Starting phenix.real_space_refine on Sun Jun 22 01:24:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h0z_34419/06_2025/8h0z_34419.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h0z_34419/06_2025/8h0z_34419.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8h0z_34419/06_2025/8h0z_34419.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h0z_34419/06_2025/8h0z_34419.map" model { file = "/net/cci-nas-00/data/ceres_data/8h0z_34419/06_2025/8h0z_34419.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h0z_34419/06_2025/8h0z_34419.cif" } resolution = 2.99 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= 0.000 sd= 0.006 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 140 5.16 5 C 16006 2.51 5 N 4066 2.21 5 O 4835 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.78s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25047 Number of models: 1 Model: "" Number of chains: 9 Chain: "B" Number of atoms: 8151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1045, 8151 Classifications: {'peptide': 1045} Link IDs: {'PTRANS': 50, 'TRANS': 994} Chain breaks: 5 Chain: "A" Number of atoms: 7992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 7992 Classifications: {'peptide': 1022} Link IDs: {'PTRANS': 49, 'TRANS': 972} Chain breaks: 8 Chain: "C" Number of atoms: 8085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8085 Classifications: {'peptide': 1035} Link IDs: {'PTRANS': 50, 'TRANS': 984} Chain breaks: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 245 Unusual residues: {'BLA': 1, 'EIC': 1, 'NAG': 13} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "A" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 265 Unusual residues: {'BLA': 1, 'EIC': 2, 'NAG': 13} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 225 Unusual residues: {'BLA': 1, 'NAG': 13} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 16.04, per 1000 atoms: 0.64 Number of scatterers: 25047 At special positions: 0 Unit cell: (120.45, 125.925, 174.105, 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 140 16.00 O 4835 8.00 N 4066 7.00 C 16006 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 159 " distance=2.05 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 288 " distance=2.03 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 348 " distance=2.04 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS B 419 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 511 " distance=2.03 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 474 " distance=2.02 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 635 " distance=2.03 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.04 Simple disulfide: pdb=" SG CYS B 720 " - pdb=" SG CYS B 742 " distance=2.03 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B 822 " - pdb=" SG CYS B 833 " distance=2.04 Simple disulfide: pdb=" SG CYS B 967 " - pdb=" SG CYS A 370 " distance=2.03 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.01 Simple disulfide: pdb=" SG CYS B1064 " - pdb=" SG CYS B1108 " distance=2.03 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.05 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 288 " distance=2.03 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 348 " distance=2.04 Simple disulfide: pdb=" SG CYS A 366 " - pdb=" SG CYS A 419 " distance=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 511 " distance=2.04 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 474 " distance=2.03 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.04 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 635 " distance=2.03 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.03 Simple disulfide: pdb=" SG CYS A 720 " - pdb=" SG CYS A 742 " distance=2.04 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS A 822 " - pdb=" SG CYS A 833 " distance=2.03 Simple disulfide: pdb=" SG CYS A 967 " - pdb=" SG CYS C 370 " distance=2.03 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.01 Simple disulfide: pdb=" SG CYS A1064 " - pdb=" SG CYS A1108 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 159 " distance=2.04 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 288 " distance=2.03 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 348 " distance=2.04 Simple disulfide: pdb=" SG CYS C 366 " - pdb=" SG CYS C 419 " distance=2.04 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 511 " distance=2.05 Simple disulfide: pdb=" SG CYS C 467 " - pdb=" SG CYS C 474 " distance=2.03 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.04 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 635 " distance=2.03 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C 657 " distance=2.03 Simple disulfide: pdb=" SG CYS C 720 " - pdb=" SG CYS C 742 " distance=2.03 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.02 Simple disulfide: pdb=" SG CYS C 822 " - pdb=" SG CYS C 833 " distance=2.03 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.01 Simple disulfide: pdb=" SG CYS C1064 " - pdb=" SG CYS C1108 " distance=2.04 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-ASN " NAG A1303 " - " ASN A 65 " " NAG A1304 " - " ASN A1080 " " NAG A1305 " - " ASN A 109 " " NAG A1306 " - " ASN A 119 " " NAG A1307 " - " ASN A 158 " " NAG A1308 " - " ASN A 269 " " NAG A1309 " - " ASN A 318 " " NAG A1310 " - " ASN A 357 " " NAG A1311 " - " ASN A 602 " " NAG A1312 " - " ASN A 691 " " NAG A1313 " - " ASN A 699 " " NAG A1314 " - " ASN A 783 " " NAG A1315 " - " ASN A1056 " " NAG B1301 " - " ASN B 65 " " NAG B1302 " - " ASN B1080 " " NAG B1303 " - " ASN B 109 " " NAG B1304 " - " ASN B 119 " " NAG B1305 " - " ASN B 158 " " NAG B1306 " - " ASN B 269 " " NAG B1307 " - " ASN B 318 " " NAG B1308 " - " ASN B 357 " " NAG B1309 " - " ASN B 602 " " NAG B1310 " - " ASN B 691 " " NAG B1311 " - " ASN B 699 " " NAG B1312 " - " ASN B 783 " " NAG B1313 " - " ASN B1056 " " NAG C1301 " - " ASN C 65 " " NAG C1302 " - " ASN C1080 " " NAG C1303 " - " ASN C 109 " " NAG C1304 " - " ASN C 119 " " NAG C1305 " - " ASN C 158 " " NAG C1306 " - " ASN C 318 " " NAG C1307 " - " ASN C 357 " " NAG C1308 " - " ASN C 602 " " NAG C1309 " - " ASN C 691 " " NAG C1310 " - " ASN C 699 " " NAG C1311 " - " ASN C 783 " " NAG C1312 " - " ASN C1056 " " NAG C1313 " - " ASN C1116 " " NAG D 1 " - " ASN B 227 " " NAG E 1 " - " ASN A 227 " " NAG F 1 " - " ASN C 227 " Time building additional restraints: 6.75 Conformation dependent library (CDL) restraints added in 3.4 seconds 6112 Ramachandran restraints generated. 3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5812 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 45 sheets defined 26.1% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.17 Creating SS restraints... Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 324 through 330 Processing helix chain 'B' and resid 351 through 356 removed outlier: 3.754A pdb=" N VAL B 354 " --> pdb=" O ASP B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 377 removed outlier: 3.848A pdb=" N ASN B 375 " --> pdb=" O THR B 372 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU B 377 " --> pdb=" O LEU B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 397 removed outlier: 4.440A pdb=" N ARG B 395 " --> pdb=" O ASP B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 409 Processing helix chain 'B' and resid 488 through 491 Processing helix chain 'B' and resid 602 through 605 removed outlier: 3.845A pdb=" N ASP B 605 " --> pdb=" O ASN B 602 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 602 through 605' Processing helix chain 'B' and resid 606 through 611 Processing helix chain 'B' and resid 612 through 615 removed outlier: 3.725A pdb=" N LEU B 615 " --> pdb=" O ALA B 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 612 through 615' Processing helix chain 'B' and resid 616 through 621 Processing helix chain 'B' and resid 719 through 725 Processing helix chain 'B' and resid 728 through 736 Processing helix chain 'B' and resid 738 through 765 removed outlier: 4.009A pdb=" N CYS B 742 " --> pdb=" O TYR B 738 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR B 743 " --> pdb=" O GLY B 739 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN B 744 " --> pdb=" O SER B 740 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU B 745 " --> pdb=" O PHE B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 808 removed outlier: 3.808A pdb=" N VAL B 808 " --> pdb=" O LEU B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 824 Processing helix chain 'B' and resid 830 through 838 removed outlier: 3.677A pdb=" N ALA B 834 " --> pdb=" O ASP B 830 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 866 Processing helix chain 'B' and resid 879 through 892 Processing helix chain 'B' and resid 894 through 901 removed outlier: 4.140A pdb=" N LEU B 898 " --> pdb=" O THR B 894 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASN B 901 " --> pdb=" O VAL B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 920 removed outlier: 3.565A pdb=" N ILE B 905 " --> pdb=" O ASN B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 924 through 926 No H-bonds generated for 'chain 'B' and resid 924 through 926' Processing helix chain 'B' and resid 927 through 947 removed outlier: 3.620A pdb=" N GLN B 931 " --> pdb=" O LEU B 927 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL B 933 " --> pdb=" O LYS B 929 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL B 945 " --> pdb=" O LEU B 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 950 No H-bonds generated for 'chain 'B' and resid 948 through 950' Processing helix chain 'B' and resid 958 through 965 removed outlier: 3.638A pdb=" N ILE B 962 " --> pdb=" O VAL B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 1015 removed outlier: 3.897A pdb=" N VAL B 973 " --> pdb=" O VAL B 969 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN B 974 " --> pdb=" O GLU B 970 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA B 998 " --> pdb=" O LEU B 994 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU B 999 " --> pdb=" O ILE B 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 324 through 329 Processing helix chain 'A' and resid 351 through 356 removed outlier: 3.810A pdb=" N VAL A 354 " --> pdb=" O ASP A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 375 removed outlier: 4.086A pdb=" N ASN A 375 " --> pdb=" O THR A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 397 removed outlier: 3.976A pdb=" N VAL A 394 " --> pdb=" O GLY A 391 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ARG A 395 " --> pdb=" O ASP A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 409 Processing helix chain 'A' and resid 425 through 430 removed outlier: 3.845A pdb=" N ASP A 429 " --> pdb=" O THR A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 492 Processing helix chain 'A' and resid 719 through 725 Processing helix chain 'A' and resid 728 through 736 Processing helix chain 'A' and resid 741 through 765 removed outlier: 3.791A pdb=" N ALA A 748 " --> pdb=" O GLN A 744 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR A 760 " --> pdb=" O GLN A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 788 removed outlier: 3.653A pdb=" N LEU A 788 " --> pdb=" O SER A 785 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 785 through 788' Processing helix chain 'A' and resid 798 through 808 removed outlier: 3.721A pdb=" N VAL A 808 " --> pdb=" O LEU A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 838 removed outlier: 3.791A pdb=" N ALA A 834 " --> pdb=" O ASP A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 864 removed outlier: 3.524A pdb=" N THR A 863 " --> pdb=" O LEU A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 891 removed outlier: 3.683A pdb=" N ILE A 891 " --> pdb=" O ARG A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 900 Processing helix chain 'A' and resid 901 through 922 Processing helix chain 'A' and resid 927 through 947 removed outlier: 3.955A pdb=" N GLN A 931 " --> pdb=" O LEU A 927 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL A 945 " --> pdb=" O LEU A 941 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS A 946 " --> pdb=" O ASN A 942 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN A 947 " --> pdb=" O THR A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 950 No H-bonds generated for 'chain 'A' and resid 948 through 950' Processing helix chain 'A' and resid 958 through 966 removed outlier: 3.655A pdb=" N ILE A 962 " --> pdb=" O VAL A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 1015 removed outlier: 3.649A pdb=" N ASP A 976 " --> pdb=" O GLU A 972 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU A 978 " --> pdb=" O GLN A 974 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA A 998 " --> pdb=" O LEU A 994 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU A 999 " --> pdb=" O ILE A 995 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER A1012 " --> pdb=" O ALA A1008 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 291 Processing helix chain 'C' and resid 324 through 330 Processing helix chain 'C' and resid 351 through 357 removed outlier: 3.818A pdb=" N VAL C 354 " --> pdb=" O ASP C 351 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASN C 357 " --> pdb=" O VAL C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 376 removed outlier: 4.100A pdb=" N ASN C 375 " --> pdb=" O THR C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 397 removed outlier: 3.556A pdb=" N ASP C 393 " --> pdb=" O LYS C 390 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL C 394 " --> pdb=" O GLY C 391 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ARG C 395 " --> pdb=" O ASP C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 409 removed outlier: 3.502A pdb=" N TYR C 408 " --> pdb=" O VAL C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 492 removed outlier: 3.663A pdb=" N GLN C 492 " --> pdb=" O ILE C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 606 through 611 Processing helix chain 'C' and resid 616 through 621 Processing helix chain 'C' and resid 719 through 724 Processing helix chain 'C' and resid 728 through 736 Processing helix chain 'C' and resid 742 through 765 Processing helix chain 'C' and resid 785 through 788 removed outlier: 3.884A pdb=" N LEU C 788 " --> pdb=" O SER C 785 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 785 through 788' Processing helix chain 'C' and resid 798 through 808 removed outlier: 3.569A pdb=" N LYS C 807 " --> pdb=" O LEU C 803 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL C 808 " --> pdb=" O LEU C 804 " (cutoff:3.500A) Processing helix chain 'C' and resid 830 through 838 removed outlier: 3.505A pdb=" N ALA C 834 " --> pdb=" O ASP C 830 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 866 Processing helix chain 'C' and resid 879 through 891 Processing helix chain 'C' and resid 894 through 901 removed outlier: 4.111A pdb=" N LEU C 898 " --> pdb=" O THR C 894 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASN C 901 " --> pdb=" O VAL C 897 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 921 removed outlier: 3.562A pdb=" N ILE C 905 " --> pdb=" O ASN C 901 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR C 921 " --> pdb=" O GLN C 917 " (cutoff:3.500A) Processing helix chain 'C' and resid 928 through 947 removed outlier: 3.828A pdb=" N VAL C 933 " --> pdb=" O LYS C 929 " (cutoff:3.500A) Processing helix chain 'C' and resid 948 through 950 No H-bonds generated for 'chain 'C' and resid 948 through 950' Processing helix chain 'C' and resid 958 through 965 removed outlier: 3.784A pdb=" N ILE C 962 " --> pdb=" O VAL C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 1015 removed outlier: 4.173A pdb=" N VAL C 973 " --> pdb=" O VAL C 969 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN C 974 " --> pdb=" O GLU C 970 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP C 976 " --> pdb=" O GLU C 972 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA C 998 " --> pdb=" O LEU C 994 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU C 999 " --> pdb=" O ILE C 995 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 32 through 34 removed outlier: 3.791A pdb=" N VAL B 66 " --> pdb=" O HIS B 33 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE B 220 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LYS B 198 " --> pdb=" O PRO B 218 " (cutoff:3.500A) removed outlier: 8.827A pdb=" N TYR B 200 " --> pdb=" O LEU B 216 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N LEU B 216 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL B 40 " --> pdb=" O LEU B 216 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 59 Processing sheet with id=AA3, first strand: chain 'B' and resid 81 through 82 removed outlier: 4.585A pdb=" N GLY B 100 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ARG B 99 " --> pdb=" O ASN B 118 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N ASN B 118 " --> pdb=" O ARG B 99 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE B 161 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ASN B 129 " --> pdb=" O CYS B 159 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N CYS B 159 " --> pdb=" O ASN B 129 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 298 through 301 removed outlier: 4.465A pdb=" N GLY B 580 " --> pdb=" O GLN B 599 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 312 through 315 removed outlier: 5.340A pdb=" N ASP B 560 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLY B 552 " --> pdb=" O ASP B 560 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 341 through 345 removed outlier: 3.576A pdb=" N GLU B 341 " --> pdb=" O SER B 386 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL B 382 " --> pdb=" O ILE B 345 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 348 through 349 removed outlier: 6.505A pdb=" N CYS B 348 " --> pdb=" O CYS B 511 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 439 through 441 Processing sheet with id=AA9, first strand: chain 'B' and resid 640 through 641 removed outlier: 6.211A pdb=" N GLU B 640 " --> pdb=" O ALA B 676 " (cutoff:3.500A) removed outlier: 8.817A pdb=" N THR B 678 " --> pdb=" O GLU B 640 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ALA B 658 " --> pdb=" O PRO B 651 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 683 through 685 removed outlier: 6.862A pdb=" N ALA B 683 " --> pdb=" O MET C 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 693 through 697 removed outlier: 4.383A pdb=" N THR B1058 " --> pdb=" O PHE B1079 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA B1060 " --> pdb=" O PHE B1077 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N PHE B1077 " --> pdb=" O ALA B1060 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 700 through 710 removed outlier: 3.574A pdb=" N MET B1032 " --> pdb=" O VAL B1047 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N TYR B1049 " --> pdb=" O HIS B1030 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N HIS B1030 " --> pdb=" O TYR B1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 715 through 718 removed outlier: 4.547A pdb=" N LYS B 715 " --> pdb=" O LEU B 843 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 769 through 771 Processing sheet with id=AB6, first strand: chain 'B' and resid 778 through 779 Processing sheet with id=AB7, first strand: chain 'B' and resid 1102 through 1104 Processing sheet with id=AB8, first strand: chain 'A' and resid 32 through 35 removed outlier: 7.653A pdb=" N ASN A 65 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N TYR A 256 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE A 220 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LYS A 198 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 8.991A pdb=" N TYR A 200 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N LEU A 216 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ARG A 38 " --> pdb=" O ASN A 214 " (cutoff:3.500A) removed outlier: 9.174A pdb=" N LEU A 216 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL A 40 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 54 through 59 removed outlier: 4.181A pdb=" N ASP A 274 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 81 through 82 removed outlier: 4.703A pdb=" N GLY A 100 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ARG A 99 " --> pdb=" O ASN A 118 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ASN A 118 " --> pdb=" O ARG A 99 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 298 through 302 removed outlier: 4.520A pdb=" N VAL A 581 " --> pdb=" O THR A 302 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 312 through 315 removed outlier: 4.793A pdb=" N ASP A 560 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER A 561 " --> pdb=" O GLY A 552 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 341 through 345 removed outlier: 4.243A pdb=" N VAL A 382 " --> pdb=" O ILE A 345 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 348 through 349 removed outlier: 6.350A pdb=" N CYS A 348 " --> pdb=" O CYS A 511 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL A 510 " --> pdb=" O PHE A 379 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 439 through 441 Processing sheet with id=AC7, first strand: chain 'A' and resid 640 through 641 removed outlier: 6.142A pdb=" N GLU A 640 " --> pdb=" O ALA A 676 " (cutoff:3.500A) removed outlier: 8.561A pdb=" N THR A 678 " --> pdb=" O GLU A 640 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ALA A 658 " --> pdb=" O PRO A 651 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 693 through 710 removed outlier: 6.553A pdb=" N THR A 693 " --> pdb=" O THR A1058 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR A1058 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ALA A 695 " --> pdb=" O ASN A1056 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASN A1056 " --> pdb=" O ALA A 695 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLU A1054 " --> pdb=" O PRO A 697 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N TYR A1049 " --> pdb=" O HIS A1030 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N HIS A1030 " --> pdb=" O TYR A1049 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 693 through 710 removed outlier: 6.553A pdb=" N THR A 693 " --> pdb=" O THR A1058 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR A1058 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ALA A 695 " --> pdb=" O ASN A1056 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASN A1056 " --> pdb=" O ALA A 695 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLU A1054 " --> pdb=" O PRO A 697 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N THR A1058 " --> pdb=" O PHE A1079 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA A1060 " --> pdb=" O PHE A1077 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N PHE A1077 " --> pdb=" O ALA A1060 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 715 through 718 removed outlier: 4.472A pdb=" N LYS A 715 " --> pdb=" O LEU A 843 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 769 through 771 removed outlier: 3.626A pdb=" N SER C 685 " --> pdb=" O MET A 770 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 778 through 779 Processing sheet with id=AD4, first strand: chain 'A' and resid 1102 through 1104 Processing sheet with id=AD5, first strand: chain 'C' and resid 32 through 34 removed outlier: 3.759A pdb=" N VAL C 66 " --> pdb=" O HIS C 33 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ASN C 65 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N TYR C 256 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LYS C 198 " --> pdb=" O PRO C 218 " (cutoff:3.500A) removed outlier: 8.919A pdb=" N TYR C 200 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N LEU C 216 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL C 40 " --> pdb=" O LEU C 216 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 51 through 59 removed outlier: 3.795A pdb=" N THR C 51 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR C 53 " --> pdb=" O LEU C 264 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 81 through 82 removed outlier: 4.713A pdb=" N GLY C 100 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ARG C 99 " --> pdb=" O ASN C 118 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ASN C 118 " --> pdb=" O ARG C 99 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N PHE C 161 " --> pdb=" O ALA C 127 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N ASN C 129 " --> pdb=" O CYS C 159 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N CYS C 159 " --> pdb=" O ASN C 129 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 298 through 301 Processing sheet with id=AD9, first strand: chain 'C' and resid 312 through 315 removed outlier: 3.538A pdb=" N SER C 561 " --> pdb=" O GLY C 552 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 341 through 344 removed outlier: 3.609A pdb=" N GLU C 341 " --> pdb=" O SER C 386 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 378 through 379 removed outlier: 3.744A pdb=" N VAL C 510 " --> pdb=" O PHE C 379 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 439 through 441 Processing sheet with id=AE4, first strand: chain 'C' and resid 640 through 641 removed outlier: 6.112A pdb=" N GLU C 640 " --> pdb=" O ALA C 676 " (cutoff:3.500A) removed outlier: 8.680A pdb=" N THR C 678 " --> pdb=" O GLU C 640 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ALA C 658 " --> pdb=" O PRO C 651 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 693 through 697 removed outlier: 3.917A pdb=" N THR C1058 " --> pdb=" O PHE C1079 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA C1060 " --> pdb=" O PHE C1077 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N PHE C1077 " --> pdb=" O ALA C1060 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 700 through 710 removed outlier: 3.516A pdb=" N MET C1032 " --> pdb=" O VAL C1047 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N TYR C1049 " --> pdb=" O HIS C1030 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N HIS C1030 " --> pdb=" O TYR C1049 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 715 through 718 removed outlier: 4.503A pdb=" N LYS C 715 " --> pdb=" O LEU C 843 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 778 through 779 Processing sheet with id=AE9, first strand: chain 'C' and resid 1102 through 1104 991 hydrogen bonds defined for protein. 2706 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: 11.42 Time building geometry restraints manager: 8.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 4052 1.32 - 1.45: 8141 1.45 - 1.59: 13233 1.59 - 1.73: 0 1.73 - 1.87: 187 Bond restraints: 25613 Sorted by residual: bond pdb=" ND BLA C1314 " pdb=" C1D BLA C1314 " ideal model delta sigma weight residual 1.319 1.488 -0.169 2.00e-02 2.50e+03 7.14e+01 bond pdb=" ND BLA A1316 " pdb=" C1D BLA A1316 " ideal model delta sigma weight residual 1.319 1.485 -0.166 2.00e-02 2.50e+03 6.92e+01 bond pdb=" C1C BLA C1314 " pdb=" NC BLA C1314 " ideal model delta sigma weight residual 1.368 1.532 -0.164 2.00e-02 2.50e+03 6.74e+01 bond pdb=" C1C BLA B1314 " pdb=" NC BLA B1314 " ideal model delta sigma weight residual 1.368 1.532 -0.164 2.00e-02 2.50e+03 6.71e+01 bond pdb=" ND BLA B1314 " pdb=" C1D BLA B1314 " ideal model delta sigma weight residual 1.319 1.482 -0.163 2.00e-02 2.50e+03 6.61e+01 ... (remaining 25608 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.28: 34380 3.28 - 6.55: 387 6.55 - 9.83: 40 9.83 - 13.11: 8 13.11 - 16.39: 2 Bond angle restraints: 34817 Sorted by residual: angle pdb=" CA CYS A 159 " pdb=" CB CYS A 159 " pdb=" SG CYS A 159 " ideal model delta sigma weight residual 114.40 130.79 -16.39 2.30e+00 1.89e-01 5.08e+01 angle pdb=" CA CYS C 159 " pdb=" CB CYS C 159 " pdb=" SG CYS C 159 " ideal model delta sigma weight residual 114.40 127.07 -12.67 2.30e+00 1.89e-01 3.04e+01 angle pdb=" N ASP B 50 " pdb=" CA ASP B 50 " pdb=" C ASP B 50 " ideal model delta sigma weight residual 110.91 104.51 6.40 1.17e+00 7.31e-01 2.99e+01 angle pdb=" N CYS A 128 " pdb=" CA CYS A 128 " pdb=" C CYS A 128 " ideal model delta sigma weight residual 108.45 115.16 -6.71 1.26e+00 6.30e-01 2.84e+01 angle pdb=" C ASP B 208 " pdb=" N LEU B 209 " pdb=" CA LEU B 209 " ideal model delta sigma weight residual 120.67 127.28 -6.61 1.34e+00 5.57e-01 2.43e+01 ... (remaining 34812 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 14571 17.89 - 35.77: 1007 35.77 - 53.66: 219 53.66 - 71.55: 39 71.55 - 89.43: 12 Dihedral angle restraints: 15848 sinusoidal: 6813 harmonic: 9035 Sorted by residual: dihedral pdb=" CA TYR A 622 " pdb=" C TYR A 622 " pdb=" N SER A 623 " pdb=" CA SER A 623 " ideal model delta harmonic sigma weight residual 180.00 -133.81 -46.19 0 5.00e+00 4.00e-02 8.53e+01 dihedral pdb=" CA PHE B 83 " pdb=" C PHE B 83 " pdb=" N LYS B 84 " pdb=" CA LYS B 84 " ideal model delta harmonic sigma weight residual 180.00 -137.93 -42.07 0 5.00e+00 4.00e-02 7.08e+01 dihedral pdb=" CA VAL A 206 " pdb=" C VAL A 206 " pdb=" N ARG A 207 " pdb=" CA ARG A 207 " ideal model delta harmonic sigma weight residual 180.00 138.89 41.11 0 5.00e+00 4.00e-02 6.76e+01 ... (remaining 15845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 3933 0.130 - 0.260: 94 0.260 - 0.390: 5 0.390 - 0.519: 1 0.519 - 0.649: 1 Chirality restraints: 4034 Sorted by residual: chirality pdb=" C1 NAG B1308 " pdb=" ND2 ASN B 357 " pdb=" C2 NAG B1308 " pdb=" O5 NAG B1308 " both_signs ideal model delta sigma weight residual False -2.40 -1.75 -0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" C1 NAG B1309 " pdb=" ND2 ASN B 602 " pdb=" C2 NAG B1309 " pdb=" O5 NAG B1309 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.00e+00 chirality pdb=" C1 NAG B1306 " pdb=" ND2 ASN B 269 " pdb=" C2 NAG B1306 " pdb=" O5 NAG B1306 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.15e+00 ... (remaining 4031 not shown) Planarity restraints: 4475 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C BLA C1314 " 0.038 2.00e-02 2.50e+03 2.02e-01 1.02e+03 pdb=" C1D BLA C1314 " 0.478 2.00e-02 2.50e+03 pdb=" C2C BLA C1314 " 0.021 2.00e-02 2.50e+03 pdb=" C3C BLA C1314 " -0.099 2.00e-02 2.50e+03 pdb=" C4C BLA C1314 " -0.162 2.00e-02 2.50e+03 pdb=" CAC BLA C1314 " -0.148 2.00e-02 2.50e+03 pdb=" CHD BLA C1314 " -0.289 2.00e-02 2.50e+03 pdb=" CMC BLA C1314 " 0.116 2.00e-02 2.50e+03 pdb=" NC BLA C1314 " -0.083 2.00e-02 2.50e+03 pdb=" OC BLA C1314 " 0.128 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND BLA C1314 " 0.161 2.00e-02 2.50e+03 1.87e-01 8.75e+02 pdb=" C1A BLA C1314 " -0.428 2.00e-02 2.50e+03 pdb=" C1D BLA C1314 " 0.024 2.00e-02 2.50e+03 pdb=" C2D BLA C1314 " -0.043 2.00e-02 2.50e+03 pdb=" C3D BLA C1314 " 0.042 2.00e-02 2.50e+03 pdb=" C4D BLA C1314 " 0.169 2.00e-02 2.50e+03 pdb=" CAD BLA C1314 " 0.007 2.00e-02 2.50e+03 pdb=" CHA BLA C1314 " 0.273 2.00e-02 2.50e+03 pdb=" CHD BLA C1314 " -0.023 2.00e-02 2.50e+03 pdb=" CMD BLA C1314 " -0.181 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB BLA A1316 " 0.104 2.00e-02 2.50e+03 1.10e-01 3.05e+02 pdb=" OB BLA A1316 " -0.010 2.00e-02 2.50e+03 pdb=" C1B BLA A1316 " 0.101 2.00e-02 2.50e+03 pdb=" C2B BLA A1316 " 0.021 2.00e-02 2.50e+03 pdb=" C3B BLA A1316 " -0.026 2.00e-02 2.50e+03 pdb=" C4A BLA A1316 " -0.251 2.00e-02 2.50e+03 pdb=" C4B BLA A1316 " 0.019 2.00e-02 2.50e+03 pdb=" CAB BLA A1316 " -0.109 2.00e-02 2.50e+03 pdb=" CHB BLA A1316 " 0.156 2.00e-02 2.50e+03 pdb=" CMB BLA A1316 " -0.004 2.00e-02 2.50e+03 ... (remaining 4472 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 4006 2.76 - 3.30: 21367 3.30 - 3.83: 38588 3.83 - 4.37: 45884 4.37 - 4.90: 82710 Nonbonded interactions: 192555 Sorted by model distance: nonbonded pdb=" OH TYR A 41 " pdb=" O LEU A 58 " model vdw 2.229 3.040 nonbonded pdb=" OG1 THR A 894 " pdb=" OD1 ASN A 896 " model vdw 2.240 3.040 nonbonded pdb=" OE1 GLN B 947 " pdb=" OG SER B 985 " model vdw 2.285 3.040 nonbonded pdb=" NZ LYS A 793 " pdb=" OG1 THR A 795 " model vdw 2.308 3.120 nonbonded pdb=" OG1 THR C 894 " pdb=" OD1 ASN C 896 " model vdw 2.311 3.040 ... (remaining 192550 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 31 through 138 or resid 152 through 810 or resid 815 throu \ gh 1123 or resid 1303 through 1313)) selection = (chain 'B' and (resid 31 through 138 or resid 152 through 604 or resid 619 throu \ gh 810 or resid 815 through 822 or resid 829 through 1123 or resid 1303 through \ 1313)) selection = (chain 'C' and (resid 31 through 604 or resid 619 through 822 or resid 829 throu \ gh 1123 or resid 1303 through 1313)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 12.700 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: 0.030 Extract box with map and model: 1.040 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 61.650 Find NCS groups from input model: 1.470 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: 0.010 Load rotamer database and sin/cos tables:12.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 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 : 0.008 0.169 25702 Z= 0.378 Angle : 0.980 18.338 35040 Z= 0.515 Chirality : 0.056 0.649 4034 Planarity : 0.008 0.202 4433 Dihedral : 12.602 89.435 9904 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.47 (0.14), residues: 3056 helix: -0.23 (0.19), residues: 696 sheet: 0.57 (0.20), residues: 687 loop : -2.08 (0.12), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 619 HIS 0.006 0.001 HIS C1030 PHE 0.062 0.002 PHE A 888 TYR 0.028 0.002 TYR C 886 ARG 0.005 0.001 ARG C 441 Details of bonding type rmsd link_NAG-ASN : bond 0.00580 ( 42) link_NAG-ASN : angle 5.28232 ( 126) link_BETA1-4 : bond 0.01015 ( 3) link_BETA1-4 : angle 2.40412 ( 9) hydrogen bonds : bond 0.14849 ( 979) hydrogen bonds : angle 6.61506 ( 2706) SS BOND : bond 0.00844 ( 44) SS BOND : angle 2.00954 ( 88) covalent geometry : bond 0.00805 (25613) covalent geometry : angle 0.92440 (34817) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6112 Ramachandran restraints generated. 3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6112 Ramachandran restraints generated. 3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 2.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 155 ASN cc_start: 0.8088 (m-40) cc_final: 0.7616 (t0) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 1.5379 time to fit residues: 374.5154 Evaluate side-chains 137 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 3.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 260 optimal weight: 0.0770 chunk 234 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 157 optimal weight: 0.9990 chunk 125 optimal weight: 0.6980 chunk 242 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 chunk 180 optimal weight: 4.9990 chunk 280 optimal weight: 0.3980 overall best weight: 0.5740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 737 GLN B 931 GLN A 437 ASN C 304 ASN ** C 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.124685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.089425 restraints weight = 37533.730| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.61 r_work: 0.2939 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.0853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25702 Z= 0.120 Angle : 0.623 11.571 35040 Z= 0.314 Chirality : 0.046 0.453 4034 Planarity : 0.005 0.064 4433 Dihedral : 7.991 77.719 4399 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.89 % Allowed : 5.88 % Favored : 93.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.89 (0.14), residues: 3056 helix: 1.02 (0.20), residues: 694 sheet: 0.66 (0.20), residues: 626 loop : -1.86 (0.13), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 868 HIS 0.003 0.001 HIS C1030 PHE 0.021 0.001 PHE A 888 TYR 0.021 0.001 TYR A1049 ARG 0.005 0.000 ARG A 449 Details of bonding type rmsd link_NAG-ASN : bond 0.00499 ( 42) link_NAG-ASN : angle 3.67940 ( 126) link_BETA1-4 : bond 0.00918 ( 3) link_BETA1-4 : angle 1.46682 ( 9) hydrogen bonds : bond 0.05220 ( 979) hydrogen bonds : angle 5.28573 ( 2706) SS BOND : bond 0.00672 ( 44) SS BOND : angle 1.52742 ( 88) covalent geometry : bond 0.00260 (25613) covalent geometry : angle 0.57913 (34817) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6112 Ramachandran restraints generated. 3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6112 Ramachandran restraints generated. 3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 5.379 Fit side-chains revert: symmetry clash REVERT: B 155 ASN cc_start: 0.8566 (m-40) cc_final: 0.7631 (t0) REVERT: B 381 ASN cc_start: 0.7717 (t0) cc_final: 0.7339 (m110) REVERT: B 553 ARG cc_start: 0.7221 (OUTLIER) cc_final: 0.7017 (mtt180) REVERT: B 939 GLN cc_start: 0.8317 (tt0) cc_final: 0.7948 (tt0) REVERT: A 733 ASN cc_start: 0.8513 (OUTLIER) cc_final: 0.8165 (m-40) outliers start: 24 outliers final: 5 residues processed: 173 average time/residue: 1.3396 time to fit residues: 277.3888 Evaluate side-chains 148 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 141 time to evaluate : 2.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 553 ARG Chi-restraints excluded: chain B residue 1100 ASP Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 733 ASN Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain C residue 561 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 227 optimal weight: 2.9990 chunk 307 optimal weight: 1.9990 chunk 176 optimal weight: 10.0000 chunk 281 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 144 optimal weight: 3.9990 chunk 254 optimal weight: 0.1980 chunk 209 optimal weight: 4.9990 chunk 277 optimal weight: 6.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 GLN ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 889 ASN A 904 GLN ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 GLN C 786 GLN C1088 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.120396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.084849 restraints weight = 37451.260| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.59 r_work: 0.2857 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 25702 Z= 0.244 Angle : 0.703 12.332 35040 Z= 0.354 Chirality : 0.050 0.513 4034 Planarity : 0.005 0.053 4433 Dihedral : 7.625 76.729 4399 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.82 % Allowed : 8.08 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.89 (0.14), residues: 3056 helix: 0.91 (0.20), residues: 719 sheet: 0.67 (0.20), residues: 649 loop : -1.89 (0.13), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 423 HIS 0.007 0.001 HIS B1046 PHE 0.036 0.002 PHE A 888 TYR 0.024 0.002 TYR C1120 ARG 0.005 0.001 ARG C 977 Details of bonding type rmsd link_NAG-ASN : bond 0.00439 ( 42) link_NAG-ASN : angle 3.79696 ( 126) link_BETA1-4 : bond 0.00562 ( 3) link_BETA1-4 : angle 1.57259 ( 9) hydrogen bonds : bond 0.06895 ( 979) hydrogen bonds : angle 5.27668 ( 2706) SS BOND : bond 0.00716 ( 44) SS BOND : angle 1.83115 ( 88) covalent geometry : bond 0.00602 (25613) covalent geometry : angle 0.66056 (34817) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6112 Ramachandran restraints generated. 3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6112 Ramachandran restraints generated. 3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 153 time to evaluate : 2.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 ASP cc_start: 0.8351 (t0) cc_final: 0.7999 (t0) REVERT: B 155 ASN cc_start: 0.8586 (m-40) cc_final: 0.7684 (t0) REVERT: B 515 LEU cc_start: 0.8002 (mm) cc_final: 0.7698 (mm) REVERT: B 553 ARG cc_start: 0.7285 (OUTLIER) cc_final: 0.7022 (mtt180) REVERT: A 733 ASN cc_start: 0.8559 (OUTLIER) cc_final: 0.8230 (m-40) REVERT: A 818 GLN cc_start: 0.7596 (mm110) cc_final: 0.6769 (tt0) REVERT: A 1112 ILE cc_start: 0.8756 (pp) cc_final: 0.8428 (mt) REVERT: C 108 ASN cc_start: 0.8886 (OUTLIER) cc_final: 0.8356 (p0) REVERT: C 181 HIS cc_start: 0.7289 (OUTLIER) cc_final: 0.7038 (m90) REVERT: C 214 ASN cc_start: 0.7854 (t0) cc_final: 0.7626 (t0) outliers start: 49 outliers final: 13 residues processed: 187 average time/residue: 1.0429 time to fit residues: 235.9400 Evaluate side-chains 158 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 2.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 553 ARG Chi-restraints excluded: chain B residue 626 ASN Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 733 ASN Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 181 HIS Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 561 SER Chi-restraints excluded: chain C residue 1047 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 240 optimal weight: 1.9990 chunk 248 optimal weight: 0.5980 chunk 173 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 186 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 238 optimal weight: 0.7980 chunk 196 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 181 HIS B 889 ASN C 108 ASN ** C 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.123207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.087824 restraints weight = 37575.439| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.61 r_work: 0.2906 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25702 Z= 0.123 Angle : 0.605 11.395 35040 Z= 0.303 Chirality : 0.046 0.464 4034 Planarity : 0.004 0.050 4433 Dihedral : 7.097 78.050 4399 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.97 % Allowed : 9.27 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.61 (0.15), residues: 3056 helix: 1.47 (0.21), residues: 705 sheet: 0.70 (0.20), residues: 673 loop : -1.82 (0.13), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 868 HIS 0.006 0.001 HIS B 181 PHE 0.028 0.001 PHE C 305 TYR 0.021 0.001 TYR A1049 ARG 0.005 0.000 ARG A 449 Details of bonding type rmsd link_NAG-ASN : bond 0.00467 ( 42) link_NAG-ASN : angle 3.42324 ( 126) link_BETA1-4 : bond 0.00657 ( 3) link_BETA1-4 : angle 1.22638 ( 9) hydrogen bonds : bond 0.05114 ( 979) hydrogen bonds : angle 5.05440 ( 2706) SS BOND : bond 0.00402 ( 44) SS BOND : angle 1.76499 ( 88) covalent geometry : bond 0.00283 (25613) covalent geometry : angle 0.56401 (34817) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6112 Ramachandran restraints generated. 3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6112 Ramachandran restraints generated. 3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 154 time to evaluate : 2.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 32 GLN cc_start: 0.7804 (OUTLIER) cc_final: 0.7509 (tm-30) REVERT: B 50 ASP cc_start: 0.8257 (t0) cc_final: 0.7890 (t0) REVERT: B 155 ASN cc_start: 0.8561 (m-40) cc_final: 0.7643 (t0) REVERT: B 515 LEU cc_start: 0.7961 (mm) cc_final: 0.7665 (mm) REVERT: B 939 GLN cc_start: 0.8269 (tt0) cc_final: 0.7991 (tt0) REVERT: A 733 ASN cc_start: 0.8588 (OUTLIER) cc_final: 0.8238 (m-40) REVERT: A 1112 ILE cc_start: 0.8772 (pp) cc_final: 0.8496 (mt) REVERT: C 46 ILE cc_start: 0.8043 (OUTLIER) cc_final: 0.7840 (mp) outliers start: 53 outliers final: 20 residues processed: 199 average time/residue: 1.0441 time to fit residues: 251.9463 Evaluate side-chains 164 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 2.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 626 ASN Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 727 ASP Chi-restraints excluded: chain A residue 733 ASN Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 CYS Chi-restraints excluded: chain C residue 561 SER Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain C residue 1047 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 9 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 307 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 127 optimal weight: 4.9990 chunk 265 optimal weight: 5.9990 chunk 256 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 133 optimal weight: 0.5980 chunk 142 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 181 HIS ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 889 ASN A 883 GLN ** C 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.121930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.086460 restraints weight = 37631.676| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.60 r_work: 0.2888 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 25702 Z= 0.173 Angle : 0.634 11.354 35040 Z= 0.318 Chirality : 0.047 0.476 4034 Planarity : 0.004 0.049 4433 Dihedral : 6.948 77.397 4399 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.27 % Allowed : 10.20 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.63 (0.15), residues: 3056 helix: 1.38 (0.20), residues: 722 sheet: 0.68 (0.19), residues: 683 loop : -1.84 (0.13), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 868 HIS 0.005 0.001 HIS B1046 PHE 0.028 0.001 PHE B 137 TYR 0.022 0.001 TYR A1049 ARG 0.006 0.000 ARG A 449 Details of bonding type rmsd link_NAG-ASN : bond 0.00442 ( 42) link_NAG-ASN : angle 3.44217 ( 126) link_BETA1-4 : bond 0.00618 ( 3) link_BETA1-4 : angle 1.22664 ( 9) hydrogen bonds : bond 0.05673 ( 979) hydrogen bonds : angle 5.02840 ( 2706) SS BOND : bond 0.00535 ( 44) SS BOND : angle 1.62611 ( 88) covalent geometry : bond 0.00424 (25613) covalent geometry : angle 0.59546 (34817) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6112 Ramachandran restraints generated. 3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6112 Ramachandran restraints generated. 3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 148 time to evaluate : 2.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 ASP cc_start: 0.8342 (t0) cc_final: 0.8026 (t0) REVERT: B 155 ASN cc_start: 0.8725 (m-40) cc_final: 0.7803 (t0) REVERT: B 515 LEU cc_start: 0.7977 (mm) cc_final: 0.7675 (mm) REVERT: B 939 GLN cc_start: 0.8325 (tt0) cc_final: 0.8061 (tt0) REVERT: A 168 PHE cc_start: 0.4049 (OUTLIER) cc_final: 0.3188 (m-80) REVERT: A 733 ASN cc_start: 0.8611 (OUTLIER) cc_final: 0.8260 (m-40) REVERT: A 1112 ILE cc_start: 0.8792 (pp) cc_final: 0.8529 (mt) REVERT: C 46 ILE cc_start: 0.8112 (OUTLIER) cc_final: 0.7874 (mp) REVERT: C 56 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7431 (tm-30) outliers start: 61 outliers final: 25 residues processed: 197 average time/residue: 1.0265 time to fit residues: 246.2007 Evaluate side-chains 169 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 2.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 417 MET Chi-restraints excluded: chain B residue 524 CYS Chi-restraints excluded: chain B residue 626 ASN Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 727 ASP Chi-restraints excluded: chain A residue 733 ASN Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 CYS Chi-restraints excluded: chain C residue 561 SER Chi-restraints excluded: chain C residue 1047 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 62 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 263 optimal weight: 0.6980 chunk 202 optimal weight: 4.9990 chunk 274 optimal weight: 0.9980 chunk 283 optimal weight: 0.9990 chunk 123 optimal weight: 0.0670 chunk 42 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 181 HIS B 889 ASN A 883 GLN A 895 GLN C 883 GLN C 947 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.123475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.088193 restraints weight = 37241.006| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.59 r_work: 0.2913 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25702 Z= 0.120 Angle : 0.592 11.951 35040 Z= 0.295 Chirality : 0.045 0.446 4034 Planarity : 0.004 0.049 4433 Dihedral : 6.663 78.091 4399 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.01 % Allowed : 11.20 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.44 (0.15), residues: 3056 helix: 1.76 (0.21), residues: 700 sheet: 0.73 (0.20), residues: 683 loop : -1.75 (0.13), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 868 HIS 0.005 0.001 HIS B 181 PHE 0.029 0.001 PHE B 137 TYR 0.021 0.001 TYR A1049 ARG 0.006 0.000 ARG A 449 Details of bonding type rmsd link_NAG-ASN : bond 0.00463 ( 42) link_NAG-ASN : angle 3.25381 ( 126) link_BETA1-4 : bond 0.00666 ( 3) link_BETA1-4 : angle 1.08660 ( 9) hydrogen bonds : bond 0.04826 ( 979) hydrogen bonds : angle 4.88468 ( 2706) SS BOND : bond 0.00469 ( 44) SS BOND : angle 1.39161 ( 88) covalent geometry : bond 0.00276 (25613) covalent geometry : angle 0.55579 (34817) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6112 Ramachandran restraints generated. 3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6112 Ramachandran restraints generated. 3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 156 time to evaluate : 3.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 ASP cc_start: 0.8284 (t0) cc_final: 0.7979 (t0) REVERT: B 155 ASN cc_start: 0.8744 (m-40) cc_final: 0.7764 (t0) REVERT: B 515 LEU cc_start: 0.7962 (mm) cc_final: 0.7656 (mm) REVERT: B 939 GLN cc_start: 0.8262 (tt0) cc_final: 0.7984 (tt0) REVERT: A 168 PHE cc_start: 0.3901 (OUTLIER) cc_final: 0.3041 (m-80) REVERT: A 181 HIS cc_start: 0.6455 (OUTLIER) cc_final: 0.5940 (p90) REVERT: A 733 ASN cc_start: 0.8595 (OUTLIER) cc_final: 0.8161 (m-40) REVERT: A 1112 ILE cc_start: 0.8767 (pp) cc_final: 0.8555 (mt) REVERT: C 181 HIS cc_start: 0.7296 (OUTLIER) cc_final: 0.6923 (m90) outliers start: 54 outliers final: 29 residues processed: 199 average time/residue: 1.0332 time to fit residues: 251.9266 Evaluate side-chains 181 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 2.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 417 MET Chi-restraints excluded: chain B residue 524 CYS Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 727 ASP Chi-restraints excluded: chain A residue 733 ASN Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 181 HIS Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 CYS Chi-restraints excluded: chain C residue 561 SER Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain C residue 967 CYS Chi-restraints excluded: chain C residue 1047 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 36 optimal weight: 4.9990 chunk 270 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 246 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 191 optimal weight: 0.9990 chunk 32 optimal weight: 0.0470 chunk 253 optimal weight: 0.3980 chunk 78 optimal weight: 3.9990 chunk 198 optimal weight: 3.9990 chunk 203 optimal weight: 4.9990 overall best weight: 1.2682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 181 HIS ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 889 ASN A 473 ASN A 883 GLN C 883 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.122377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.086896 restraints weight = 37542.628| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.61 r_work: 0.2893 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25702 Z= 0.156 Angle : 0.618 12.497 35040 Z= 0.309 Chirality : 0.046 0.456 4034 Planarity : 0.004 0.048 4433 Dihedral : 6.614 77.697 4399 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.20 % Allowed : 11.76 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.50 (0.15), residues: 3056 helix: 1.64 (0.21), residues: 705 sheet: 0.72 (0.20), residues: 683 loop : -1.77 (0.13), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 868 HIS 0.005 0.001 HIS B1046 PHE 0.030 0.001 PHE B 137 TYR 0.021 0.001 TYR A1049 ARG 0.006 0.000 ARG A 449 Details of bonding type rmsd link_NAG-ASN : bond 0.00439 ( 42) link_NAG-ASN : angle 3.30195 ( 126) link_BETA1-4 : bond 0.00640 ( 3) link_BETA1-4 : angle 1.11005 ( 9) hydrogen bonds : bond 0.05356 ( 979) hydrogen bonds : angle 4.89727 ( 2706) SS BOND : bond 0.00564 ( 44) SS BOND : angle 1.64648 ( 88) covalent geometry : bond 0.00377 (25613) covalent geometry : angle 0.58160 (34817) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6112 Ramachandran restraints generated. 3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6112 Ramachandran restraints generated. 3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 152 time to evaluate : 2.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 ASP cc_start: 0.8307 (t0) cc_final: 0.7952 (t0) REVERT: B 155 ASN cc_start: 0.8707 (m-40) cc_final: 0.7716 (t0) REVERT: B 515 LEU cc_start: 0.7979 (mm) cc_final: 0.7670 (mm) REVERT: B 877 GLN cc_start: 0.9006 (OUTLIER) cc_final: 0.8239 (pp30) REVERT: B 939 GLN cc_start: 0.8309 (tt0) cc_final: 0.8045 (tt0) REVERT: A 168 PHE cc_start: 0.4068 (OUTLIER) cc_final: 0.3211 (m-80) REVERT: A 181 HIS cc_start: 0.6526 (OUTLIER) cc_final: 0.5956 (p90) REVERT: A 733 ASN cc_start: 0.8611 (OUTLIER) cc_final: 0.8203 (m-40) REVERT: C 181 HIS cc_start: 0.7290 (OUTLIER) cc_final: 0.6919 (m90) outliers start: 59 outliers final: 33 residues processed: 196 average time/residue: 0.9878 time to fit residues: 237.9584 Evaluate side-chains 181 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 143 time to evaluate : 2.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 417 MET Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 877 GLN Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 727 ASP Chi-restraints excluded: chain A residue 733 ASN Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 181 HIS Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 CYS Chi-restraints excluded: chain C residue 561 SER Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain C residue 967 CYS Chi-restraints excluded: chain C residue 1047 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 300 optimal weight: 0.5980 chunk 269 optimal weight: 2.9990 chunk 189 optimal weight: 3.9990 chunk 171 optimal weight: 3.9990 chunk 175 optimal weight: 4.9990 chunk 260 optimal weight: 0.0020 chunk 282 optimal weight: 0.9980 chunk 292 optimal weight: 3.9990 chunk 288 optimal weight: 0.7980 chunk 176 optimal weight: 0.4980 chunk 148 optimal weight: 7.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 181 HIS B 883 GLN B 889 ASN A 473 ASN C 883 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.124168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.088790 restraints weight = 37681.703| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.64 r_work: 0.2927 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 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 0.057 25702 Z= 0.110 Angle : 0.576 13.757 35040 Z= 0.287 Chirality : 0.045 0.425 4034 Planarity : 0.004 0.049 4433 Dihedral : 6.390 78.725 4399 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.82 % Allowed : 12.39 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.34 (0.15), residues: 3056 helix: 1.87 (0.21), residues: 700 sheet: 0.79 (0.20), residues: 673 loop : -1.68 (0.13), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 868 HIS 0.005 0.001 HIS B 181 PHE 0.030 0.001 PHE B 137 TYR 0.021 0.001 TYR A1049 ARG 0.007 0.000 ARG A 449 Details of bonding type rmsd link_NAG-ASN : bond 0.00459 ( 42) link_NAG-ASN : angle 3.08676 ( 126) link_BETA1-4 : bond 0.00510 ( 3) link_BETA1-4 : angle 0.98598 ( 9) hydrogen bonds : bond 0.04431 ( 979) hydrogen bonds : angle 4.76255 ( 2706) SS BOND : bond 0.00486 ( 44) SS BOND : angle 1.40952 ( 88) covalent geometry : bond 0.00252 (25613) covalent geometry : angle 0.54196 (34817) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6112 Ramachandran restraints generated. 3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6112 Ramachandran restraints generated. 3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 157 time to evaluate : 2.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 ASP cc_start: 0.8254 (t0) cc_final: 0.7907 (t0) REVERT: B 155 ASN cc_start: 0.8692 (m-40) cc_final: 0.7688 (t0) REVERT: B 515 LEU cc_start: 0.7985 (mm) cc_final: 0.7681 (mm) REVERT: B 939 GLN cc_start: 0.8329 (tt0) cc_final: 0.8033 (tt0) REVERT: A 168 PHE cc_start: 0.4005 (OUTLIER) cc_final: 0.3149 (m-80) REVERT: A 181 HIS cc_start: 0.6439 (OUTLIER) cc_final: 0.5865 (p90) REVERT: A 733 ASN cc_start: 0.8629 (OUTLIER) cc_final: 0.8192 (m-40) REVERT: C 181 HIS cc_start: 0.7294 (OUTLIER) cc_final: 0.6931 (m90) REVERT: C 501 PHE cc_start: 0.8450 (m-10) cc_final: 0.8211 (m-10) outliers start: 49 outliers final: 30 residues processed: 196 average time/residue: 1.0106 time to fit residues: 243.1454 Evaluate side-chains 180 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 146 time to evaluate : 3.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 727 ASP Chi-restraints excluded: chain A residue 733 ASN Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 181 HIS Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 CYS Chi-restraints excluded: chain C residue 561 SER Chi-restraints excluded: chain C residue 819 TYR Chi-restraints excluded: chain C residue 967 CYS Chi-restraints excluded: chain C residue 1047 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 306 optimal weight: 0.0000 chunk 195 optimal weight: 0.1980 chunk 39 optimal weight: 0.5980 chunk 197 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 280 optimal weight: 1.9990 chunk 240 optimal weight: 2.9990 chunk 307 optimal weight: 0.8980 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 181 HIS B 889 ASN A 473 ASN C 937 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.125421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.090279 restraints weight = 37546.266| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.61 r_work: 0.2953 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 25702 Z= 0.100 Angle : 0.560 15.107 35040 Z= 0.278 Chirality : 0.044 0.397 4034 Planarity : 0.004 0.049 4433 Dihedral : 6.159 78.906 4399 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.53 % Allowed : 12.84 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 (0.15), residues: 3056 helix: 2.09 (0.21), residues: 690 sheet: 0.79 (0.20), residues: 635 loop : -1.56 (0.13), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 868 HIS 0.005 0.001 HIS B 181 PHE 0.031 0.001 PHE B 137 TYR 0.020 0.001 TYR A1049 ARG 0.007 0.000 ARG A 449 Details of bonding type rmsd link_NAG-ASN : bond 0.00454 ( 42) link_NAG-ASN : angle 2.91440 ( 126) link_BETA1-4 : bond 0.00621 ( 3) link_BETA1-4 : angle 0.87299 ( 9) hydrogen bonds : bond 0.04009 ( 979) hydrogen bonds : angle 4.64653 ( 2706) SS BOND : bond 0.00361 ( 44) SS BOND : angle 1.18529 ( 88) covalent geometry : bond 0.00226 (25613) covalent geometry : angle 0.53034 (34817) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6112 Ramachandran restraints generated. 3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6112 Ramachandran restraints generated. 3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 160 time to evaluate : 2.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 ASP cc_start: 0.8245 (t0) cc_final: 0.7898 (t0) REVERT: B 155 ASN cc_start: 0.8730 (m-40) cc_final: 0.7692 (t0) REVERT: B 515 LEU cc_start: 0.7958 (mm) cc_final: 0.7657 (mm) REVERT: B 768 LYS cc_start: 0.8337 (ptpp) cc_final: 0.8084 (mptt) REVERT: B 877 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.8237 (pp30) REVERT: B 939 GLN cc_start: 0.8316 (tt0) cc_final: 0.8037 (tt0) REVERT: A 168 PHE cc_start: 0.3969 (OUTLIER) cc_final: 0.3150 (m-80) REVERT: A 181 HIS cc_start: 0.6327 (OUTLIER) cc_final: 0.5791 (p90) REVERT: A 473 ASN cc_start: 0.8392 (m-40) cc_final: 0.8150 (m110) REVERT: C 181 HIS cc_start: 0.7270 (OUTLIER) cc_final: 0.6910 (m90) REVERT: C 491 TYR cc_start: 0.8460 (m-80) cc_final: 0.8099 (m-80) REVERT: C 501 PHE cc_start: 0.8346 (m-10) cc_final: 0.8068 (m-10) REVERT: C 816 MET cc_start: 0.5436 (ppp) cc_final: 0.4701 (ppp) outliers start: 41 outliers final: 30 residues processed: 194 average time/residue: 0.9676 time to fit residues: 229.8554 Evaluate side-chains 183 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 149 time to evaluate : 2.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 877 GLN Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 727 ASP Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 181 HIS Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 376 ASP Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 CYS Chi-restraints excluded: chain C residue 561 SER Chi-restraints excluded: chain C residue 819 TYR Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain C residue 967 CYS Chi-restraints excluded: chain C residue 1047 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 204 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 212 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 157 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 chunk 236 optimal weight: 4.9990 chunk 261 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 181 HIS B 889 ASN A 818 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.124830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.089510 restraints weight = 37386.399| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.61 r_work: 0.2936 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 25702 Z= 0.112 Angle : 0.567 16.200 35040 Z= 0.283 Chirality : 0.045 0.399 4034 Planarity : 0.004 0.050 4433 Dihedral : 6.116 78.645 4399 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.49 % Allowed : 12.99 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.23 (0.15), residues: 3056 helix: 2.03 (0.21), residues: 696 sheet: 0.81 (0.20), residues: 632 loop : -1.55 (0.13), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 868 HIS 0.005 0.001 HIS B 181 PHE 0.032 0.001 PHE B 137 TYR 0.021 0.001 TYR A1049 ARG 0.007 0.000 ARG A 449 Details of bonding type rmsd link_NAG-ASN : bond 0.00442 ( 42) link_NAG-ASN : angle 2.91109 ( 126) link_BETA1-4 : bond 0.00541 ( 3) link_BETA1-4 : angle 0.89135 ( 9) hydrogen bonds : bond 0.04323 ( 979) hydrogen bonds : angle 4.67627 ( 2706) SS BOND : bond 0.00404 ( 44) SS BOND : angle 1.21738 ( 88) covalent geometry : bond 0.00262 (25613) covalent geometry : angle 0.53784 (34817) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6112 Ramachandran restraints generated. 3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6112 Ramachandran restraints generated. 3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 153 time to evaluate : 2.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 ASP cc_start: 0.8271 (t0) cc_final: 0.7929 (t0) REVERT: B 155 ASN cc_start: 0.8743 (m-40) cc_final: 0.7712 (t0) REVERT: B 515 LEU cc_start: 0.7948 (mm) cc_final: 0.7646 (mm) REVERT: B 768 LYS cc_start: 0.8352 (ptpp) cc_final: 0.8093 (mptt) REVERT: B 877 GLN cc_start: 0.8927 (OUTLIER) cc_final: 0.8267 (pp30) REVERT: B 939 GLN cc_start: 0.8312 (tt0) cc_final: 0.8029 (tt0) REVERT: A 168 PHE cc_start: 0.3955 (OUTLIER) cc_final: 0.3158 (m-80) REVERT: A 181 HIS cc_start: 0.6316 (OUTLIER) cc_final: 0.5782 (p90) REVERT: C 181 HIS cc_start: 0.7256 (OUTLIER) cc_final: 0.6883 (m90) REVERT: C 501 PHE cc_start: 0.8380 (m-10) cc_final: 0.8106 (m-10) REVERT: C 816 MET cc_start: 0.5346 (ppp) cc_final: 0.4776 (ppp) outliers start: 40 outliers final: 31 residues processed: 187 average time/residue: 1.2147 time to fit residues: 285.2060 Evaluate side-chains 183 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 148 time to evaluate : 3.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 773 THR Chi-restraints excluded: chain B residue 877 GLN Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 727 ASP Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 181 HIS Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 376 ASP Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 CYS Chi-restraints excluded: chain C residue 561 SER Chi-restraints excluded: chain C residue 967 CYS Chi-restraints excluded: chain C residue 1047 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 272 optimal weight: 1.9990 chunk 287 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 183 optimal weight: 3.9990 chunk 288 optimal weight: 0.6980 chunk 252 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 244 optimal weight: 0.3980 chunk 235 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 158 optimal weight: 0.0270 overall best weight: 0.5440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 181 HIS B 769 GLN B 889 ASN C 818 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.125375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.090123 restraints weight = 37393.766| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.61 r_work: 0.2948 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 25702 Z= 0.103 Angle : 0.557 14.977 35040 Z= 0.278 Chirality : 0.044 0.386 4034 Planarity : 0.004 0.049 4433 Dihedral : 6.022 78.930 4399 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.53 % Allowed : 12.99 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (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 (0.15), residues: 3056 helix: 2.14 (0.21), residues: 688 sheet: 0.81 (0.20), residues: 631 loop : -1.50 (0.13), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 868 HIS 0.006 0.001 HIS B 181 PHE 0.031 0.001 PHE B 137 TYR 0.021 0.001 TYR A1049 ARG 0.007 0.000 ARG A 449 Details of bonding type rmsd link_NAG-ASN : bond 0.00451 ( 42) link_NAG-ASN : angle 2.85643 ( 126) link_BETA1-4 : bond 0.00560 ( 3) link_BETA1-4 : angle 0.88703 ( 9) hydrogen bonds : bond 0.04100 ( 979) hydrogen bonds : angle 4.65045 ( 2706) SS BOND : bond 0.00383 ( 44) SS BOND : angle 1.17770 ( 88) covalent geometry : bond 0.00234 (25613) covalent geometry : angle 0.52781 (34817) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16883.86 seconds wall clock time: 298 minutes 56.00 seconds (17936.00 seconds total)