Starting phenix.real_space_refine on Mon Aug 25 05:02:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h0z_34419/08_2025/8h0z_34419.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h0z_34419/08_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_34419/08_2025/8h0z_34419.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h0z_34419/08_2025/8h0z_34419.map" model { file = "/net/cci-nas-00/data/ceres_data/8h0z_34419/08_2025/8h0z_34419.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h0z_34419/08_2025/8h0z_34419.cif" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.16, per 1000 atoms: 0.21 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: 1.73 Conformation dependent library (CDL) restraints added in 843.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.05 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: 5.54 Time building geometry restraints manager: 2.30 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: 3.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 21.790 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.090 ------------------------------------------------------------------------------- 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 : 3.14 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.005 0.001 ARG C 441 TYR 0.028 0.002 TYR C 886 PHE 0.062 0.002 PHE A 888 TRP 0.024 0.002 TRP C 619 HIS 0.006 0.001 HIS C1030 Details of bonding type rmsd covalent geometry : bond 0.00805 (25613) covalent geometry : angle 0.92440 (34817) SS BOND : bond 0.00844 ( 44) SS BOND : angle 2.00954 ( 88) hydrogen bonds : bond 0.14849 ( 979) hydrogen bonds : angle 6.61506 ( 2706) link_BETA1-4 : bond 0.01015 ( 3) link_BETA1-4 : angle 2.40412 ( 9) link_NAG-ASN : bond 0.00580 ( 42) link_NAG-ASN : angle 5.28232 ( 126) *********************** 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 : 0.945 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: 0.5258 time to fit residues: 127.3138 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 : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 C 304 ASN ** C 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.123893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.088480 restraints weight = 37690.278| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.62 r_work: 0.2924 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.0799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 25702 Z= 0.137 Angle : 0.641 11.979 35040 Z= 0.323 Chirality : 0.047 0.463 4034 Planarity : 0.005 0.065 4433 Dihedral : 8.040 77.589 4399 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.04 % Allowed : 6.10 % Favored : 92.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.14), residues: 3056 helix: 0.91 (0.20), residues: 695 sheet: 0.65 (0.20), residues: 624 loop : -1.87 (0.12), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 449 TYR 0.021 0.001 TYR A1049 PHE 0.024 0.001 PHE A 888 TRP 0.018 0.001 TRP A 868 HIS 0.004 0.001 HIS C1030 Details of bonding type rmsd covalent geometry : bond 0.00312 (25613) covalent geometry : angle 0.59481 (34817) SS BOND : bond 0.00528 ( 44) SS BOND : angle 1.72497 ( 88) hydrogen bonds : bond 0.05684 ( 979) hydrogen bonds : angle 5.33635 ( 2706) link_BETA1-4 : bond 0.00830 ( 3) link_BETA1-4 : angle 1.67660 ( 9) link_NAG-ASN : bond 0.00487 ( 42) link_NAG-ASN : angle 3.77599 ( 126) *********************** 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: 28 poor density : 156 time to evaluate : 0.815 Fit side-chains revert: symmetry clash REVERT: B 155 ASN cc_start: 0.8566 (m-40) cc_final: 0.7637 (t0) REVERT: B 939 GLN cc_start: 0.8327 (tt0) cc_final: 0.7987 (tt0) REVERT: A 733 ASN cc_start: 0.8541 (OUTLIER) cc_final: 0.8201 (m-40) outliers start: 28 outliers final: 9 residues processed: 172 average time/residue: 0.5119 time to fit residues: 104.7889 Evaluate side-chains 149 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 139 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 626 ASN Chi-restraints excluded: chain B residue 1100 ASP Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 733 ASN Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain C residue 181 HIS Chi-restraints excluded: chain C residue 261 THR 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 12 optimal weight: 6.9990 chunk 167 optimal weight: 0.6980 chunk 285 optimal weight: 0.9980 chunk 234 optimal weight: 1.9990 chunk 157 optimal weight: 0.7980 chunk 241 optimal weight: 0.0870 chunk 35 optimal weight: 0.4980 chunk 158 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 255 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 889 ASN A 437 ASN ** C 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.125152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.089852 restraints weight = 37502.694| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.61 r_work: 0.2942 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 25702 Z= 0.110 Angle : 0.581 11.348 35040 Z= 0.291 Chirality : 0.045 0.432 4034 Planarity : 0.004 0.053 4433 Dihedral : 7.222 78.502 4399 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.19 % Allowed : 8.15 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.14), residues: 3056 helix: 1.42 (0.21), residues: 704 sheet: 0.69 (0.20), residues: 638 loop : -1.77 (0.13), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 449 TYR 0.022 0.001 TYR C1120 PHE 0.023 0.001 PHE B 137 TRP 0.014 0.001 TRP A 868 HIS 0.003 0.001 HIS C1030 Details of bonding type rmsd covalent geometry : bond 0.00247 (25613) covalent geometry : angle 0.54271 (34817) SS BOND : bond 0.00396 ( 44) SS BOND : angle 1.32696 ( 88) hydrogen bonds : bond 0.04694 ( 979) hydrogen bonds : angle 4.98264 ( 2706) link_BETA1-4 : bond 0.00559 ( 3) link_BETA1-4 : angle 1.21361 ( 9) link_NAG-ASN : bond 0.00472 ( 42) link_NAG-ASN : angle 3.32572 ( 126) *********************** 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 191 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 159 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 ASP cc_start: 0.8193 (t0) cc_final: 0.7817 (t0) REVERT: B 155 ASN cc_start: 0.8554 (m-40) cc_final: 0.7660 (t0) REVERT: B 939 GLN cc_start: 0.8271 (tt0) cc_final: 0.7926 (tt0) REVERT: A 733 ASN cc_start: 0.8508 (OUTLIER) cc_final: 0.8156 (m-40) outliers start: 32 outliers final: 8 residues processed: 182 average time/residue: 0.4526 time to fit residues: 98.6974 Evaluate side-chains 150 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 141 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 727 ASP Chi-restraints excluded: chain A residue 733 ASN 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 215 optimal weight: 6.9990 chunk 189 optimal weight: 0.0770 chunk 272 optimal weight: 0.8980 chunk 288 optimal weight: 0.6980 chunk 163 optimal weight: 5.9990 chunk 202 optimal weight: 4.9990 chunk 182 optimal weight: 0.9990 chunk 267 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 296 optimal weight: 0.6980 chunk 263 optimal weight: 0.0970 overall best weight: 0.4936 ------------------------------------------------------------------------------- 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 883 GLN B 889 ASN C 181 HIS C 883 GLN C 937 ASN C 947 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.125827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.090669 restraints weight = 37281.596| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.60 r_work: 0.2955 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 25702 Z= 0.102 Angle : 0.567 11.195 35040 Z= 0.283 Chirality : 0.045 0.424 4034 Planarity : 0.004 0.049 4433 Dihedral : 6.780 78.600 4399 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.64 % Allowed : 9.08 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.15), residues: 3056 helix: 1.74 (0.21), residues: 700 sheet: 0.76 (0.20), residues: 625 loop : -1.71 (0.13), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 449 TYR 0.021 0.001 TYR A1049 PHE 0.024 0.001 PHE B 137 TRP 0.013 0.001 TRP A 868 HIS 0.006 0.001 HIS B 181 Details of bonding type rmsd covalent geometry : bond 0.00231 (25613) covalent geometry : angle 0.53053 (34817) SS BOND : bond 0.00323 ( 44) SS BOND : angle 1.45221 ( 88) hydrogen bonds : bond 0.04311 ( 979) hydrogen bonds : angle 4.87588 ( 2706) link_BETA1-4 : bond 0.00483 ( 3) link_BETA1-4 : angle 1.06586 ( 9) link_NAG-ASN : bond 0.00471 ( 42) link_NAG-ASN : angle 3.16551 ( 126) *********************** 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 211 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 167 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 32 GLN cc_start: 0.7592 (OUTLIER) cc_final: 0.7322 (mm-40) REVERT: B 50 ASP cc_start: 0.8146 (t0) cc_final: 0.7744 (t0) REVERT: B 155 ASN cc_start: 0.8732 (m-40) cc_final: 0.7831 (t0) REVERT: B 707 GLU cc_start: 0.9098 (tt0) cc_final: 0.8732 (tt0) REVERT: B 939 GLN cc_start: 0.8260 (tt0) cc_final: 0.7941 (tt0) REVERT: A 168 PHE cc_start: 0.3790 (OUTLIER) cc_final: 0.3319 (m-80) REVERT: A 644 THR cc_start: 0.8617 (p) cc_final: 0.8296 (t) REVERT: A 733 ASN cc_start: 0.8586 (OUTLIER) cc_final: 0.8221 (m-40) REVERT: C 321 ASN cc_start: 0.7915 (p0) cc_final: 0.7694 (p0) outliers start: 44 outliers final: 13 residues processed: 200 average time/residue: 0.4468 time to fit residues: 108.9617 Evaluate side-chains 160 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 0.982 ------------------------------------------------------------------------------- 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 357 ASN Chi-restraints excluded: chain B residue 904 GLN Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 504 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 1047 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 474 CYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 65 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 124 optimal weight: 8.9990 chunk 279 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 chunk 181 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 302 optimal weight: 0.5980 chunk 221 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 112 GLN B 181 HIS ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 883 GLN B 889 ASN B 937 ASN A 904 GLN C 550 GLN C 883 GLN C 937 ASN C1088 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.120537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.084914 restraints weight = 37552.748| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.60 r_work: 0.2859 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1285 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= 0.253 Angle : 0.696 12.055 35040 Z= 0.352 Chirality : 0.050 0.505 4034 Planarity : 0.005 0.049 4433 Dihedral : 6.964 76.575 4399 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.38 % Allowed : 9.45 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.14), residues: 3056 helix: 1.19 (0.20), residues: 723 sheet: 0.66 (0.19), residues: 681 loop : -1.84 (0.13), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 395 TYR 0.022 0.002 TYR A1049 PHE 0.034 0.002 PHE A 888 TRP 0.011 0.002 TRP B 868 HIS 0.007 0.001 HIS B1046 Details of bonding type rmsd covalent geometry : bond 0.00627 (25613) covalent geometry : angle 0.65671 (34817) SS BOND : bond 0.00691 ( 44) SS BOND : angle 1.84651 ( 88) hydrogen bonds : bond 0.06745 ( 979) hydrogen bonds : angle 5.15311 ( 2706) link_BETA1-4 : bond 0.00565 ( 3) link_BETA1-4 : angle 1.43458 ( 9) link_NAG-ASN : bond 0.00429 ( 42) link_NAG-ASN : angle 3.59765 ( 126) *********************** 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 208 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 144 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 ASP cc_start: 0.8363 (t0) cc_final: 0.8025 (t0) REVERT: B 155 ASN cc_start: 0.8750 (m-40) cc_final: 0.7814 (t0) REVERT: B 515 LEU cc_start: 0.7975 (mm) cc_final: 0.7659 (mm) REVERT: B 768 LYS cc_start: 0.8478 (pttm) cc_final: 0.8211 (mptt) REVERT: A 168 PHE cc_start: 0.4041 (OUTLIER) cc_final: 0.3203 (m-80) REVERT: A 733 ASN cc_start: 0.8578 (OUTLIER) cc_final: 0.8241 (m-40) REVERT: C 46 ILE cc_start: 0.8110 (OUTLIER) cc_final: 0.7874 (mp) outliers start: 64 outliers final: 25 residues processed: 193 average time/residue: 0.4198 time to fit residues: 98.1740 Evaluate side-chains 167 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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 524 CYS Chi-restraints excluded: chain B residue 626 ASN Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain A residue 168 PHE 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 1047 VAL Chi-restraints excluded: chain C residue 46 ILE 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 916 ILE 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 48 optimal weight: 3.9990 chunk 218 optimal weight: 0.9990 chunk 205 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 chunk 240 optimal weight: 0.9980 chunk 147 optimal weight: 1.9990 chunk 248 optimal weight: 0.6980 chunk 54 optimal weight: 10.0000 chunk 307 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 129 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.122311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.086780 restraints weight = 37473.845| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.63 r_work: 0.2896 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25702 Z= 0.146 Angle : 0.610 11.704 35040 Z= 0.306 Chirality : 0.046 0.457 4034 Planarity : 0.004 0.049 4433 Dihedral : 6.702 77.874 4399 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.82 % Allowed : 10.79 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.15), residues: 3056 helix: 1.52 (0.21), residues: 711 sheet: 0.71 (0.20), residues: 683 loop : -1.79 (0.13), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 449 TYR 0.022 0.001 TYR A1049 PHE 0.030 0.001 PHE C 305 TRP 0.012 0.001 TRP B 868 HIS 0.005 0.001 HIS B1046 Details of bonding type rmsd covalent geometry : bond 0.00348 (25613) covalent geometry : angle 0.57264 (34817) SS BOND : bond 0.00542 ( 44) SS BOND : angle 1.54127 ( 88) hydrogen bonds : bond 0.05299 ( 979) hydrogen bonds : angle 4.95432 ( 2706) link_BETA1-4 : bond 0.00506 ( 3) link_BETA1-4 : angle 1.24553 ( 9) link_NAG-ASN : bond 0.00450 ( 42) link_NAG-ASN : angle 3.34690 ( 126) *********************** 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 199 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 150 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 ASP cc_start: 0.8333 (t0) cc_final: 0.7973 (t0) REVERT: B 155 ASN cc_start: 0.8736 (m-40) cc_final: 0.7819 (t0) REVERT: B 515 LEU cc_start: 0.7974 (mm) cc_final: 0.7661 (mm) REVERT: B 707 GLU cc_start: 0.9114 (tt0) cc_final: 0.8773 (tt0) REVERT: B 768 LYS cc_start: 0.8416 (pttm) cc_final: 0.8206 (mptt) REVERT: B 939 GLN cc_start: 0.8360 (tt0) cc_final: 0.8089 (tt0) REVERT: A 168 PHE cc_start: 0.4065 (OUTLIER) cc_final: 0.3212 (m-80) REVERT: A 733 ASN cc_start: 0.8640 (OUTLIER) cc_final: 0.8280 (m-40) REVERT: C 46 ILE cc_start: 0.8041 (OUTLIER) cc_final: 0.7826 (mp) REVERT: C 181 HIS cc_start: 0.7166 (OUTLIER) cc_final: 0.6826 (m90) outliers start: 49 outliers final: 21 residues processed: 187 average time/residue: 0.4533 time to fit residues: 102.3233 Evaluate side-chains 165 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 0.974 ------------------------------------------------------------------------------- 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 114 VAL Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 524 CYS Chi-restraints excluded: chain A residue 168 PHE 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 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 1047 VAL Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 181 HIS Chi-restraints excluded: chain C residue 474 CYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 244 optimal weight: 0.6980 chunk 193 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 192 optimal weight: 2.9990 chunk 288 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 271 optimal weight: 0.9980 chunk 246 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 264 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.121887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.086279 restraints weight = 37403.626| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.63 r_work: 0.2879 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25702 Z= 0.162 Angle : 0.623 13.667 35040 Z= 0.313 Chirality : 0.047 0.460 4034 Planarity : 0.004 0.049 4433 Dihedral : 6.618 77.362 4399 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.05 % Allowed : 11.20 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.15), residues: 3056 helix: 1.52 (0.21), residues: 711 sheet: 0.71 (0.20), residues: 681 loop : -1.78 (0.13), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 449 TYR 0.021 0.001 TYR A1049 PHE 0.030 0.001 PHE B 137 TRP 0.011 0.001 TRP A 868 HIS 0.006 0.001 HIS B1046 Details of bonding type rmsd covalent geometry : bond 0.00395 (25613) covalent geometry : angle 0.58616 (34817) SS BOND : bond 0.00551 ( 44) SS BOND : angle 1.55933 ( 88) hydrogen bonds : bond 0.05523 ( 979) hydrogen bonds : angle 4.94016 ( 2706) link_BETA1-4 : bond 0.00506 ( 3) link_BETA1-4 : angle 1.20205 ( 9) link_NAG-ASN : bond 0.00429 ( 42) link_NAG-ASN : angle 3.34671 ( 126) *********************** 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 200 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 145 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 ASP cc_start: 0.8341 (t0) cc_final: 0.7983 (t0) REVERT: B 155 ASN cc_start: 0.8739 (m-40) cc_final: 0.7778 (t0) REVERT: B 515 LEU cc_start: 0.7959 (mm) cc_final: 0.7644 (mm) REVERT: B 768 LYS cc_start: 0.8432 (pttm) cc_final: 0.8203 (mptt) REVERT: B 939 GLN cc_start: 0.8337 (tt0) cc_final: 0.8070 (tt0) REVERT: A 168 PHE cc_start: 0.4198 (OUTLIER) cc_final: 0.3324 (m-80) REVERT: A 181 HIS cc_start: 0.6525 (OUTLIER) cc_final: 0.5893 (p90) REVERT: A 733 ASN cc_start: 0.8627 (OUTLIER) cc_final: 0.8223 (m-40) REVERT: A 1112 ILE cc_start: 0.8690 (pp) cc_final: 0.8452 (mt) REVERT: C 56 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7408 (tm-30) REVERT: C 181 HIS cc_start: 0.7149 (OUTLIER) cc_final: 0.6814 (m90) outliers start: 55 outliers final: 29 residues processed: 188 average time/residue: 0.4664 time to fit residues: 107.1358 Evaluate side-chains 177 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 143 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 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 489 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 515 LEU 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 1047 VAL 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 181 HIS Chi-restraints excluded: chain C residue 184 GLU 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 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 269 optimal weight: 2.9990 chunk 270 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 147 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 27 optimal weight: 0.0040 chunk 163 optimal weight: 6.9990 chunk 301 optimal weight: 0.4980 chunk 57 optimal weight: 2.9990 overall best weight: 0.8594 ------------------------------------------------------------------------------- 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 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 = 0.3584 r_free = 0.3584 target = 0.122775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.087300 restraints weight = 37562.139| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.63 r_work: 0.2903 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25702 Z= 0.125 Angle : 0.597 14.729 35040 Z= 0.299 Chirality : 0.045 0.440 4034 Planarity : 0.004 0.048 4433 Dihedral : 6.471 78.191 4399 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.82 % Allowed : 11.65 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.15), residues: 3056 helix: 1.80 (0.21), residues: 698 sheet: 0.75 (0.20), residues: 673 loop : -1.71 (0.13), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 449 TYR 0.021 0.001 TYR A1049 PHE 0.032 0.001 PHE B 137 TRP 0.012 0.001 TRP A 868 HIS 0.005 0.001 HIS B 181 Details of bonding type rmsd covalent geometry : bond 0.00294 (25613) covalent geometry : angle 0.56161 (34817) SS BOND : bond 0.00520 ( 44) SS BOND : angle 1.60791 ( 88) hydrogen bonds : bond 0.04852 ( 979) hydrogen bonds : angle 4.83968 ( 2706) link_BETA1-4 : bond 0.00603 ( 3) link_BETA1-4 : angle 1.07575 ( 9) link_NAG-ASN : bond 0.00460 ( 42) link_NAG-ASN : angle 3.19018 ( 126) *********************** 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 200 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 151 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 ASP cc_start: 0.8297 (t0) cc_final: 0.7945 (t0) REVERT: B 155 ASN cc_start: 0.8685 (m-40) cc_final: 0.7693 (t0) REVERT: B 515 LEU cc_start: 0.7959 (mm) cc_final: 0.7649 (mm) REVERT: B 768 LYS cc_start: 0.8416 (pttm) cc_final: 0.8201 (mptt) REVERT: B 939 GLN cc_start: 0.8322 (tt0) cc_final: 0.8064 (tt0) REVERT: A 168 PHE cc_start: 0.4089 (OUTLIER) cc_final: 0.3227 (m-80) REVERT: A 181 HIS cc_start: 0.6466 (OUTLIER) cc_final: 0.5831 (p90) REVERT: A 733 ASN cc_start: 0.8635 (OUTLIER) cc_final: 0.8202 (m-40) REVERT: A 1112 ILE cc_start: 0.8696 (pp) cc_final: 0.8486 (mt) REVERT: C 138 PHE cc_start: 0.6100 (m-80) cc_final: 0.5872 (m-10) REVERT: C 181 HIS cc_start: 0.7316 (OUTLIER) cc_final: 0.6876 (m90) outliers start: 49 outliers final: 27 residues processed: 192 average time/residue: 0.4547 time to fit residues: 106.2819 Evaluate side-chains 175 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 144 time to evaluate : 0.853 ------------------------------------------------------------------------------- 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 421 LEU Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 882 MET Chi-restraints excluded: chain B residue 1047 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 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 421 LEU Chi-restraints excluded: chain C residue 474 CYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 215 optimal weight: 3.9990 chunk 252 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 180 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 14 optimal weight: 20.0000 chunk 118 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 818 GLN A 883 GLN C 883 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.120560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.085085 restraints weight = 37667.189| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.60 r_work: 0.2861 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 25702 Z= 0.217 Angle : 0.678 14.083 35040 Z= 0.341 Chirality : 0.048 0.473 4034 Planarity : 0.004 0.048 4433 Dihedral : 6.693 76.743 4399 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.82 % Allowed : 12.02 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.15), residues: 3056 helix: 1.39 (0.20), residues: 710 sheet: 0.65 (0.20), residues: 672 loop : -1.80 (0.13), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 395 TYR 0.020 0.002 TYR C1120 PHE 0.033 0.002 PHE B 137 TRP 0.010 0.002 TRP B 868 HIS 0.007 0.001 HIS B1046 Details of bonding type rmsd covalent geometry : bond 0.00537 (25613) covalent geometry : angle 0.63893 (34817) SS BOND : bond 0.00707 ( 44) SS BOND : angle 2.06502 ( 88) hydrogen bonds : bond 0.06289 ( 979) hydrogen bonds : angle 5.05113 ( 2706) link_BETA1-4 : bond 0.00480 ( 3) link_BETA1-4 : angle 1.32000 ( 9) link_NAG-ASN : bond 0.00434 ( 42) link_NAG-ASN : angle 3.44855 ( 126) *********************** 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 194 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 145 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 ASP cc_start: 0.8414 (t0) cc_final: 0.8064 (t0) REVERT: B 155 ASN cc_start: 0.8700 (m-40) cc_final: 0.7713 (t0) REVERT: B 515 LEU cc_start: 0.7909 (mm) cc_final: 0.7617 (mm) REVERT: A 37 MET cc_start: 0.8258 (mtm) cc_final: 0.7920 (mtm) REVERT: A 181 HIS cc_start: 0.6545 (OUTLIER) cc_final: 0.5826 (p90) REVERT: A 733 ASN cc_start: 0.8621 (OUTLIER) cc_final: 0.8282 (m-40) REVERT: C 138 PHE cc_start: 0.6256 (m-80) cc_final: 0.6039 (m-10) REVERT: C 181 HIS cc_start: 0.7254 (OUTLIER) cc_final: 0.6916 (m90) outliers start: 49 outliers final: 29 residues processed: 182 average time/residue: 0.4732 time to fit residues: 105.2888 Evaluate side-chains 174 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 142 time to evaluate : 0.681 ------------------------------------------------------------------------------- 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 114 VAL Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 224 LEU 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 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 402 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 916 ILE Chi-restraints excluded: chain C residue 945 VAL 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 209 optimal weight: 1.9990 chunk 226 optimal weight: 3.9990 chunk 129 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 101 optimal weight: 0.0030 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.7194 ------------------------------------------------------------------------------- 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 A 883 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.123345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.088046 restraints weight = 37520.189| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.61 r_work: 0.2914 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25702 Z= 0.119 Angle : 0.596 14.153 35040 Z= 0.298 Chirality : 0.045 0.435 4034 Planarity : 0.004 0.049 4433 Dihedral : 6.447 78.430 4399 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.19 % Allowed : 12.77 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.15), residues: 3056 helix: 1.79 (0.21), residues: 699 sheet: 0.71 (0.20), residues: 674 loop : -1.67 (0.13), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 449 TYR 0.021 0.001 TYR A1049 PHE 0.033 0.001 PHE B 137 TRP 0.013 0.001 TRP A 868 HIS 0.005 0.001 HIS B 181 Details of bonding type rmsd covalent geometry : bond 0.00277 (25613) covalent geometry : angle 0.56142 (34817) SS BOND : bond 0.00414 ( 44) SS BOND : angle 1.54013 ( 88) hydrogen bonds : bond 0.04720 ( 979) hydrogen bonds : angle 4.84473 ( 2706) link_BETA1-4 : bond 0.00610 ( 3) link_BETA1-4 : angle 1.08006 ( 9) link_NAG-ASN : bond 0.00455 ( 42) link_NAG-ASN : angle 3.15918 ( 126) ********************** 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 183 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 151 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 ASP cc_start: 0.8346 (t0) cc_final: 0.8011 (t0) REVERT: B 155 ASN cc_start: 0.8708 (m-40) cc_final: 0.7678 (t0) REVERT: B 515 LEU cc_start: 0.7897 (mm) cc_final: 0.7616 (mm) REVERT: B 877 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.8230 (pp30) REVERT: B 939 GLN cc_start: 0.8329 (tt0) cc_final: 0.8052 (tt0) REVERT: A 37 MET cc_start: 0.8245 (mtm) cc_final: 0.7909 (mtm) REVERT: A 181 HIS cc_start: 0.6464 (OUTLIER) cc_final: 0.5749 (p90) REVERT: A 473 ASN cc_start: 0.8421 (m-40) cc_final: 0.8204 (m110) REVERT: A 733 ASN cc_start: 0.8636 (OUTLIER) cc_final: 0.8203 (m-40) REVERT: C 138 PHE cc_start: 0.6130 (m-80) cc_final: 0.5917 (m-10) REVERT: C 181 HIS cc_start: 0.7282 (OUTLIER) cc_final: 0.6882 (m90) REVERT: C 491 TYR cc_start: 0.8522 (m-80) cc_final: 0.8230 (m-80) REVERT: C 816 MET cc_start: 0.5755 (ppp) cc_final: 0.5088 (ppp) outliers start: 32 outliers final: 24 residues processed: 179 average time/residue: 0.5090 time to fit residues: 110.8154 Evaluate side-chains 173 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 0.967 ------------------------------------------------------------------------------- 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 877 GLN Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain A residue 102 VAL 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 227 optimal weight: 0.9990 chunk 241 optimal weight: 4.9990 chunk 251 optimal weight: 0.5980 chunk 88 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 274 optimal weight: 0.0570 chunk 127 optimal weight: 0.7980 chunk 302 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- 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 181 HIS B 889 ASN B 937 ASN C 883 GLN C 937 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.124195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.089506 restraints weight = 37354.627| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.71 r_work: 0.2916 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1725 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= 0.113 Angle : 0.579 15.986 35040 Z= 0.289 Chirality : 0.045 0.420 4034 Planarity : 0.004 0.049 4433 Dihedral : 6.214 78.146 4399 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.38 % Allowed : 12.54 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.15), residues: 3056 helix: 1.98 (0.21), residues: 693 sheet: 0.74 (0.20), residues: 673 loop : -1.60 (0.13), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 449 TYR 0.021 0.001 TYR A1049 PHE 0.032 0.001 PHE B 137 TRP 0.013 0.001 TRP A 868 HIS 0.005 0.001 HIS B 181 Details of bonding type rmsd covalent geometry : bond 0.00264 (25613) covalent geometry : angle 0.54690 (34817) SS BOND : bond 0.00378 ( 44) SS BOND : angle 1.36936 ( 88) hydrogen bonds : bond 0.04447 ( 979) hydrogen bonds : angle 4.74807 ( 2706) link_BETA1-4 : bond 0.00606 ( 3) link_BETA1-4 : angle 0.96281 ( 9) link_NAG-ASN : bond 0.00439 ( 42) link_NAG-ASN : angle 3.01800 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6929.81 seconds wall clock time: 119 minutes 10.37 seconds (7150.37 seconds total)