 HIS C1048 PHE 0.015 0.001 PHE C 400 TYR 0.022 0.001 TYR A1067 ARG 0.003 0.000 ARG B 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00373 ( 34) link_NAG-ASN : angle 2.67013 ( 102) link_BETA1-4 : bond 0.00501 ( 8) link_BETA1-4 : angle 1.08340 ( 24) hydrogen bonds : bond 0.06234 ( 936) hydrogen bonds : angle 5.10605 ( 2739) SS BOND : bond 0.00453 ( 42) SS BOND : angle 1.59924 ( 84) covalent geometry : bond 0.00348 (26133) covalent geometry : angle 0.54709 (35561) *********************** 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 220 residues out of total 2789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 172 time to evaluate : 2.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 THR cc_start: 0.6654 (OUTLIER) cc_final: 0.6019 (m) REVERT: A 188 ASN cc_start: 0.8127 (OUTLIER) cc_final: 0.7645 (p0) REVERT: A 254 SER cc_start: 0.3186 (OUTLIER) cc_final: 0.2297 (p) REVERT: A 319 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7713 (mtt-85) REVERT: A 378 LYS cc_start: 0.7325 (mttp) cc_final: 0.6985 (mttp) REVERT: A 455 LEU cc_start: 0.8106 (tt) cc_final: 0.7700 (tm) REVERT: A 508 TYR cc_start: 0.7377 (m-80) cc_final: 0.7028 (m-80) REVERT: A 745 ASP cc_start: 0.8168 (p0) cc_final: 0.7664 (p0) REVERT: A 916 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8573 (tp) REVERT: B 129 LYS cc_start: 0.8384 (mmmt) cc_final: 0.8030 (mmmt) REVERT: B 177 MET cc_start: 0.4237 (ttm) cc_final: 0.2288 (pmt) REVERT: B 229 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.6697 (mt) REVERT: B 619 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.6721 (mp0) REVERT: C 81 ASN cc_start: 0.8099 (p0) cc_final: 0.7773 (p0) REVERT: C 153 MET cc_start: 0.7519 (pmm) cc_final: 0.6789 (pp-130) REVERT: C 177 MET cc_start: 0.3402 (pmt) cc_final: 0.3110 (pmm) REVERT: C 237 ARG cc_start: 0.7907 (mtm-85) cc_final: 0.7597 (mpp-170) REVERT: C 529 LYS cc_start: 0.8352 (mmtt) cc_final: 0.8119 (mmpt) REVERT: C 988 GLU cc_start: 0.6897 (tp30) cc_final: 0.6416 (tp30) outliers start: 48 outliers final: 31 residues processed: 204 average time/residue: 1.0619 time to fit residues: 264.8418 Evaluate side-chains 207 residues out of total 2789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 169 time to evaluate : 3.068 ------------------------------------------------------------------------------- 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 108 THR 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 319 ARG 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 646 ARG 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 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 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 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 785 VAL 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 128 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 309 optimal weight: 0.6980 chunk 314 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 279 optimal weight: 0.7980 chunk 34 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 317 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 969 ASN B 334 ASN B 532 ASN C 196 ASN C 394 ASN C 675 GLN C 901 GLN C1002 GLN C1005 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.202180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.133466 restraints weight = 29344.163| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.96 r_work: 0.3258 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 26217 Z= 0.137 Angle : 0.562 11.640 35771 Z= 0.286 Chirality : 0.045 0.261 4143 Planarity : 0.004 0.048 4562 Dihedral : 5.429 59.549 4303 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.90 % Allowed : 10.54 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.14), residues: 3157 helix: 2.01 (0.21), residues: 659 sheet: 0.54 (0.19), residues: 735 loop : -1.35 (0.13), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 64 HIS 0.005 0.001 HIS C1048 PHE 0.015 0.001 PHE C 400 TYR 0.021 0.001 TYR A1067 ARG 0.009 0.000 ARG C 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00389 ( 34) link_NAG-ASN : angle 2.49794 ( 102) link_BETA1-4 : bond 0.00504 ( 8) link_BETA1-4 : angle 1.06039 ( 24) hydrogen bonds : bond 0.06018 ( 936) hydrogen bonds : angle 5.06550 ( 2739) SS BOND : bond 0.00430 ( 42) SS BOND : angle 1.64272 ( 84) covalent geometry : bond 0.00322 (26133) covalent geometry : angle 0.54113 (35561) *********************** 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 223 residues out of total 2789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 170 time to evaluate : 2.746 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 THR cc_start: 0.6674 (OUTLIER) cc_final: 0.6047 (m) REVERT: A 188 ASN cc_start: 0.8111 (p0) cc_final: 0.7825 (p0) REVERT: A 207 HIS cc_start: 0.7406 (t-90) cc_final: 0.7065 (m-70) REVERT: A 319 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.7646 (mtt-85) REVERT: A 378 LYS cc_start: 0.7328 (mttp) cc_final: 0.6977 (mttp) REVERT: A 455 LEU cc_start: 0.8215 (tt) cc_final: 0.7839 (tm) REVERT: A 508 TYR cc_start: 0.7400 (m-80) cc_final: 0.7056 (m-80) REVERT: A 556 ASN cc_start: 0.7715 (p0) cc_final: 0.7278 (p0) REVERT: A 745 ASP cc_start: 0.8089 (p0) cc_final: 0.7562 (p0) REVERT: A 916 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8538 (tp) REVERT: B 129 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.7960 (mmmt) REVERT: B 177 MET cc_start: 0.4201 (ttm) cc_final: 0.2295 (pmt) REVERT: B 229 LEU cc_start: 0.7280 (OUTLIER) cc_final: 0.6677 (mt) REVERT: B 619 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.6666 (mp0) REVERT: C 80 ASP cc_start: 0.6788 (p0) cc_final: 0.5523 (m-30) REVERT: C 81 ASN cc_start: 0.8112 (p0) cc_final: 0.7756 (p0) REVERT: C 120 VAL cc_start: 0.7336 (OUTLIER) cc_final: 0.7094 (m) REVERT: C 153 MET cc_start: 0.7507 (pmm) cc_final: 0.6812 (pp-130) REVERT: C 177 MET cc_start: 0.3418 (pmt) cc_final: 0.3128 (pmm) REVERT: C 237 ARG cc_start: 0.7801 (mtm-85) cc_final: 0.7071 (mtp85) REVERT: C 529 LYS cc_start: 0.8312 (mmtt) cc_final: 0.8071 (mmpt) REVERT: C 988 GLU cc_start: 0.6828 (tp30) cc_final: 0.6355 (tp30) outliers start: 53 outliers final: 32 residues processed: 207 average time/residue: 1.0251 time to fit residues: 258.9041 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 : 2.606 ------------------------------------------------------------------------------- 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 108 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 319 ARG 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 646 ARG 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 934 ILE Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 129 LYS 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 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 120 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 163 optimal weight: 0.6980 chunk 162 optimal weight: 1.9990 chunk 193 optimal weight: 2.9990 chunk 176 optimal weight: 0.3980 chunk 212 optimal weight: 20.0000 chunk 118 optimal weight: 7.9990 chunk 131 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 177 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 104 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 394 ASN C 675 GLN C1005 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.202854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.135243 restraints weight = 29425.462| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 3.25 r_work: 0.3279 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 26217 Z= 0.121 Angle : 0.545 14.258 35771 Z= 0.277 Chirality : 0.044 0.245 4143 Planarity : 0.004 0.050 4562 Dihedral : 5.327 58.196 4303 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.58 % Allowed : 11.15 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.15), residues: 3157 helix: 2.05 (0.21), residues: 665 sheet: 0.57 (0.19), residues: 737 loop : -1.31 (0.13), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 64 HIS 0.004 0.001 HIS B 207 PHE 0.016 0.001 PHE A 565 TYR 0.019 0.001 TYR A1067 ARG 0.012 0.000 ARG C 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00386 ( 34) link_NAG-ASN : angle 2.35532 ( 102) link_BETA1-4 : bond 0.00500 ( 8) link_BETA1-4 : angle 1.01072 ( 24) hydrogen bonds : bond 0.05572 ( 936) hydrogen bonds : angle 4.98029 ( 2739) SS BOND : bond 0.00556 ( 42) SS BOND : angle 1.55774 ( 84) covalent geometry : bond 0.00275 (26133) covalent geometry : angle 0.52597 (35561) *********************** 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 221 residues out of total 2789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 177 time to evaluate : 2.855 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 THR cc_start: 0.6816 (OUTLIER) cc_final: 0.6165 (m) REVERT: A 129 LYS cc_start: 0.5942 (mtpp) cc_final: 0.5618 (ttmm) REVERT: A 188 ASN cc_start: 0.8162 (p0) cc_final: 0.7891 (p0) REVERT: A 207 HIS cc_start: 0.7420 (t-90) cc_final: 0.7102 (m-70) REVERT: A 378 LYS cc_start: 0.7336 (mttp) cc_final: 0.7052 (mttp) REVERT: A 455 LEU cc_start: 0.8218 (tt) cc_final: 0.7847 (tm) REVERT: A 508 TYR cc_start: 0.7395 (m-80) cc_final: 0.7057 (m-80) REVERT: A 556 ASN cc_start: 0.7738 (p0) cc_final: 0.7324 (p0) REVERT: A 745 ASP cc_start: 0.8156 (p0) cc_final: 0.7624 (p0) REVERT: A 916 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8565 (tp) REVERT: B 129 LYS cc_start: 0.8439 (mmmt) cc_final: 0.8062 (mmmt) REVERT: B 177 MET cc_start: 0.4296 (ttm) cc_final: 0.2463 (pmt) REVERT: B 190 ARG cc_start: 0.7142 (mmm160) cc_final: 0.6887 (mmp80) REVERT: B 229 LEU cc_start: 0.7220 (OUTLIER) cc_final: 0.6702 (mt) REVERT: B 619 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.6548 (mp0) REVERT: C 80 ASP cc_start: 0.6698 (p0) cc_final: 0.5322 (m-30) REVERT: C 81 ASN cc_start: 0.8100 (p0) cc_final: 0.7746 (p0) REVERT: C 120 VAL cc_start: 0.7400 (OUTLIER) cc_final: 0.7177 (m) REVERT: C 153 MET cc_start: 0.7540 (pmm) cc_final: 0.6853 (pp-130) REVERT: C 177 MET cc_start: 0.3602 (pmt) cc_final: 0.3385 (pmm) REVERT: C 237 ARG cc_start: 0.7917 (mtm-85) cc_final: 0.7209 (mtp85) REVERT: C 529 LYS cc_start: 0.8313 (mmtt) cc_final: 0.8076 (mmpt) REVERT: C 988 GLU cc_start: 0.6899 (tp30) cc_final: 0.6424 (tp30) outliers start: 44 outliers final: 29 residues processed: 208 average time/residue: 1.0370 time to fit residues: 262.1820 Evaluate side-chains 206 residues out of total 2789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 172 time to evaluate : 2.713 ------------------------------------------------------------------------------- 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 108 THR Chi-restraints excluded: chain A residue 117 LEU 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 553 THR Chi-restraints excluded: chain A residue 646 ARG 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 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 525 CYS Chi-restraints excluded: chain B residue 619 GLU 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 120 VAL 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 785 VAL 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 113 optimal weight: 4.9990 chunk 199 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 171 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 259 optimal weight: 9.9990 chunk 234 optimal weight: 6.9990 chunk 130 optimal weight: 0.8980 chunk 141 optimal weight: 7.9990 chunk 210 optimal weight: 1.9990 chunk 188 optimal weight: 0.0970 overall best weight: 0.9780 ------------------------------------------------------------------------------- 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 66 HIS B 532 ASN C 394 ASN C 556 ASN C 675 GLN C 901 GLN C1005 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.201866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.133632 restraints weight = 29410.791| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.94 r_work: 0.3284 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 26217 Z= 0.148 Angle : 0.572 14.087 35771 Z= 0.292 Chirality : 0.045 0.249 4143 Planarity : 0.004 0.055 4562 Dihedral : 5.406 59.800 4303 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.47 % Allowed : 11.33 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.14), residues: 3157 helix: 2.00 (0.21), residues: 659 sheet: 0.56 (0.19), residues: 725 loop : -1.36 (0.13), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 64 HIS 0.006 0.001 HIS C1048 PHE 0.016 0.001 PHE A 565 TYR 0.022 0.001 TYR A1067 ARG 0.012 0.000 ARG C 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00395 ( 34) link_NAG-ASN : angle 2.36269 ( 102) link_BETA1-4 : bond 0.00493 ( 8) link_BETA1-4 : angle 1.07495 ( 24) hydrogen bonds : bond 0.06196 ( 936) hydrogen bonds : angle 5.05221 ( 2739) SS BOND : bond 0.00502 ( 42) SS BOND : angle 1.57708 ( 84) covalent geometry : bond 0.00354 (26133) covalent geometry : angle 0.55407 (35561) ********************** 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 214 residues out of total 2789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 173 time to evaluate : 2.887 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 THR cc_start: 0.6706 (OUTLIER) cc_final: 0.6082 (m) REVERT: A 129 LYS cc_start: 0.5885 (mtpp) cc_final: 0.5621 (ttmm) REVERT: A 188 ASN cc_start: 0.8115 (p0) cc_final: 0.7666 (p0) REVERT: A 378 LYS cc_start: 0.7317 (mttp) cc_final: 0.7036 (mttp) REVERT: A 455 LEU cc_start: 0.8219 (tt) cc_final: 0.7842 (tm) REVERT: A 508 TYR cc_start: 0.7413 (m-80) cc_final: 0.7129 (m-80) REVERT: A 745 ASP cc_start: 0.8094 (p0) cc_final: 0.7577 (p0) REVERT: A 916 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8532 (tp) REVERT: B 129 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.7967 (mmmt) REVERT: B 177 MET cc_start: 0.4287 (ttm) cc_final: 0.2432 (pmt) REVERT: B 208 THR cc_start: 0.8023 (m) cc_final: 0.7818 (m) REVERT: B 619 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.6517 (mp0) REVERT: C 80 ASP cc_start: 0.6734 (p0) cc_final: 0.5374 (m-30) REVERT: C 81 ASN cc_start: 0.8112 (p0) cc_final: 0.7735 (p0) REVERT: C 120 VAL cc_start: 0.7359 (OUTLIER) cc_final: 0.7122 (m) REVERT: C 153 MET cc_start: 0.7512 (pmm) cc_final: 0.6836 (pp-130) REVERT: C 237 ARG cc_start: 0.7885 (mtm-85) cc_final: 0.7166 (mtp85) REVERT: C 529 LYS cc_start: 0.8303 (mmtt) cc_final: 0.8060 (mmpt) REVERT: C 988 GLU cc_start: 0.6878 (tp30) cc_final: 0.6404 (tp30) outliers start: 41 outliers final: 31 residues processed: 204 average time/residue: 1.0658 time to fit residues: 265.0898 Evaluate side-chains 203 residues out of total 2789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 167 time to evaluate : 2.889 ------------------------------------------------------------------------------- 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 117 LEU 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 646 ARG 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 934 ILE Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 129 LYS 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 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 120 VAL 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 960 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 231 optimal weight: 3.9990 chunk 284 optimal weight: 1.9990 chunk 290 optimal weight: 5.9990 chunk 139 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 161 optimal weight: 4.9990 chunk 291 optimal weight: 0.8980 chunk 146 optimal weight: 3.9990 chunk 200 optimal weight: 0.6980 chunk 206 optimal weight: 0.3980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 234 ASN C 394 ASN C 556 ASN C 675 GLN C 901 GLN C1005 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.202634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.133425 restraints weight = 29347.371| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 3.19 r_work: 0.3263 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 26217 Z= 0.126 Angle : 0.549 13.826 35771 Z= 0.280 Chirality : 0.044 0.247 4143 Planarity : 0.004 0.052 4562 Dihedral : 5.330 58.393 4303 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.40 % Allowed : 11.62 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.14), residues: 3157 helix: 2.00 (0.21), residues: 667 sheet: 0.57 (0.19), residues: 727 loop : -1.31 (0.13), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 64 HIS 0.005 0.001 HIS B 207 PHE 0.015 0.001 PHE A 565 TYR 0.020 0.001 TYR A1067 ARG 0.012 0.000 ARG C 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00390 ( 34) link_NAG-ASN : angle 2.26906 ( 102) link_BETA1-4 : bond 0.00476 ( 8) link_BETA1-4 : angle 1.01939 ( 24) hydrogen bonds : bond 0.05671 ( 936) hydrogen bonds : angle 4.97202 ( 2739) SS BOND : bond 0.00459 ( 42) SS BOND : angle 1.44784 ( 84) covalent geometry : bond 0.00292 (26133) covalent geometry : angle 0.53186 (35561) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24866.48 seconds wall clock time: 428 minutes 41.61 seconds (25721.61 seconds total)