Starting phenix.real_space_refine on Mon Sep 30 13:28:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0z_34419/09_2024/8h0z_34419.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0z_34419/09_2024/8h0z_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0z_34419/09_2024/8h0z_34419.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0z_34419/09_2024/8h0z_34419.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0z_34419/09_2024/8h0z_34419.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0z_34419/09_2024/8h0z_34419.cif" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 140 5.16 5 C 16006 2.51 5 N 4066 2.21 5 O 4835 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 25047 Number of models: 1 Model: "" Number of chains: 9 Chain: "B" Number of atoms: 8151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1045, 8151 Classifications: {'peptide': 1045} Link IDs: {'PTRANS': 50, 'TRANS': 994} Chain breaks: 5 Chain: "A" Number of atoms: 7992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 7992 Classifications: {'peptide': 1022} Link IDs: {'PTRANS': 49, 'TRANS': 972} Chain breaks: 8 Chain: "C" Number of atoms: 8085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8085 Classifications: {'peptide': 1035} Link IDs: {'PTRANS': 50, 'TRANS': 984} Chain breaks: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 245 Unusual residues: {'BLA': 1, 'EIC': 1, 'NAG': 13} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "A" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 265 Unusual residues: {'BLA': 1, 'EIC': 2, 'NAG': 13} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 225 Unusual residues: {'BLA': 1, 'NAG': 13} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 16.36, per 1000 atoms: 0.65 Number of scatterers: 25047 At special positions: 0 Unit cell: (120.45, 125.925, 174.105, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 140 16.00 O 4835 8.00 N 4066 7.00 C 16006 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 159 " distance=2.05 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 288 " distance=2.03 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 348 " distance=2.04 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS B 419 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 511 " distance=2.03 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 474 " distance=2.02 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 635 " distance=2.03 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.04 Simple disulfide: pdb=" SG CYS B 720 " - pdb=" SG CYS B 742 " distance=2.03 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B 822 " - pdb=" SG CYS B 833 " distance=2.04 Simple disulfide: pdb=" SG CYS B 967 " - pdb=" SG CYS A 370 " distance=2.03 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.01 Simple disulfide: pdb=" SG CYS B1064 " - pdb=" SG CYS B1108 " distance=2.03 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.05 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 288 " distance=2.03 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 348 " distance=2.04 Simple disulfide: pdb=" SG CYS A 366 " - pdb=" SG CYS A 419 " distance=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 511 " distance=2.04 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 474 " distance=2.03 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.04 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 635 " distance=2.03 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.03 Simple disulfide: pdb=" SG CYS A 720 " - pdb=" SG CYS A 742 " distance=2.04 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS A 822 " - pdb=" SG CYS A 833 " distance=2.03 Simple disulfide: pdb=" SG CYS A 967 " - pdb=" SG CYS C 370 " distance=2.03 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.01 Simple disulfide: pdb=" SG CYS A1064 " - pdb=" SG CYS A1108 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 159 " distance=2.04 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 288 " distance=2.03 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 348 " distance=2.04 Simple disulfide: pdb=" SG CYS C 366 " - pdb=" SG CYS C 419 " distance=2.04 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 511 " distance=2.05 Simple disulfide: pdb=" SG CYS C 467 " - pdb=" SG CYS C 474 " distance=2.03 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.04 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 635 " distance=2.03 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C 657 " distance=2.03 Simple disulfide: pdb=" SG CYS C 720 " - pdb=" SG CYS C 742 " distance=2.03 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.02 Simple disulfide: pdb=" SG CYS C 822 " - pdb=" SG CYS C 833 " distance=2.03 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.01 Simple disulfide: pdb=" SG CYS C1064 " - pdb=" SG CYS C1108 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1303 " - " ASN A 65 " " NAG A1304 " - " ASN A1080 " " NAG A1305 " - " ASN A 109 " " NAG A1306 " - " ASN A 119 " " NAG A1307 " - " ASN A 158 " " NAG A1308 " - " ASN A 269 " " NAG A1309 " - " ASN A 318 " " NAG A1310 " - " ASN A 357 " " NAG A1311 " - " ASN A 602 " " NAG A1312 " - " ASN A 691 " " NAG A1313 " - " ASN A 699 " " NAG A1314 " - " ASN A 783 " " NAG A1315 " - " ASN A1056 " " NAG B1301 " - " ASN B 65 " " NAG B1302 " - " ASN B1080 " " NAG B1303 " - " ASN B 109 " " NAG B1304 " - " ASN B 119 " " NAG B1305 " - " ASN B 158 " " NAG B1306 " - " ASN B 269 " " NAG B1307 " - " ASN B 318 " " NAG B1308 " - " ASN B 357 " " NAG B1309 " - " ASN B 602 " " NAG B1310 " - " ASN B 691 " " NAG B1311 " - " ASN B 699 " " NAG B1312 " - " ASN B 783 " " NAG B1313 " - " ASN B1056 " " NAG C1301 " - " ASN C 65 " " NAG C1302 " - " ASN C1080 " " NAG C1303 " - " ASN C 109 " " NAG C1304 " - " ASN C 119 " " NAG C1305 " - " ASN C 158 " " NAG C1306 " - " ASN C 318 " " NAG C1307 " - " ASN C 357 " " NAG C1308 " - " ASN C 602 " " NAG C1309 " - " ASN C 691 " " NAG C1310 " - " ASN C 699 " " NAG C1311 " - " ASN C 783 " " NAG C1312 " - " ASN C1056 " " NAG C1313 " - " ASN C1116 " " NAG D 1 " - " ASN B 227 " " NAG E 1 " - " ASN A 227 " " NAG F 1 " - " ASN C 227 " Time building additional restraints: 6.51 Conformation dependent library (CDL) restraints added in 3.1 seconds 6112 Ramachandran restraints generated. 3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5812 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 45 sheets defined 26.1% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.27 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: 16.45 Time building geometry restraints manager: 7.49 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: 1.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.130 Check model and map are aligned: 0.210 Set scattering table: 0.250 Process input model: 68.430 Find NCS groups from input model: 1.680 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.760 ------------------------------------------------------------------------------- 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 25613 Z= 0.517 Angle : 0.924 16.385 34817 Z= 0.504 Chirality : 0.056 0.649 4034 Planarity : 0.008 0.202 4433 Dihedral : 12.602 89.435 9904 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.14), residues: 3056 helix: -0.23 (0.19), residues: 696 sheet: 0.57 (0.20), residues: 687 loop : -2.08 (0.12), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 619 HIS 0.006 0.001 HIS C1030 PHE 0.062 0.002 PHE A 888 TYR 0.028 0.002 TYR C 886 ARG 0.005 0.001 ARG C 441 *********************** 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 fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 3.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 155 ASN cc_start: 0.8088 (m-40) cc_final: 0.7616 (t0) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 1.2671 time to fit residues: 306.6179 Evaluate side-chains 137 residues out of total 2687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 2.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 260 optimal weight: 0.0770 chunk 234 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 157 optimal weight: 0.9990 chunk 125 optimal weight: 0.9980 chunk 242 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 chunk 180 optimal weight: 4.9990 chunk 280 optimal weight: 0.3980 overall best weight: 0.6340 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.0814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25613 Z= 0.176 Angle : 0.585 8.453 34817 Z= 0.307 Chirality : 0.046 0.459 4034 Planarity : 0.005 0.065 4433 Dihedral : 8.041 77.789 4399 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.93 % Allowed : 5.81 % Favored : 93.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.14), residues: 3056 helix: 0.96 (0.20), residues: 695 sheet: 0.66 (0.20), residues: 624 loop : -1.87 (0.12), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 868 HIS 0.003 0.001 HIS C1030 PHE 0.022 0.001 PHE A 888 TYR 0.021 0.001 TYR A1049 ARG 0.004 0.000 ARG A 449 *********************** 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 fitting. rotamer outliers: 25 poor density : 159 time to evaluate : 3.320 Fit side-chains revert: symmetry clash REVERT: B 155 ASN cc_start: 0.8132 (m-40) cc_final: 0.7632 (t0) REVERT: B 553 ARG cc_start: 0.7156 (OUTLIER) cc_final: 0.6933 (mtt180) REVERT: B 939 GLN cc_start: 0.7739 (tt0) cc_final: 0.7430 (tt0) REVERT: A 733 ASN cc_start: 0.8278 (OUTLIER) cc_final: 0.7920 (m-40) REVERT: C 107 MET cc_start: 0.7871 (mmm) cc_final: 0.7671 (mmt) outliers start: 25 outliers final: 5 residues processed: 173 average time/residue: 1.2325 time to fit residues: 252.8483 Evaluate side-chains 147 residues out of total 2687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 140 time to evaluate : 2.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 553 ARG Chi-restraints excluded: chain B residue 1100 ASP Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 733 ASN Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain C residue 561 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 155 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 233 optimal weight: 0.8980 chunk 191 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 281 optimal weight: 1.9990 chunk 303 optimal weight: 0.8980 chunk 250 optimal weight: 0.9980 chunk 278 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 225 optimal weight: 8.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 A 904 GLN ** C 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25613 Z= 0.200 Angle : 0.561 10.041 34817 Z= 0.292 Chirality : 0.046 0.449 4034 Planarity : 0.004 0.053 4433 Dihedral : 7.256 78.079 4399 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.53 % Allowed : 8.00 % Favored : 90.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.14), residues: 3056 helix: 1.38 (0.21), residues: 704 sheet: 0.70 (0.20), residues: 665 loop : -1.81 (0.13), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 868 HIS 0.004 0.001 HIS B1046 PHE 0.023 0.001 PHE A 888 TYR 0.022 0.001 TYR C1120 ARG 0.005 0.000 ARG A 449 *********************** 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 195 residues out of total 2687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 154 time to evaluate : 2.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 ASP cc_start: 0.7769 (t0) cc_final: 0.7461 (t0) REVERT: B 155 ASN cc_start: 0.8074 (m-40) cc_final: 0.7634 (t0) REVERT: B 553 ARG cc_start: 0.7195 (OUTLIER) cc_final: 0.6927 (mtt180) REVERT: B 939 GLN cc_start: 0.7747 (tt0) cc_final: 0.7446 (tt0) REVERT: A 733 ASN cc_start: 0.8258 (OUTLIER) cc_final: 0.7897 (m-40) REVERT: C 214 ASN cc_start: 0.7625 (t0) cc_final: 0.7412 (t0) outliers start: 41 outliers final: 12 residues processed: 184 average time/residue: 1.1125 time to fit residues: 247.3551 Evaluate side-chains 149 residues out of total 2687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 135 time to evaluate : 2.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 553 ARG Chi-restraints excluded: chain B residue 626 ASN Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 727 ASP Chi-restraints excluded: chain A residue 733 ASN Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain A residue 1047 VAL 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 277 optimal weight: 0.0020 chunk 211 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 188 optimal weight: 1.9990 chunk 282 optimal weight: 2.9990 chunk 298 optimal weight: 0.9980 chunk 147 optimal weight: 0.7980 chunk 267 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.1592 ------------------------------------------------------------------------------- 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 889 ASN A 883 GLN C 883 GLN ** C 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 25613 Z= 0.230 Angle : 0.573 10.973 34817 Z= 0.297 Chirality : 0.046 0.460 4034 Planarity : 0.004 0.049 4433 Dihedral : 6.941 77.856 4399 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.08 % Allowed : 8.75 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.15), residues: 3056 helix: 1.51 (0.21), residues: 706 sheet: 0.72 (0.20), residues: 663 loop : -1.78 (0.13), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 868 HIS 0.005 0.001 HIS B 181 PHE 0.028 0.001 PHE B 578 TYR 0.021 0.001 TYR A1049 ARG 0.005 0.000 ARG A 449 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6112 Ramachandran restraints generated. 3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6112 Ramachandran restraints generated. 3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 151 time to evaluate : 3.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 32 GLN cc_start: 0.7695 (OUTLIER) cc_final: 0.7441 (tm-30) REVERT: B 50 ASP cc_start: 0.7787 (t0) cc_final: 0.7485 (t0) REVERT: B 155 ASN cc_start: 0.8279 (m-40) cc_final: 0.7790 (t0) REVERT: B 939 GLN cc_start: 0.7738 (tt0) cc_final: 0.7500 (tt0) REVERT: A 168 PHE cc_start: 0.4194 (OUTLIER) cc_final: 0.3429 (m-80) REVERT: A 733 ASN cc_start: 0.8344 (OUTLIER) cc_final: 0.7961 (m-40) REVERT: A 1112 ILE cc_start: 0.8710 (pp) cc_final: 0.8446 (mt) REVERT: C 46 ILE cc_start: 0.8174 (OUTLIER) cc_final: 0.7965 (mp) outliers start: 56 outliers final: 20 residues processed: 193 average time/residue: 1.0687 time to fit residues: 252.6847 Evaluate side-chains 164 residues out of total 2687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 140 time to evaluate : 3.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 626 ASN Chi-restraints excluded: chain B residue 904 GLN 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 515 LEU Chi-restraints excluded: chain A residue 600 ASP 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 985 SER Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 261 THR 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 248 optimal weight: 0.9990 chunk 169 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 222 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 254 optimal weight: 4.9990 chunk 206 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 152 optimal weight: 3.9990 chunk 268 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 181 HIS B 889 ASN A 883 GLN C 883 GLN ** C 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 25613 Z= 0.281 Angle : 0.591 11.375 34817 Z= 0.307 Chirality : 0.047 0.471 4034 Planarity : 0.004 0.049 4433 Dihedral : 6.849 77.586 4399 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.94 % Allowed : 10.01 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.15), residues: 3056 helix: 1.44 (0.21), residues: 717 sheet: 0.68 (0.19), residues: 683 loop : -1.81 (0.13), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 868 HIS 0.006 0.001 HIS B1046 PHE 0.027 0.001 PHE B 137 TYR 0.023 0.001 TYR A1049 ARG 0.005 0.000 ARG A 449 *********************** 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 200 residues out of total 2687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 148 time to evaluate : 2.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 ASP cc_start: 0.7883 (t0) cc_final: 0.7662 (t0) REVERT: B 155 ASN cc_start: 0.8256 (m-40) cc_final: 0.7774 (t0) REVERT: B 515 LEU cc_start: 0.7942 (mm) cc_final: 0.7665 (mm) REVERT: B 939 GLN cc_start: 0.7749 (tt0) cc_final: 0.7527 (tt0) REVERT: A 168 PHE cc_start: 0.4154 (OUTLIER) cc_final: 0.3312 (m-80) REVERT: A 733 ASN cc_start: 0.8341 (OUTLIER) cc_final: 0.7976 (m-40) REVERT: A 1112 ILE cc_start: 0.8766 (pp) cc_final: 0.8530 (mt) REVERT: C 46 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7985 (mp) REVERT: C 56 GLN cc_start: 0.7820 (OUTLIER) cc_final: 0.7311 (tm-30) REVERT: C 214 ASN cc_start: 0.7527 (t0) cc_final: 0.7276 (t0) outliers start: 52 outliers final: 26 residues processed: 191 average time/residue: 1.0437 time to fit residues: 243.4510 Evaluate side-chains 176 residues out of total 2687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 146 time to evaluate : 3.109 ------------------------------------------------------------------------------- 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 904 GLN 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 985 SER Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 CYS Chi-restraints excluded: chain C residue 561 SER Chi-restraints excluded: chain C residue 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 100 optimal weight: 0.9990 chunk 268 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 175 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 298 optimal weight: 0.5980 chunk 248 optimal weight: 0.6980 chunk 138 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 156 optimal weight: 0.3980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 181 HIS B 889 ASN A 883 GLN A 895 GLN C 883 GLN C 947 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25613 Z= 0.173 Angle : 0.541 12.194 34817 Z= 0.279 Chirality : 0.045 0.433 4034 Planarity : 0.004 0.048 4433 Dihedral : 6.509 78.605 4399 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.01 % Allowed : 10.76 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.15), residues: 3056 helix: 1.79 (0.21), residues: 700 sheet: 0.80 (0.20), residues: 673 loop : -1.71 (0.13), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 868 HIS 0.005 0.001 HIS B 181 PHE 0.027 0.001 PHE B 137 TYR 0.021 0.001 TYR A1049 ARG 0.005 0.000 ARG A 449 *********************** 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 220 residues out of total 2687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 166 time to evaluate : 2.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 ASP cc_start: 0.7786 (t0) cc_final: 0.7584 (t0) REVERT: B 155 ASN cc_start: 0.8268 (m-40) cc_final: 0.7755 (t0) REVERT: B 515 LEU cc_start: 0.7919 (mm) cc_final: 0.7640 (mm) REVERT: B 939 GLN cc_start: 0.7717 (tt0) cc_final: 0.7466 (tt0) REVERT: A 181 HIS cc_start: 0.6460 (OUTLIER) cc_final: 0.5950 (p90) REVERT: A 733 ASN cc_start: 0.8363 (OUTLIER) cc_final: 0.7885 (m-40) REVERT: A 1112 ILE cc_start: 0.8747 (pp) cc_final: 0.8543 (mt) REVERT: C 501 PHE cc_start: 0.8253 (m-10) cc_final: 0.8027 (m-10) REVERT: C 1097 ILE cc_start: 0.8807 (OUTLIER) cc_final: 0.8593 (mt) outliers start: 54 outliers final: 28 residues processed: 209 average time/residue: 1.0392 time to fit residues: 264.0487 Evaluate side-chains 181 residues out of total 2687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 150 time to evaluate : 2.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 524 CYS Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1100 ASP Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 727 ASP Chi-restraints excluded: chain A residue 733 ASN Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 376 ASP Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 CYS Chi-restraints excluded: chain C residue 561 SER Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain C residue 967 CYS Chi-restraints excluded: chain C residue 1047 VAL Chi-restraints excluded: chain C residue 1097 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 288 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 218 optimal weight: 4.9990 chunk 169 optimal weight: 0.3980 chunk 251 optimal weight: 0.5980 chunk 166 optimal weight: 3.9990 chunk 297 optimal weight: 0.7980 chunk 186 optimal weight: 0.0070 chunk 181 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- 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 C 937 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 25613 Z= 0.148 Angle : 0.533 13.399 34817 Z= 0.274 Chirality : 0.044 0.414 4034 Planarity : 0.004 0.048 4433 Dihedral : 6.284 78.944 4399 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.90 % Allowed : 11.72 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.15), residues: 3056 helix: 1.93 (0.21), residues: 702 sheet: 0.81 (0.20), residues: 673 loop : -1.63 (0.13), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 868 HIS 0.005 0.001 HIS B 181 PHE 0.030 0.001 PHE B 137 TYR 0.021 0.001 TYR A1049 ARG 0.006 0.000 ARG A 449 *********************** 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 209 residues out of total 2687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 158 time to evaluate : 2.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 155 ASN cc_start: 0.8212 (m-40) cc_final: 0.7710 (t0) REVERT: B 515 LEU cc_start: 0.7902 (mm) cc_final: 0.7624 (mm) REVERT: B 939 GLN cc_start: 0.7690 (tt0) cc_final: 0.7460 (tt0) REVERT: A 168 PHE cc_start: 0.4022 (OUTLIER) cc_final: 0.3205 (m-80) REVERT: A 181 HIS cc_start: 0.6363 (OUTLIER) cc_final: 0.5842 (p90) REVERT: A 644 THR cc_start: 0.8413 (p) cc_final: 0.8131 (t) REVERT: C 1097 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8513 (mt) outliers start: 51 outliers final: 29 residues processed: 195 average time/residue: 0.9837 time to fit residues: 235.7109 Evaluate side-chains 181 residues out of total 2687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 149 time to evaluate : 2.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 417 MET Chi-restraints excluded: chain B residue 882 MET Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 727 ASP Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 376 ASP Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 CYS Chi-restraints excluded: chain C residue 561 SER Chi-restraints excluded: chain C residue 819 TYR Chi-restraints excluded: chain C residue 967 CYS Chi-restraints excluded: chain C residue 1047 VAL Chi-restraints excluded: chain C residue 1097 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 184 optimal weight: 0.7980 chunk 118 optimal weight: 9.9990 chunk 177 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 189 optimal weight: 0.0370 chunk 202 optimal weight: 3.9990 chunk 147 optimal weight: 0.9980 chunk 27 optimal weight: 0.0060 chunk 234 optimal weight: 1.9990 overall best weight: 0.7676 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25613 Z= 0.178 Angle : 0.547 14.074 34817 Z= 0.281 Chirality : 0.045 0.412 4034 Planarity : 0.004 0.048 4433 Dihedral : 6.248 78.690 4399 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.60 % Allowed : 12.24 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.15), residues: 3056 helix: 1.95 (0.21), residues: 701 sheet: 0.81 (0.20), residues: 674 loop : -1.62 (0.13), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 868 HIS 0.005 0.001 HIS B 181 PHE 0.031 0.001 PHE B 137 TYR 0.021 0.001 TYR A1049 ARG 0.006 0.000 ARG A 449 *********************** 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 197 residues out of total 2687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 154 time to evaluate : 2.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 155 ASN cc_start: 0.8174 (m-40) cc_final: 0.7627 (t0) REVERT: B 515 LEU cc_start: 0.7900 (mm) cc_final: 0.7619 (mm) REVERT: B 939 GLN cc_start: 0.7704 (tt0) cc_final: 0.7469 (tt0) REVERT: A 168 PHE cc_start: 0.4024 (OUTLIER) cc_final: 0.3218 (m-80) REVERT: A 181 HIS cc_start: 0.6336 (OUTLIER) cc_final: 0.5796 (p90) REVERT: A 644 THR cc_start: 0.8407 (p) cc_final: 0.8130 (t) REVERT: A 733 ASN cc_start: 0.8365 (OUTLIER) cc_final: 0.7915 (m-40) REVERT: C 107 MET cc_start: 0.7841 (mmt) cc_final: 0.7640 (mmt) REVERT: C 1097 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8411 (mt) outliers start: 43 outliers final: 28 residues processed: 185 average time/residue: 1.0393 time to fit residues: 233.5300 Evaluate side-chains 179 residues out of total 2687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 147 time to evaluate : 2.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 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 882 MET Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 727 ASP Chi-restraints excluded: chain A residue 733 ASN Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 376 ASP Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 CYS Chi-restraints excluded: chain C residue 561 SER Chi-restraints excluded: chain C residue 967 CYS Chi-restraints excluded: chain C residue 1047 VAL Chi-restraints excluded: chain C residue 1097 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 270 optimal weight: 0.9980 chunk 285 optimal weight: 0.9980 chunk 260 optimal weight: 0.7980 chunk 277 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 217 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 250 optimal weight: 2.9990 chunk 262 optimal weight: 4.9990 chunk 276 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 818 GLN C 818 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25613 Z= 0.193 Angle : 0.553 14.570 34817 Z= 0.284 Chirality : 0.045 0.412 4034 Planarity : 0.004 0.048 4433 Dihedral : 6.242 78.590 4399 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.79 % Allowed : 12.36 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.15), residues: 3056 helix: 1.99 (0.21), residues: 693 sheet: 0.79 (0.20), residues: 674 loop : -1.59 (0.13), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 868 HIS 0.005 0.001 HIS B 181 PHE 0.032 0.001 PHE B 137 TYR 0.021 0.001 TYR A1049 ARG 0.006 0.000 ARG A 449 *********************** 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 202 residues out of total 2687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 154 time to evaluate : 3.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 155 ASN cc_start: 0.8218 (m-40) cc_final: 0.7680 (t0) REVERT: B 515 LEU cc_start: 0.7898 (mm) cc_final: 0.7623 (mm) REVERT: A 181 HIS cc_start: 0.6331 (OUTLIER) cc_final: 0.5727 (p90) REVERT: A 644 THR cc_start: 0.8401 (p) cc_final: 0.8124 (t) REVERT: A 733 ASN cc_start: 0.8369 (OUTLIER) cc_final: 0.7918 (m-40) REVERT: C 491 TYR cc_start: 0.7878 (m-80) cc_final: 0.7563 (m-80) REVERT: C 816 MET cc_start: 0.5487 (ppp) cc_final: 0.4720 (ppp) REVERT: C 882 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.8657 (mtp) outliers start: 48 outliers final: 29 residues processed: 190 average time/residue: 1.0304 time to fit residues: 240.8342 Evaluate side-chains 179 residues out of total 2687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 147 time to evaluate : 2.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 537 VAL 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 985 SER Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 376 ASP Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 CYS Chi-restraints excluded: chain C residue 561 SER Chi-restraints excluded: chain C residue 882 MET 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 182 optimal weight: 1.9990 chunk 293 optimal weight: 0.0970 chunk 179 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 204 optimal weight: 0.7980 chunk 307 optimal weight: 3.9990 chunk 283 optimal weight: 4.9990 chunk 245 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 189 optimal weight: 0.9980 chunk 150 optimal weight: 4.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25613 Z= 0.201 Angle : 0.561 17.378 34817 Z= 0.287 Chirality : 0.045 0.414 4034 Planarity : 0.004 0.048 4433 Dihedral : 6.250 78.501 4399 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.41 % Allowed : 12.77 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.15), residues: 3056 helix: 1.97 (0.21), residues: 693 sheet: 0.80 (0.20), residues: 672 loop : -1.58 (0.13), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 868 HIS 0.005 0.001 HIS B 181 PHE 0.033 0.001 PHE A 137 TYR 0.021 0.001 TYR A1049 ARG 0.006 0.000 ARG A 449 ********************** 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 192 residues out of total 2687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 154 time to evaluate : 2.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 155 ASN cc_start: 0.8220 (m-40) cc_final: 0.7676 (t0) REVERT: B 515 LEU cc_start: 0.7901 (mm) cc_final: 0.7634 (mm) REVERT: A 168 PHE cc_start: 0.4226 (OUTLIER) cc_final: 0.3326 (m-80) REVERT: A 181 HIS cc_start: 0.6333 (OUTLIER) cc_final: 0.5725 (p90) REVERT: A 733 ASN cc_start: 0.8366 (OUTLIER) cc_final: 0.7919 (m-40) REVERT: C 491 TYR cc_start: 0.7913 (m-80) cc_final: 0.7582 (m-80) REVERT: C 816 MET cc_start: 0.5322 (ppp) cc_final: 0.4583 (ppp) REVERT: C 882 MET cc_start: 0.8914 (OUTLIER) cc_final: 0.8660 (mtp) outliers start: 38 outliers final: 30 residues processed: 184 average time/residue: 1.0138 time to fit residues: 227.4655 Evaluate side-chains 185 residues out of total 2687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 151 time to evaluate : 2.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 727 ASP Chi-restraints excluded: chain A residue 733 ASN Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 376 ASP Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 CYS Chi-restraints excluded: chain C residue 561 SER Chi-restraints excluded: chain C residue 882 MET 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 194 optimal weight: 0.9990 chunk 261 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 226 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 245 optimal weight: 0.4980 chunk 102 optimal weight: 0.6980 chunk 252 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.124221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.088817 restraints weight = 37320.883| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.61 r_work: 0.2925 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25613 Z= 0.185 Angle : 0.554 16.122 34817 Z= 0.284 Chirality : 0.045 0.409 4034 Planarity : 0.004 0.048 4433 Dihedral : 6.216 78.651 4399 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.56 % Allowed : 12.80 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.15), residues: 3056 helix: 2.00 (0.21), residues: 693 sheet: 0.80 (0.20), residues: 674 loop : -1.57 (0.13), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 868 HIS 0.005 0.001 HIS B 181 PHE 0.032 0.001 PHE B 137 TYR 0.021 0.001 TYR A1049 ARG 0.006 0.000 ARG A 449 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6252.54 seconds wall clock time: 113 minutes 15.21 seconds (6795.21 seconds total)