Starting phenix.real_space_refine on Sun Jul 5 00:02:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zh2_14718/07_2026/7zh2_14718.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zh2_14718/07_2026/7zh2_14718.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zh2_14718/07_2026/7zh2_14718.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zh2_14718/07_2026/7zh2_14718.map" model { file = "/net/cci-nas-00/data/ceres_data/7zh2_14718/07_2026/7zh2_14718.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zh2_14718/07_2026/7zh2_14718.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7zh2_14718/07_2026/7zh2_14718.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zh2_14718/07_2026/7zh2_14718.cif" } resolution = 2.71 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.012 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 132 5.16 5 C 15597 2.51 5 N 3986 2.21 5 O 4704 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24419 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 7969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 7969 Classifications: {'peptide': 1020} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 48, 'TRANS': 971} Chain breaks: 6 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 7969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 7969 Classifications: {'peptide': 1020} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 48, 'TRANS': 971} Chain breaks: 6 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 7959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 7959 Classifications: {'peptide': 1020} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 48, 'TRANS': 971} Chain breaks: 6 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 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 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 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 chiralities: 2 Chain: "A" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 146 Unusual residues: {'EIC': 1, 'NAG': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 146 Unusual residues: {'EIC': 1, 'NAG': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 146 Unusual residues: {'EIC': 1, 'NAG': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 5.20, per 1000 atoms: 0.21 Number of scatterers: 24419 At special positions: 0 Unit cell: (131.25, 143.85, 158.55, 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 132 16.00 O 4704 8.00 N 3986 7.00 C 15597 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A 366 " - pdb=" SG CYS A 419 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 511 " distance=2.03 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=2.03 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 725 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS A 822 " - pdb=" SG CYS A 833 " distance=2.04 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 159 " distance=2.03 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=2.03 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=2.03 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=2.03 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 B1014 " - pdb=" SG CYS B1025 " 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=2.03 Simple disulfide: pdb=" SG CYS C 366 " - pdb=" SG CYS C 419 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 511 " distance=2.03 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=2.03 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 725 " - pdb=" SG CYS C 731 " distance=2.03 Simple disulfide: pdb=" SG CYS C 822 " - pdb=" SG CYS C 833 " distance=2.04 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1302 " - " ASN A 109 " " NAG A1303 " - " ASN A 119 " " NAG A1304 " - " ASN A 158 " " NAG A1305 " - " ASN A 269 " " NAG A1306 " - " ASN A 318 " " NAG A1307 " - " ASN A 357 " " NAG A1308 " - " ASN A 602 " " NAG A1309 " - " ASN A 783 " " NAG A1310 " - " ASN A 699 " " NAG B1302 " - " ASN B 109 " " NAG B1303 " - " ASN B 119 " " NAG B1304 " - " ASN B 158 " " NAG B1305 " - " ASN B 269 " " NAG B1306 " - " ASN B 318 " " NAG B1307 " - " ASN B 357 " " NAG B1308 " - " ASN B 602 " " NAG B1309 " - " ASN B 783 " " NAG B1310 " - " ASN B 699 " " NAG C1302 " - " ASN C 109 " " NAG C1303 " - " ASN C 119 " " NAG C1304 " - " ASN C 158 " " NAG C1305 " - " ASN C 269 " " NAG C1306 " - " ASN C 318 " " NAG C1307 " - " ASN C 357 " " NAG C1308 " - " ASN C 602 " " NAG C1309 " - " ASN C 783 " " NAG C1310 " - " ASN C 699 " " NAG D 1 " - " ASN A 227 " " NAG E 1 " - " ASN B 227 " " NAG F 1 " - " ASN C 227 " Time building additional restraints: 1.84 Conformation dependent library (CDL) restraints added in 1.1 seconds 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5748 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 47 sheets defined 26.1% alpha, 32.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 354 through 359 removed outlier: 4.228A pdb=" N SER A 358 " --> pdb=" O VAL A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 376 removed outlier: 3.917A pdb=" N LEU A 374 " --> pdb=" O ALA A 371 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ASN A 375 " --> pdb=" O THR A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 397 removed outlier: 4.365A 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 Processing helix chain 'A' and resid 488 through 491 Processing helix chain 'A' and resid 719 through 724 Processing helix chain 'A' and resid 728 through 738 Processing helix chain 'A' and resid 741 through 765 removed outlier: 3.908A pdb=" N LEU A 745 " --> pdb=" O PHE A 741 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 808 removed outlier: 3.553A pdb=" N ASN A 806 " --> pdb=" O ASP A 802 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS A 807 " --> pdb=" O LEU A 803 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL A 808 " --> pdb=" O LEU A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 825 Processing helix chain 'A' and resid 830 through 838 removed outlier: 3.604A pdb=" N ALA A 834 " --> pdb=" O ASP A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 865 Processing helix chain 'A' and resid 882 through 891 Processing helix chain 'A' and resid 895 through 901 removed outlier: 3.667A pdb=" N TYR A 899 " --> pdb=" O GLN A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 922 Processing helix chain 'A' and resid 927 through 947 removed outlier: 3.555A pdb=" N LEU A 941 " --> pdb=" O ASN A 937 " (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: 3.704A pdb=" N ARG A 965 " --> pdb=" O ASP A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 1015 removed outlier: 3.544A pdb=" N VAL A 973 " --> pdb=" O VAL A 969 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN A 974 " --> pdb=" O GLU A 970 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 324 through 330 Processing helix chain 'B' and resid 353 through 357 Processing helix chain 'B' and resid 370 through 376 removed outlier: 3.864A pdb=" N LEU B 374 " --> pdb=" O ALA B 371 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ASN B 375 " --> pdb=" O THR B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 397 removed outlier: 4.209A 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 425 through 430 Processing helix chain 'B' and resid 488 through 491 Processing helix chain 'B' and resid 719 through 724 Processing helix chain 'B' and resid 728 through 739 Processing helix chain 'B' and resid 741 through 765 removed outlier: 3.737A pdb=" N ASP B 757 " --> pdb=" O ALA B 753 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 763 " --> pdb=" O ASN B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 808 removed outlier: 3.734A pdb=" N VAL B 808 " --> pdb=" O LEU B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 825 Processing helix chain 'B' and resid 830 through 838 removed outlier: 3.510A pdb=" N ALA B 834 " --> pdb=" O ASP B 830 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 865 Processing helix chain 'B' and resid 881 through 891 Processing helix chain 'B' and resid 894 through 901 removed outlier: 4.218A pdb=" N LEU B 898 " --> pdb=" O THR B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 922 removed outlier: 3.558A pdb=" N THR B 922 " --> pdb=" O GLU B 918 " (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: 3.508A pdb=" N VAL B 934 " --> pdb=" O LEU B 930 " (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 966 removed outlier: 3.679A pdb=" N ARG B 965 " --> pdb=" O ASP B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 1015 removed outlier: 3.587A pdb=" N VAL B 973 " --> pdb=" O VAL B 969 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN B 974 " --> pdb=" O GLU B 970 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG B 977 " --> pdb=" O VAL B 973 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU B 999 " --> pdb=" O ILE B 995 " (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 354 through 359 removed outlier: 4.505A pdb=" N SER C 358 " --> pdb=" O VAL C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 374 removed outlier: 3.883A pdb=" N LEU C 374 " --> pdb=" O ALA C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 397 removed outlier: 4.507A pdb=" N ARG C 395 " --> pdb=" O ASP C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 409 Processing helix chain 'C' and resid 425 through 430 Processing helix chain 'C' and resid 488 through 491 Processing helix chain 'C' and resid 719 through 724 Processing helix chain 'C' and resid 728 through 739 Processing helix chain 'C' and resid 741 through 765 removed outlier: 3.658A pdb=" N LEU C 745 " --> pdb=" O PHE C 741 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP C 757 " --> pdb=" O ALA C 753 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL C 763 " --> pdb=" O ASN C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 808 removed outlier: 3.528A pdb=" N LEU C 803 " --> pdb=" O PHE C 799 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL C 808 " --> pdb=" O LEU C 804 " (cutoff:3.500A) Processing helix chain 'C' and resid 818 through 825 removed outlier: 3.542A pdb=" N CYS C 822 " --> pdb=" O GLN C 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 830 through 837 Processing helix chain 'C' and resid 848 through 864 Processing helix chain 'C' and resid 881 through 892 removed outlier: 3.506A pdb=" N GLY C 890 " --> pdb=" O TYR C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 901 removed outlier: 4.254A pdb=" N LEU C 898 " --> pdb=" O THR C 894 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR C 899 " --> pdb=" O GLN C 895 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 922 removed outlier: 3.628A pdb=" N SER C 919 " --> pdb=" O GLN C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 927 through 947 removed outlier: 3.533A pdb=" N VAL C 934 " --> pdb=" O LEU C 930 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL C 945 " --> pdb=" O LEU C 941 " (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 966 removed outlier: 3.584A pdb=" N ARG C 965 " --> pdb=" O ASP C 961 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 1015 removed outlier: 3.823A pdb=" N VAL C 973 " --> pdb=" O VAL C 969 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN C 974 " --> pdb=" O GLU C 970 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 1098 through 1102 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 35 removed outlier: 3.674A pdb=" N SER A 64 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ASN A 65 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N TYR A 256 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU A 194 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LYS A 221 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL A 196 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N TYR A 200 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N THR A 215 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N VAL A 40 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 59 removed outlier: 4.069A pdb=" N ASP A 274 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 81 through 82 removed outlier: 6.999A pdb=" N ASN A 230 " --> pdb=" O PHE A 103 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N PHE A 103 " --> pdb=" O ASN A 230 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ARG A 232 " --> pdb=" O TRP A 101 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TRP A 101 " --> pdb=" O ARG A 232 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE A 234 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ARG A 99 " --> pdb=" O ASN A 118 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA A 127 " --> pdb=" O PHE A 161 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N PHE A 161 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ASN A 129 " --> pdb=" O CYS A 159 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N CYS A 159 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N GLU A 131 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 9.854A pdb=" N PHE A 157 " --> pdb=" O GLU A 131 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N CYS A 133 " --> pdb=" O ASN A 155 " (cutoff:3.500A) removed outlier: 10.923A pdb=" N ASN A 155 " --> pdb=" O CYS A 133 " (cutoff:3.500A) removed outlier: 10.440A pdb=" N ASN A 135 " --> pdb=" O PHE A 153 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N PHE A 153 " --> pdb=" O ASN A 135 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 298 through 301 Processing sheet with id=AA5, first strand: chain 'A' and resid 312 through 315 removed outlier: 5.092A pdb=" N ASP A 560 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER A 561 " --> pdb=" O GLY A 552 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 341 through 344 removed outlier: 3.649A pdb=" N GLU A 341 " --> pdb=" O SER A 386 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N CYS A 348 " --> pdb=" O CYS A 511 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 341 through 344 removed outlier: 3.649A pdb=" N GLU A 341 " --> pdb=" O SER A 386 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ASN A 381 " --> pdb=" O GLU A 502 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLU A 502 " --> pdb=" O ASN A 381 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 439 through 441 Processing sheet with id=AA9, first strand: chain 'A' and resid 640 through 641 removed outlier: 6.272A pdb=" N GLU A 640 " --> pdb=" O ALA A 676 " (cutoff:3.500A) removed outlier: 8.529A pdb=" N THR A 678 " --> pdb=" O GLU A 640 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 683 through 685 removed outlier: 6.509A pdb=" N ALA A 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 'A' and resid 693 through 710 removed outlier: 6.785A pdb=" N THR A 693 " --> pdb=" O THR A1058 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N THR A1058 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ALA A 695 " --> pdb=" O ASN A1056 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ASN A1056 " --> pdb=" O ALA A 695 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLU A1054 " --> pdb=" O PRO A 697 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET A1032 " --> pdb=" O VAL A1047 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N TYR A1049 " --> pdb=" O HIS A1030 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N HIS A1030 " --> pdb=" O TYR A1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 693 through 710 removed outlier: 6.785A pdb=" N THR A 693 " --> pdb=" O THR A1058 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N THR A1058 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ALA A 695 " --> pdb=" O ASN A1056 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ASN A1056 " --> pdb=" O ALA A 695 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLU A1054 " --> pdb=" O PRO A 697 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR A1058 " --> pdb=" O PHE A1079 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA A1060 " --> pdb=" O PHE A1077 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N PHE A1077 " --> pdb=" O ALA A1060 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 715 through 718 removed outlier: 4.693A pdb=" N LYS A 715 " --> pdb=" O LEU A 843 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 769 through 771 Processing sheet with id=AB6, first strand: chain 'A' and resid 778 through 779 Processing sheet with id=AB7, first strand: chain 'A' and resid 1070 through 1071 removed outlier: 3.546A pdb=" N PHE A1103 " --> pdb=" O PHE A1071 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 31 through 35 removed outlier: 3.665A pdb=" N THR B 31 " --> pdb=" O GLY B 68 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER B 64 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA B 251 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N HIS B 181 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N LEU B 194 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LYS B 221 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL B 196 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N TYR B 200 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N THR B 215 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N VAL B 40 " --> pdb=" O LEU B 216 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 51 through 59 removed outlier: 4.080A pdb=" N ASP B 274 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 81 through 82 removed outlier: 6.922A pdb=" N ASN B 230 " --> pdb=" O PHE B 103 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N PHE B 103 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ARG B 232 " --> pdb=" O TRP B 101 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N TRP B 101 " --> pdb=" O ARG B 232 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE B 234 " --> pdb=" O ARG B 99 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ARG B 99 " --> pdb=" O ASN B 118 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL B 123 " --> pdb=" O TYR B 163 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N TYR B 163 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ILE B 125 " --> pdb=" O PHE B 161 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N PHE B 161 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ALA B 127 " --> pdb=" O CYS B 159 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N CYS B 159 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE B 157 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ASN B 155 " --> pdb=" O GLU B 131 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N CYS B 133 " --> pdb=" O PHE B 153 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N PHE B 153 " --> pdb=" O CYS B 133 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ASN B 135 " --> pdb=" O MET B 151 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N MET B 151 " --> pdb=" O ASN B 135 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 81 through 82 removed outlier: 13.520A pdb=" N PHE B 231 " --> pdb=" O PHE B 130 " (cutoff:3.500A) removed outlier: 13.168A pdb=" N LEU B 132 " --> pdb=" O PHE B 231 " (cutoff:3.500A) removed outlier: 12.567A pdb=" N ALA B 233 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 10.062A pdb=" N ASP B 134 " --> pdb=" O ALA B 233 " (cutoff:3.500A) removed outlier: 10.091A pdb=" N LEU B 235 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ALA B 237 " --> pdb=" O PRO B 136 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N PHE B 138 " --> pdb=" O ALA B 237 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL B 123 " --> pdb=" O TYR B 163 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N TYR B 163 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ILE B 125 " --> pdb=" O PHE B 161 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N PHE B 161 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ALA B 127 " --> pdb=" O CYS B 159 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N CYS B 159 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE B 157 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ASN B 155 " --> pdb=" O GLU B 131 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N CYS B 133 " --> pdb=" O PHE B 153 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N PHE B 153 " --> pdb=" O CYS B 133 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ASN B 135 " --> pdb=" O MET B 151 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N MET B 151 " --> pdb=" O ASN B 135 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 298 through 302 removed outlier: 4.791A pdb=" N VAL B 581 " --> pdb=" O THR B 302 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU B 636 " --> pdb=" O PHE B 629 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 312 through 315 removed outlier: 5.024A pdb=" N ASP B 560 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER B 561 " --> pdb=" O GLY B 552 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 341 through 344 removed outlier: 3.686A pdb=" N GLU B 341 " --> pdb=" O SER B 386 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N CYS B 348 " --> pdb=" O CYS B 511 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 341 through 344 removed outlier: 3.686A pdb=" N GLU B 341 " --> pdb=" O SER B 386 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N VAL B 382 " --> pdb=" O SER B 500 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N SER B 500 " --> pdb=" O VAL B 382 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ALA B 384 " --> pdb=" O VAL B 498 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL B 498 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N SER B 386 " --> pdb=" O VAL B 496 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL B 496 " --> pdb=" O SER B 386 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N VAL B 388 " --> pdb=" O TYR B 494 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N TYR B 494 " --> pdb=" O VAL B 388 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 439 through 441 Processing sheet with id=AC8, first strand: chain 'B' and resid 640 through 641 removed outlier: 6.305A pdb=" N GLU B 640 " --> pdb=" O ALA B 676 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N THR B 678 " --> pdb=" O GLU B 640 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE B 656 " --> pdb=" O ILE B 652 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 693 through 710 removed outlier: 6.666A pdb=" N THR B 693 " --> pdb=" O THR B1058 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N THR B1058 " --> pdb=" O THR B 693 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ALA B 695 " --> pdb=" O ASN B1056 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ASN B1056 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N GLU B1054 " --> pdb=" O PRO B 697 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET B1032 " --> pdb=" O VAL B1047 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N TYR B1049 " --> pdb=" O HIS B1030 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N HIS B1030 " --> pdb=" O TYR B1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 715 through 718 removed outlier: 4.590A pdb=" N LYS B 715 " --> pdb=" O LEU B 843 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 769 through 771 Processing sheet with id=AD3, first strand: chain 'B' and resid 778 through 779 Processing sheet with id=AD4, first strand: chain 'B' and resid 1070 through 1071 Processing sheet with id=AD5, first strand: chain 'B' and resid 1076 through 1079 Processing sheet with id=AD6, first strand: chain 'C' and resid 31 through 35 removed outlier: 3.925A pdb=" N THR C 31 " --> pdb=" O GLY C 68 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER C 64 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ASN C 65 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N TYR C 256 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N HIS C 181 " --> pdb=" O GLU C 93 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N LEU C 194 " --> pdb=" O LYS C 221 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LYS C 221 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL C 196 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N TYR C 200 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N THR C 215 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL C 40 " --> pdb=" O LEU C 216 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 51 through 59 removed outlier: 4.129A pdb=" N ASP C 274 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 81 through 82 removed outlier: 3.682A pdb=" N GLY C 100 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ARG C 99 " --> pdb=" O ASN C 118 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N GLU C 131 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 9.896A pdb=" N PHE C 157 " --> pdb=" O GLU C 131 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N CYS C 133 " --> pdb=" O ASN C 155 " (cutoff:3.500A) removed outlier: 10.908A pdb=" N ASN C 155 " --> pdb=" O CYS C 133 " (cutoff:3.500A) removed outlier: 10.494A pdb=" N ASN C 135 " --> pdb=" O PHE C 153 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N PHE C 153 " --> pdb=" O ASN C 135 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 81 through 82 removed outlier: 3.682A pdb=" N GLY C 100 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ARG C 99 " --> pdb=" O ASN C 118 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 298 through 302 removed outlier: 4.591A pdb=" N VAL C 581 " --> pdb=" O THR C 302 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 312 through 315 removed outlier: 5.189A pdb=" N ASP C 560 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER C 561 " --> pdb=" O GLY C 552 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 341 through 344 removed outlier: 3.664A pdb=" N GLU C 341 " --> pdb=" O SER C 386 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N CYS C 348 " --> pdb=" O CYS C 511 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 341 through 344 removed outlier: 3.664A pdb=" N GLU C 341 " --> pdb=" O SER C 386 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N ASN C 381 " --> pdb=" O GLU C 502 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N GLU C 502 " --> pdb=" O ASN C 381 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 439 through 441 Processing sheet with id=AE6, first strand: chain 'C' and resid 640 through 641 removed outlier: 6.466A pdb=" N ILE C 656 " --> pdb=" O ILE C 652 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 693 through 710 removed outlier: 6.636A pdb=" N THR C 693 " --> pdb=" O THR C1058 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR C1058 " --> pdb=" O THR C 693 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ALA C 695 " --> pdb=" O ASN C1056 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ASN C1056 " --> pdb=" O ALA C 695 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N GLU C1054 " --> pdb=" O PRO C 697 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N MET C1032 " --> pdb=" O VAL C1047 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N TYR C1049 " --> pdb=" O HIS C1030 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N HIS C1030 " --> pdb=" O TYR C1049 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 693 through 710 removed outlier: 6.636A pdb=" N THR C 693 " --> pdb=" O THR C1058 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR C1058 " --> pdb=" O THR C 693 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ALA C 695 " --> pdb=" O ASN C1056 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ASN C1056 " --> pdb=" O ALA C 695 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N GLU C1054 " --> pdb=" O PRO C 697 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N THR C1058 " --> pdb=" O PHE C1079 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 715 through 718 removed outlier: 4.565A pdb=" N LYS C 715 " --> pdb=" O LEU C 843 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 778 through 779 Processing sheet with id=AF2, first strand: chain 'C' and resid 1069 through 1071 removed outlier: 4.147A pdb=" N ALA C1069 " --> pdb=" O SER C1105 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE C1103 " --> pdb=" O PHE C1071 " (cutoff:3.500A) 1032 hydrogen bonds defined for protein. 2856 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.96 Time building geometry restraints manager: 2.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6006 1.33 - 1.46: 6550 1.46 - 1.58: 12235 1.58 - 1.71: 0 1.71 - 1.84: 180 Bond restraints: 24971 Sorted by residual: bond pdb=" N GLN C 786 " pdb=" CA GLN C 786 " ideal model delta sigma weight residual 1.457 1.506 -0.049 1.29e-02 6.01e+03 1.42e+01 bond pdb=" N ILE C 787 " pdb=" CA ILE C 787 " ideal model delta sigma weight residual 1.455 1.494 -0.038 1.04e-02 9.25e+03 1.36e+01 bond pdb=" N ILE C 81 " pdb=" CA ILE C 81 " ideal model delta sigma weight residual 1.460 1.494 -0.034 9.30e-03 1.16e+04 1.32e+01 bond pdb=" N ALA A 881 " pdb=" CA ALA A 881 " ideal model delta sigma weight residual 1.457 1.500 -0.042 1.29e-02 6.01e+03 1.08e+01 bond pdb=" N CYS A 159 " pdb=" CA CYS A 159 " ideal model delta sigma weight residual 1.454 1.497 -0.042 1.31e-02 5.83e+03 1.05e+01 ... (remaining 24966 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 33488 2.41 - 4.82: 400 4.82 - 7.23: 40 7.23 - 9.64: 3 9.64 - 12.05: 2 Bond angle restraints: 33933 Sorted by residual: angle pdb=" C PHE A 880 " pdb=" N ALA A 881 " pdb=" CA ALA A 881 " ideal model delta sigma weight residual 121.54 133.59 -12.05 1.91e+00 2.74e-01 3.98e+01 angle pdb=" CA PHE A 880 " pdb=" C PHE A 880 " pdb=" O PHE A 880 " ideal model delta sigma weight residual 121.16 114.28 6.88 1.12e+00 7.97e-01 3.78e+01 angle pdb=" C SER C 785 " pdb=" N GLN C 786 " pdb=" CA GLN C 786 " ideal model delta sigma weight residual 121.54 133.21 -11.67 1.91e+00 2.74e-01 3.73e+01 angle pdb=" C ASN A 158 " pdb=" CA ASN A 158 " pdb=" CB ASN A 158 " ideal model delta sigma weight residual 111.86 119.38 -7.52 1.34e+00 5.57e-01 3.15e+01 angle pdb=" CA SER C 785 " pdb=" C SER C 785 " pdb=" O SER C 785 " ideal model delta sigma weight residual 121.16 114.88 6.28 1.12e+00 7.97e-01 3.14e+01 ... (remaining 33928 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 13414 17.96 - 35.91: 968 35.91 - 53.87: 150 53.87 - 71.83: 41 71.83 - 89.78: 23 Dihedral angle restraints: 14596 sinusoidal: 5665 harmonic: 8931 Sorted by residual: dihedral pdb=" CA THR C 468 " pdb=" C THR C 468 " pdb=" N PRO C 469 " pdb=" CA PRO C 469 " ideal model delta harmonic sigma weight residual 180.00 -158.44 -21.56 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA THR B 468 " pdb=" C THR B 468 " pdb=" N PRO B 469 " pdb=" CA PRO B 469 " ideal model delta harmonic sigma weight residual 180.00 -159.92 -20.08 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CB CYS C 725 " pdb=" SG CYS C 725 " pdb=" SG CYS C 731 " pdb=" CB CYS C 731 " ideal model delta sinusoidal sigma weight residual -86.00 -53.86 -32.14 1 1.00e+01 1.00e-02 1.47e+01 ... (remaining 14593 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 3151 0.048 - 0.096: 485 0.096 - 0.145: 265 0.145 - 0.193: 9 0.193 - 0.241: 7 Chirality restraints: 3917 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 2.55e+00 chirality pdb=" CA ILE A 878 " pdb=" N ILE A 878 " pdb=" C ILE A 878 " pdb=" CB ILE A 878 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.38 -0.02 2.00e-02 2.50e+03 1.43e+00 ... (remaining 3914 not shown) Planarity restraints: 4382 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 158 " 0.049 2.00e-02 2.50e+03 4.71e-02 2.78e+01 pdb=" CG ASN A 158 " -0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN A 158 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 158 " -0.066 2.00e-02 2.50e+03 pdb=" C1 NAG A1304 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 158 " -0.043 2.00e-02 2.50e+03 4.57e-02 2.61e+01 pdb=" CG ASN C 158 " 0.018 2.00e-02 2.50e+03 pdb=" OD1 ASN C 158 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN C 158 " 0.073 2.00e-02 2.50e+03 pdb=" C1 NAG C1304 " -0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A1093 " 0.072 5.00e-02 4.00e+02 1.06e-01 1.81e+01 pdb=" N PRO A1094 " -0.184 5.00e-02 4.00e+02 pdb=" CA PRO A1094 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO A1094 " 0.057 5.00e-02 4.00e+02 ... (remaining 4379 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 129 2.61 - 3.18: 20288 3.18 - 3.76: 33875 3.76 - 4.33: 50875 4.33 - 4.90: 84404 Nonbonded interactions: 189571 Sorted by model distance: nonbonded pdb=" O ASN C 119 " pdb=" OG SER C 120 " model vdw 2.038 3.040 nonbonded pdb=" O ASN A 119 " pdb=" OG SER A 120 " model vdw 2.042 3.040 nonbonded pdb=" OG1 THR B 106 " pdb=" OD1 ASN B 108 " model vdw 2.216 3.040 nonbonded pdb=" O PRO B 462 " pdb=" NZ LYS B 465 " model vdw 2.271 3.120 nonbonded pdb=" OH TYR C 436 " pdb=" OH TYR C 484 " model vdw 2.278 3.040 ... (remaining 189566 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 30 through 864 or (resid 865 through 875 and (name N or na \ me CA or name C or name O or name CB )) or resid 876 through 899 or (resid 900 a \ nd (name N or name CA or name C or name O or name CB )) or resid 901 through 106 \ 7 or (resid 1068 through 1069 and (name N or name CA or name C or name O or name \ CB )) or resid 1070 through 1310)) selection = (chain 'B' and (resid 30 through 864 or (resid 865 through 875 and (name N or na \ me CA or name C or name O or name CB )) or resid 876 through 899 or (resid 900 a \ nd (name N or name CA or name C or name O or name CB )) or resid 901 through 106 \ 7 or (resid 1068 through 1069 and (name N or name CA or name C or name O or name \ CB )) or resid 1070 through 1310)) selection = chain 'C' } 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=1.00 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 23.560 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 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 : 0.003 0.095 25040 Z= 0.205 Angle : 0.630 12.049 34104 Z= 0.362 Chirality : 0.045 0.241 3917 Planarity : 0.004 0.106 4352 Dihedral : 13.208 89.781 8740 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.28 % Favored : 96.62 % Rotamer: Outliers : 0.30 % Allowed : 0.30 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.14), residues: 3018 helix: 0.51 (0.20), residues: 684 sheet: 0.70 (0.20), residues: 627 loop : -1.53 (0.13), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 495 TYR 0.009 0.001 TYR C 491 PHE 0.027 0.001 PHE A 334 TRP 0.008 0.001 TRP B 423 HIS 0.007 0.001 HIS A1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.20 (24971) covalent geometry : angle 0.62221 / 0.36 (33933) SS BOND : bond 0.00280 / 0.17 ( 36) SS BOND : angle 0.91755 / 0.67 ( 72) hydrogen bonds : bond 0.25617 / 16.78 ( 977) hydrogen bonds : angle 8.31679 / 5.73 ( 2856) link_BETA1-4 : bond 0.00151 / 0.07 ( 3) link_BETA1-4 : angle 1.07238 / 0.64 ( 9) link_NAG-ASN : bond 0.02330 / 1.36 ( 30) link_NAG-ASN : angle 1.92051 / 1.35 ( 90) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 343 time to evaluate : 0.889 Fit side-chains revert: symmetry clash REVERT: A 713 MET cc_start: 0.8644 (ptm) cc_final: 0.8203 (ptm) REVERT: A 1058 THR cc_start: 0.7318 (m) cc_final: 0.6923 (p) REVERT: A 1103 PHE cc_start: 0.6377 (p90) cc_final: 0.5884 (p90) REVERT: B 484 TYR cc_start: 0.7637 (m-80) cc_final: 0.7388 (m-80) REVERT: B 758 ARG cc_start: 0.7574 (ttm170) cc_final: 0.7195 (ttp80) REVERT: B 790 ASP cc_start: 0.6752 (t0) cc_final: 0.6065 (t70) REVERT: B 884 MET cc_start: 0.7678 (tpt) cc_final: 0.7226 (tpt) REVERT: B 1079 PHE cc_start: 0.6356 (t80) cc_final: 0.5602 (t80) REVERT: C 32 GLN cc_start: 0.7308 (mm110) cc_final: 0.7094 (mm110) outliers start: 8 outliers final: 4 residues processed: 346 average time/residue: 0.7066 time to fit residues: 277.5529 Evaluate side-chains 257 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 253 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 878 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 917 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.0770 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 8.9990 overall best weight: 2.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 435 ASN A 479 ASN A 627 ASN A 766 GLN A 877 GLN A 889 ASN A 908 GLN A 936 GLN A1088 GLN B 70 HIS B 321 ASN B 479 ASN B 769 GLN B 827 ASN B 883 GLN B 889 ASN B 992 GLN C 546 GLN C 769 GLN C 786 GLN C 883 GLN ** C 901 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 917 GLN C 992 GLN C1088 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.131402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.104287 restraints weight = 28448.863| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.63 r_work: 0.2927 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25040 Z= 0.162 Angle : 0.627 7.826 34104 Z= 0.341 Chirality : 0.047 0.225 3917 Planarity : 0.005 0.067 4352 Dihedral : 6.153 77.972 3341 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.31 % Favored : 95.63 % Rotamer: Outliers : 2.12 % Allowed : 5.83 % Favored : 92.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.14), residues: 3018 helix: 1.32 (0.20), residues: 708 sheet: 0.89 (0.21), residues: 567 loop : -1.50 (0.13), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 426 TYR 0.023 0.002 TYR B 352 PHE 0.035 0.002 PHE A 334 TRP 0.014 0.001 TRP B 423 HIS 0.008 0.002 HIS A1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (24971) covalent geometry : angle 0.61688 / 0.34 (33933) SS BOND : bond 0.00537 / 0.32 ( 36) SS BOND : angle 1.58340 / 1.08 ( 72) hydrogen bonds : bond 0.07758 / 5.01 ( 977) hydrogen bonds : angle 5.94195 / 4.11 ( 2856) link_BETA1-4 : bond 0.00493 / 0.25 ( 3) link_BETA1-4 : angle 1.42405 / 0.83 ( 9) link_NAG-ASN : bond 0.00344 / 0.20 ( 30) link_NAG-ASN : angle 1.75005 / 1.24 ( 90) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 269 time to evaluate : 0.768 Fit side-chains revert: symmetry clash REVERT: A 319 ILE cc_start: 0.8400 (OUTLIER) cc_final: 0.8185 (mp) REVERT: A 359 THR cc_start: 0.7414 (m) cc_final: 0.7201 (t) REVERT: A 449 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.8428 (mtt90) REVERT: A 544 ARG cc_start: 0.7362 (OUTLIER) cc_final: 0.7149 (mtp85) REVERT: A 713 MET cc_start: 0.8791 (ptm) cc_final: 0.8521 (ptm) REVERT: A 911 LYS cc_start: 0.7718 (ttpp) cc_final: 0.7068 (mppt) REVERT: A 1054 GLU cc_start: 0.7027 (OUTLIER) cc_final: 0.6680 (pm20) REVERT: A 1103 PHE cc_start: 0.5956 (p90) cc_final: 0.5339 (p90) REVERT: B 306 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7183 (mtt90) REVERT: B 484 TYR cc_start: 0.7877 (m-80) cc_final: 0.7633 (m-80) REVERT: B 758 ARG cc_start: 0.8289 (ttm170) cc_final: 0.7914 (ttp80) REVERT: B 762 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8240 (mt-10) REVERT: B 790 ASP cc_start: 0.6989 (t0) cc_final: 0.6346 (t70) REVERT: B 884 MET cc_start: 0.8095 (tpt) cc_final: 0.7818 (tpt) REVERT: C 32 GLN cc_start: 0.7621 (mm110) cc_final: 0.7358 (mm110) REVERT: C 54 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8346 (tp) REVERT: C 449 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.7723 (mtp180) REVERT: C 687 ILE cc_start: 0.6870 (OUTLIER) cc_final: 0.6638 (mm) REVERT: C 736 LEU cc_start: 0.7399 (tp) cc_final: 0.7177 (tp) REVERT: C 786 GLN cc_start: 0.7180 (mt0) cc_final: 0.6932 (mt0) REVERT: C 809 THR cc_start: 0.7407 (m) cc_final: 0.6761 (p) REVERT: C 882 MET cc_start: 0.7518 (mtp) cc_final: 0.7315 (mtm) REVERT: C 911 LYS cc_start: 0.8022 (OUTLIER) cc_final: 0.7483 (tmtt) outliers start: 56 outliers final: 25 residues processed: 298 average time/residue: 0.6879 time to fit residues: 233.6459 Evaluate side-chains 283 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 248 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 449 ARG Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 544 ARG Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 679 MET Chi-restraints excluded: chain A residue 769 GLN Chi-restraints excluded: chain A residue 894 THR Chi-restraints excluded: chain A residue 939 GLN Chi-restraints excluded: chain A residue 1054 GLU Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 306 ARG Chi-restraints excluded: chain B residue 762 GLU Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 904 GLN Chi-restraints excluded: chain B residue 911 LYS Chi-restraints excluded: chain B residue 972 GLU Chi-restraints excluded: chain B residue 1086 ILE Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 647 GLU Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 911 LYS Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain C residue 1080 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 87 optimal weight: 8.9990 chunk 120 optimal weight: 9.9990 chunk 185 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 183 optimal weight: 10.0000 chunk 281 optimal weight: 5.9990 chunk 112 optimal weight: 20.0000 chunk 134 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 chunk 67 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 523 GLN A 889 ASN A 908 GLN B 70 HIS B 827 ASN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 ASN B 992 GLN C 74 HIS C 96 ASN C 201 GLN C 301 GLN C 479 ASN C 546 GLN C 737 GLN C 769 GLN C 901 ASN C 917 GLN C1065 HIS C1095 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.128542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.101235 restraints weight = 28519.559| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.64 r_work: 0.2897 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 25040 Z= 0.250 Angle : 0.776 14.900 34104 Z= 0.420 Chirality : 0.053 0.309 3917 Planarity : 0.006 0.056 4352 Dihedral : 6.595 67.047 3336 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.17 % Favored : 94.76 % Rotamer: Outliers : 2.92 % Allowed : 7.92 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.14), residues: 3018 helix: 0.86 (0.19), residues: 741 sheet: 0.74 (0.21), residues: 564 loop : -1.65 (0.12), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 48 TYR 0.024 0.003 TYR A 367 PHE 0.033 0.003 PHE A 334 TRP 0.017 0.002 TRP B 423 HIS 0.010 0.003 HIS C1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00581 / 0.25 (24971) covalent geometry : angle 0.76142 / 0.42 (33933) SS BOND : bond 0.00811 / 0.47 ( 36) SS BOND : angle 2.38446 / 1.73 ( 72) hydrogen bonds : bond 0.09280 / 6.00 ( 977) hydrogen bonds : angle 6.00454 / 4.15 ( 2856) link_BETA1-4 : bond 0.00692 / 0.35 ( 3) link_BETA1-4 : angle 1.58579 / 0.93 ( 9) link_NAG-ASN : bond 0.00457 / 0.26 ( 30) link_NAG-ASN : angle 2.17233 / 1.51 ( 90) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 254 time to evaluate : 0.955 Fit side-chains revert: symmetry clash REVERT: A 31 THR cc_start: 0.7003 (OUTLIER) cc_final: 0.6702 (t) REVERT: A 359 THR cc_start: 0.7514 (m) cc_final: 0.7304 (t) REVERT: A 449 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8526 (mtt-85) REVERT: A 589 ASN cc_start: 0.6775 (OUTLIER) cc_final: 0.6250 (p0) REVERT: A 593 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6863 (tt0) REVERT: A 730 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.7208 (pm20) REVERT: A 1053 GLN cc_start: 0.6747 (OUTLIER) cc_final: 0.6341 (mt0) REVERT: A 1054 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6754 (pm20) REVERT: B 285 GLU cc_start: 0.7908 (tp30) cc_final: 0.7663 (tp30) REVERT: B 758 ARG cc_start: 0.8213 (ttm170) cc_final: 0.7919 (ttp80) REVERT: B 762 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8359 (mt-10) REVERT: C 32 GLN cc_start: 0.7478 (mm110) cc_final: 0.7082 (mm110) REVERT: C 54 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8345 (tp) REVERT: C 449 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.7783 (mtp180) REVERT: C 491 TYR cc_start: 0.7218 (m-80) cc_final: 0.6988 (m-80) REVERT: C 624 THR cc_start: 0.6363 (OUTLIER) cc_final: 0.6068 (t) REVERT: C 786 GLN cc_start: 0.7458 (mt0) cc_final: 0.7253 (mm-40) REVERT: C 809 THR cc_start: 0.7610 (m) cc_final: 0.7097 (p) REVERT: C 825 ASP cc_start: 0.6169 (OUTLIER) cc_final: 0.5915 (p0) REVERT: C 911 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7609 (tmtt) REVERT: C 917 GLN cc_start: 0.7433 (tt0) cc_final: 0.6904 (tt0) outliers start: 77 outliers final: 36 residues processed: 304 average time/residue: 0.6953 time to fit residues: 241.0648 Evaluate side-chains 291 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 242 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 449 ARG Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 589 ASN Chi-restraints excluded: chain A residue 593 GLU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 730 GLU Chi-restraints excluded: chain A residue 769 GLN Chi-restraints excluded: chain A residue 816 MET Chi-restraints excluded: chain A residue 882 MET Chi-restraints excluded: chain A residue 894 THR Chi-restraints excluded: chain A residue 939 GLN Chi-restraints excluded: chain A residue 1053 GLN Chi-restraints excluded: chain A residue 1054 GLU Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 762 GLU Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 904 GLN Chi-restraints excluded: chain B residue 911 LYS Chi-restraints excluded: chain B residue 972 GLU Chi-restraints excluded: chain B residue 1086 ILE Chi-restraints excluded: chain B residue 1093 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 333 LYS Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 632 GLN Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 772 LYS Chi-restraints excluded: chain C residue 825 ASP Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 911 LYS Chi-restraints excluded: chain C residue 1088 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 109 optimal weight: 3.9990 chunk 192 optimal weight: 5.9990 chunk 216 optimal weight: 4.9990 chunk 213 optimal weight: 2.9990 chunk 205 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 224 optimal weight: 2.9990 chunk 188 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 505 ASN A 889 ASN A 908 GLN B 827 ASN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN C 445 HIS C 546 GLN ** C 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1053 GLN C1095 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.130356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.103057 restraints weight = 28346.452| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.66 r_work: 0.2913 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 25040 Z= 0.156 Angle : 0.620 11.065 34104 Z= 0.335 Chirality : 0.046 0.237 3917 Planarity : 0.005 0.071 4352 Dihedral : 6.191 55.428 3336 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.64 % Favored : 95.33 % Rotamer: Outliers : 2.50 % Allowed : 9.20 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.14), residues: 3018 helix: 1.36 (0.20), residues: 708 sheet: 0.75 (0.21), residues: 576 loop : -1.63 (0.13), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 99 TYR 0.020 0.002 TYR B 352 PHE 0.019 0.002 PHE A 179 TRP 0.013 0.001 TRP B 423 HIS 0.008 0.001 HIS A1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 (24971) covalent geometry : angle 0.60674 / 0.33 (33933) SS BOND : bond 0.00531 / 0.32 ( 36) SS BOND : angle 1.87441 / 1.44 ( 72) hydrogen bonds : bond 0.07327 / 4.72 ( 977) hydrogen bonds : angle 5.64013 / 3.88 ( 2856) link_BETA1-4 : bond 0.00535 / 0.27 ( 3) link_BETA1-4 : angle 1.51927 / 0.89 ( 9) link_NAG-ASN : bond 0.00328 / 0.19 ( 30) link_NAG-ASN : angle 1.95524 / 1.34 ( 90) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 257 time to evaluate : 1.076 Fit side-chains REVERT: A 277 ASP cc_start: 0.8437 (t0) cc_final: 0.8193 (t0) REVERT: A 359 THR cc_start: 0.7493 (m) cc_final: 0.7244 (t) REVERT: A 589 ASN cc_start: 0.6622 (OUTLIER) cc_final: 0.6167 (p0) REVERT: A 730 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.7168 (pm20) REVERT: A 1053 GLN cc_start: 0.6639 (OUTLIER) cc_final: 0.6270 (mt0) REVERT: A 1054 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6815 (pm20) REVERT: A 1088 GLN cc_start: 0.7218 (pt0) cc_final: 0.6819 (pt0) REVERT: B 285 GLU cc_start: 0.7925 (tp30) cc_final: 0.7695 (tp30) REVERT: B 484 TYR cc_start: 0.7810 (m-80) cc_final: 0.7601 (m-80) REVERT: B 758 ARG cc_start: 0.8309 (ttm170) cc_final: 0.7816 (ttp-110) REVERT: B 762 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8294 (mt-10) REVERT: B 823 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7648 (tp) REVERT: B 884 MET cc_start: 0.8161 (tpt) cc_final: 0.7833 (tpt) REVERT: B 1098 THR cc_start: 0.5445 (m) cc_final: 0.4903 (p) REVERT: C 32 GLN cc_start: 0.7521 (mm110) cc_final: 0.7265 (mm110) REVERT: C 54 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8350 (tp) REVERT: C 107 MET cc_start: 0.8381 (mmm) cc_final: 0.8036 (mmt) REVERT: C 449 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.7814 (mtp180) REVERT: C 624 THR cc_start: 0.6017 (OUTLIER) cc_final: 0.5738 (t) REVERT: C 647 GLU cc_start: 0.6986 (tp30) cc_final: 0.6425 (tm-30) REVERT: C 809 THR cc_start: 0.7583 (m) cc_final: 0.7110 (p) REVERT: C 882 MET cc_start: 0.7825 (OUTLIER) cc_final: 0.7568 (mtm) REVERT: C 894 THR cc_start: 0.7926 (OUTLIER) cc_final: 0.7642 (p) REVERT: C 911 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7564 (tmtt) REVERT: C 1065 HIS cc_start: 0.3483 (OUTLIER) cc_final: 0.1609 (m-70) outliers start: 66 outliers final: 30 residues processed: 298 average time/residue: 0.6513 time to fit residues: 221.3453 Evaluate side-chains 297 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 254 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 589 ASN Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 730 GLU Chi-restraints excluded: chain A residue 816 MET Chi-restraints excluded: chain A residue 882 MET Chi-restraints excluded: chain A residue 939 GLN Chi-restraints excluded: chain A residue 1053 GLN Chi-restraints excluded: chain A residue 1054 GLU Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 447 LYS Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 762 GLU Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 904 GLN Chi-restraints excluded: chain B residue 911 LYS Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1086 ILE Chi-restraints excluded: chain B residue 1093 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 333 LYS Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 632 GLN Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 882 MET Chi-restraints excluded: chain C residue 894 THR Chi-restraints excluded: chain C residue 911 LYS Chi-restraints excluded: chain C residue 1065 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 179 optimal weight: 8.9990 chunk 225 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 chunk 220 optimal weight: 3.9990 chunk 189 optimal weight: 9.9990 chunk 132 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 205 optimal weight: 3.9990 chunk 172 optimal weight: 4.9990 chunk 215 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 73 ASN A 889 ASN A 908 GLN A 915 GLN A1088 GLN B 445 HIS B 827 ASN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN C 546 GLN C 786 GLN ** C 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 917 GLN C1053 GLN C1065 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.129026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.101625 restraints weight = 28316.767| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.66 r_work: 0.2878 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 25040 Z= 0.201 Angle : 0.688 12.182 34104 Z= 0.372 Chirality : 0.049 0.238 3917 Planarity : 0.005 0.066 4352 Dihedral : 6.341 54.648 3334 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.47 % Favored : 94.50 % Rotamer: Outliers : 3.30 % Allowed : 9.32 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.14), residues: 3018 helix: 1.17 (0.19), residues: 720 sheet: 0.69 (0.21), residues: 570 loop : -1.70 (0.13), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 48 TYR 0.022 0.002 TYR B 352 PHE 0.020 0.002 PHE B 799 TRP 0.015 0.002 TRP B 423 HIS 0.007 0.002 HIS B1046 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.20 (24971) covalent geometry : angle 0.67430 / 0.37 (33933) SS BOND : bond 0.00672 / 0.39 ( 36) SS BOND : angle 2.09452 / 1.58 ( 72) hydrogen bonds : bond 0.08170 / 5.27 ( 977) hydrogen bonds : angle 5.71052 / 3.94 ( 2856) link_BETA1-4 : bond 0.00620 / 0.31 ( 3) link_BETA1-4 : angle 1.59885 / 0.93 ( 9) link_NAG-ASN : bond 0.00419 / 0.24 ( 30) link_NAG-ASN : angle 2.05675 / 1.42 ( 90) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 259 time to evaluate : 1.095 Fit side-chains revert: symmetry clash REVERT: A 31 THR cc_start: 0.6971 (OUTLIER) cc_final: 0.6653 (t) REVERT: A 132 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.6537 (mm) REVERT: A 277 ASP cc_start: 0.8510 (t0) cc_final: 0.8295 (t0) REVERT: A 589 ASN cc_start: 0.6771 (OUTLIER) cc_final: 0.6266 (p0) REVERT: A 593 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6859 (tt0) REVERT: A 632 GLN cc_start: 0.7606 (tp40) cc_final: 0.7138 (mt0) REVERT: A 730 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.7238 (pm20) REVERT: A 1053 GLN cc_start: 0.6721 (OUTLIER) cc_final: 0.6342 (mt0) REVERT: A 1054 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6829 (pm20) REVERT: B 285 GLU cc_start: 0.7979 (tp30) cc_final: 0.7750 (tp30) REVERT: B 484 TYR cc_start: 0.7877 (m-80) cc_final: 0.7675 (m-80) REVERT: B 762 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8362 (mt-10) REVERT: B 769 GLN cc_start: 0.7736 (OUTLIER) cc_final: 0.7531 (tt0) REVERT: B 790 ASP cc_start: 0.7076 (t0) cc_final: 0.6453 (t70) REVERT: B 823 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7704 (tp) REVERT: B 884 MET cc_start: 0.8170 (tpt) cc_final: 0.7858 (tpt) REVERT: B 946 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8133 (mtpt) REVERT: B 972 GLU cc_start: 0.7752 (tt0) cc_final: 0.7519 (tt0) REVERT: B 984 GLN cc_start: 0.8243 (tm-30) cc_final: 0.8002 (tm-30) REVERT: B 1098 THR cc_start: 0.5307 (m) cc_final: 0.4769 (p) REVERT: C 32 GLN cc_start: 0.7510 (mm110) cc_final: 0.7235 (mm110) REVERT: C 54 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8346 (tp) REVERT: C 164 ILE cc_start: 0.8334 (OUTLIER) cc_final: 0.8112 (mm) REVERT: C 449 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.7835 (mtp180) REVERT: C 624 THR cc_start: 0.6205 (OUTLIER) cc_final: 0.5862 (t) REVERT: C 707 GLU cc_start: 0.8442 (tt0) cc_final: 0.8241 (tt0) REVERT: C 809 THR cc_start: 0.7682 (m) cc_final: 0.7418 (p) REVERT: C 882 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.7677 (mtm) REVERT: C 894 THR cc_start: 0.7901 (OUTLIER) cc_final: 0.7609 (p) REVERT: C 911 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7605 (tmtt) REVERT: C 917 GLN cc_start: 0.7384 (tt0) cc_final: 0.7086 (tt0) outliers start: 87 outliers final: 44 residues processed: 320 average time/residue: 0.6598 time to fit residues: 242.0225 Evaluate side-chains 312 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 250 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 589 ASN Chi-restraints excluded: chain A residue 593 GLU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 730 GLU Chi-restraints excluded: chain A residue 816 MET Chi-restraints excluded: chain A residue 882 MET Chi-restraints excluded: chain A residue 894 THR Chi-restraints excluded: chain A residue 939 GLN Chi-restraints excluded: chain A residue 1053 GLN Chi-restraints excluded: chain A residue 1054 GLU Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 426 ARG Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 762 GLU Chi-restraints excluded: chain B residue 769 GLN Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 904 GLN Chi-restraints excluded: chain B residue 911 LYS Chi-restraints excluded: chain B residue 946 LYS Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1086 ILE Chi-restraints excluded: chain B residue 1093 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 159 CYS Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 333 LYS Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 632 GLN Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 882 MET Chi-restraints excluded: chain C residue 894 THR Chi-restraints excluded: chain C residue 898 LEU Chi-restraints excluded: chain C residue 911 LYS Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain C residue 1088 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 240 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 197 optimal weight: 1.9990 chunk 257 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 263 optimal weight: 1.9990 chunk 278 optimal weight: 0.2980 chunk 223 optimal weight: 9.9990 chunk 33 optimal weight: 0.3980 chunk 267 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 HIS ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 GLN A 915 GLN B 827 ASN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN C 112 GLN C 546 GLN C 627 ASN C 786 GLN ** C 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1053 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.132645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.105193 restraints weight = 28457.080| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.65 r_work: 0.2949 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 25040 Z= 0.119 Angle : 0.545 10.754 34104 Z= 0.292 Chirality : 0.044 0.215 3917 Planarity : 0.004 0.053 4352 Dihedral : 5.718 56.136 3334 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.98 % Favored : 95.96 % Rotamer: Outliers : 2.23 % Allowed : 10.64 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.14), residues: 3018 helix: 1.66 (0.20), residues: 708 sheet: 0.77 (0.21), residues: 546 loop : -1.55 (0.13), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 99 TYR 0.019 0.001 TYR A 352 PHE 0.019 0.001 PHE B 799 TRP 0.011 0.001 TRP B 423 HIS 0.004 0.001 HIS A1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.12 (24971) covalent geometry : angle 0.53362 / 0.29 (33933) SS BOND : bond 0.00390 / 0.24 ( 36) SS BOND : angle 1.47624 / 1.14 ( 72) hydrogen bonds : bond 0.05976 / 3.84 ( 977) hydrogen bonds : angle 5.30052 / 3.64 ( 2856) link_BETA1-4 : bond 0.00372 / 0.19 ( 3) link_BETA1-4 : angle 1.37236 / 0.80 ( 9) link_NAG-ASN : bond 0.00260 / 0.14 ( 30) link_NAG-ASN : angle 1.76728 / 1.19 ( 90) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 267 time to evaluate : 0.970 Fit side-chains revert: symmetry clash REVERT: A 72 ILE cc_start: 0.2081 (OUTLIER) cc_final: 0.1215 (tt) REVERT: A 132 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.6553 (mm) REVERT: A 359 THR cc_start: 0.7378 (m) cc_final: 0.7114 (t) REVERT: A 632 GLN cc_start: 0.7588 (tp40) cc_final: 0.7080 (mt0) REVERT: A 730 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.7074 (pm20) REVERT: A 911 LYS cc_start: 0.7845 (ttpp) cc_final: 0.7068 (mmtm) REVERT: B 285 GLU cc_start: 0.7940 (tp30) cc_final: 0.7720 (tp30) REVERT: B 758 ARG cc_start: 0.8293 (ttm170) cc_final: 0.7825 (ttp-110) REVERT: B 762 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8147 (mt-10) REVERT: B 884 MET cc_start: 0.8130 (tpt) cc_final: 0.7709 (tpt) REVERT: B 918 GLU cc_start: 0.6712 (mt-10) cc_final: 0.6422 (mp0) REVERT: B 1098 THR cc_start: 0.5192 (m) cc_final: 0.4722 (p) REVERT: C 32 GLN cc_start: 0.7514 (mm110) cc_final: 0.7224 (mm110) REVERT: C 54 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8349 (tp) REVERT: C 107 MET cc_start: 0.8333 (mmm) cc_final: 0.8073 (mmt) REVERT: C 117 ILE cc_start: 0.8616 (pt) cc_final: 0.8396 (pp) REVERT: C 449 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.7779 (mtp180) REVERT: C 624 THR cc_start: 0.5901 (OUTLIER) cc_final: 0.5609 (t) REVERT: C 647 GLU cc_start: 0.6939 (tp30) cc_final: 0.6362 (tm-30) REVERT: C 707 GLU cc_start: 0.8404 (tt0) cc_final: 0.8160 (tt0) REVERT: C 882 MET cc_start: 0.7828 (OUTLIER) cc_final: 0.7627 (mtm) REVERT: C 1065 HIS cc_start: 0.3435 (OUTLIER) cc_final: 0.1671 (m-70) outliers start: 59 outliers final: 21 residues processed: 309 average time/residue: 0.6538 time to fit residues: 231.3639 Evaluate side-chains 279 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 249 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 730 GLU Chi-restraints excluded: chain A residue 939 GLN Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 426 ARG Chi-restraints excluded: chain B residue 447 LYS Chi-restraints excluded: chain B residue 762 GLU Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 904 GLN Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1093 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 159 CYS Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 333 LYS Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 882 MET Chi-restraints excluded: chain C residue 1065 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 184 optimal weight: 7.9990 chunk 151 optimal weight: 7.9990 chunk 242 optimal weight: 9.9990 chunk 224 optimal weight: 9.9990 chunk 186 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 129 optimal weight: 7.9990 chunk 185 optimal weight: 6.9990 chunk 274 optimal weight: 9.9990 chunk 118 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 GLN A 915 GLN A1040 HIS A1065 HIS B 827 ASN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN C 546 GLN ** C 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 917 GLN C1053 GLN C1065 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.130128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.102804 restraints weight = 28438.917| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.66 r_work: 0.2914 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 25040 Z= 0.176 Angle : 0.638 10.503 34104 Z= 0.344 Chirality : 0.047 0.204 3917 Planarity : 0.005 0.056 4352 Dihedral : 6.030 55.303 3333 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.20 % Favored : 94.73 % Rotamer: Outliers : 2.42 % Allowed : 10.87 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.14), residues: 3018 helix: 1.41 (0.20), residues: 714 sheet: 0.84 (0.21), residues: 558 loop : -1.63 (0.13), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 758 TYR 0.022 0.002 TYR B 352 PHE 0.022 0.002 PHE B 799 TRP 0.013 0.001 TRP B 423 HIS 0.006 0.001 HIS C1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.18 (24971) covalent geometry : angle 0.62654 / 0.34 (33933) SS BOND : bond 0.00574 / 0.33 ( 36) SS BOND : angle 1.79797 / 1.36 ( 72) hydrogen bonds : bond 0.07423 / 4.79 ( 977) hydrogen bonds : angle 5.48365 / 3.77 ( 2856) link_BETA1-4 : bond 0.00512 / 0.26 ( 3) link_BETA1-4 : angle 1.51052 / 0.89 ( 9) link_NAG-ASN : bond 0.00353 / 0.20 ( 30) link_NAG-ASN : angle 1.89369 / 1.29 ( 90) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 250 time to evaluate : 0.946 Fit side-chains revert: symmetry clash REVERT: A 132 LEU cc_start: 0.7491 (OUTLIER) cc_final: 0.6580 (mm) REVERT: A 593 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6912 (tt0) REVERT: A 632 GLN cc_start: 0.7500 (tp40) cc_final: 0.7028 (mt0) REVERT: A 730 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.7192 (pm20) REVERT: A 1053 GLN cc_start: 0.6819 (OUTLIER) cc_final: 0.6457 (mt0) REVERT: A 1054 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6837 (pm20) REVERT: B 285 GLU cc_start: 0.7899 (tp30) cc_final: 0.7685 (tp30) REVERT: B 758 ARG cc_start: 0.8318 (ttm170) cc_final: 0.7820 (ttp-110) REVERT: B 762 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8319 (mt-10) REVERT: B 790 ASP cc_start: 0.6883 (t0) cc_final: 0.6239 (t70) REVERT: B 884 MET cc_start: 0.8098 (tpt) cc_final: 0.7788 (tpt) REVERT: B 946 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.7817 (mtpt) REVERT: B 972 GLU cc_start: 0.7590 (tt0) cc_final: 0.7344 (tt0) REVERT: B 1098 THR cc_start: 0.5316 (m) cc_final: 0.4829 (p) REVERT: C 32 GLN cc_start: 0.7478 (mm110) cc_final: 0.7210 (mm110) REVERT: C 54 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8340 (tp) REVERT: C 164 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.8078 (mm) REVERT: C 449 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.7793 (mtp180) REVERT: C 624 THR cc_start: 0.6269 (OUTLIER) cc_final: 0.5904 (t) REVERT: C 647 GLU cc_start: 0.7069 (tp30) cc_final: 0.6436 (tm-30) REVERT: C 707 GLU cc_start: 0.8406 (tt0) cc_final: 0.8145 (tt0) REVERT: C 882 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.7679 (mtm) REVERT: C 894 THR cc_start: 0.7779 (OUTLIER) cc_final: 0.7455 (p) REVERT: C 917 GLN cc_start: 0.7421 (tt0) cc_final: 0.6881 (tt0) outliers start: 64 outliers final: 40 residues processed: 298 average time/residue: 0.7005 time to fit residues: 238.2787 Evaluate side-chains 304 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 251 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 593 GLU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 730 GLU Chi-restraints excluded: chain A residue 816 MET Chi-restraints excluded: chain A residue 939 GLN Chi-restraints excluded: chain A residue 1053 GLN Chi-restraints excluded: chain A residue 1054 GLU Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 426 ARG Chi-restraints excluded: chain B residue 447 LYS Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 762 GLU Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 904 GLN Chi-restraints excluded: chain B residue 946 LYS Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1086 ILE Chi-restraints excluded: chain B residue 1093 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 159 CYS Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 333 LYS Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 632 GLN Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 823 LEU Chi-restraints excluded: chain C residue 882 MET Chi-restraints excluded: chain C residue 894 THR Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain C residue 934 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 144 optimal weight: 1.9990 chunk 264 optimal weight: 20.0000 chunk 84 optimal weight: 6.9990 chunk 200 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 chunk 280 optimal weight: 9.9990 chunk 234 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 210 optimal weight: 10.0000 chunk 101 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 889 ASN A 908 GLN A 915 GLN A 917 GLN B 827 ASN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN C 546 GLN C1053 GLN C1065 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.127771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.100369 restraints weight = 28398.605| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.67 r_work: 0.2878 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 25040 Z= 0.270 Angle : 0.791 11.955 34104 Z= 0.427 Chirality : 0.053 0.261 3917 Planarity : 0.006 0.056 4352 Dihedral : 6.641 51.284 3333 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.80 % Allowed : 10.98 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.14), residues: 3018 helix: 0.77 (0.19), residues: 744 sheet: 0.48 (0.20), residues: 615 loop : -1.74 (0.13), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 982 TYR 0.024 0.003 TYR B 352 PHE 0.024 0.003 PHE B 799 TRP 0.015 0.002 TRP B 423 HIS 0.010 0.002 HIS B1046 Details of bonding type rmsd/Z covalent geometry : bond 0.00635 / 0.27 (24971) covalent geometry : angle 0.77684 / 0.42 (33933) SS BOND : bond 0.00857 / 0.49 ( 36) SS BOND : angle 2.31243 / 1.71 ( 72) hydrogen bonds : bond 0.09222 / 5.97 ( 977) hydrogen bonds : angle 5.87654 / 4.06 ( 2856) link_BETA1-4 : bond 0.00761 / 0.38 ( 3) link_BETA1-4 : angle 1.63926 / 0.96 ( 9) link_NAG-ASN : bond 0.00566 / 0.33 ( 30) link_NAG-ASN : angle 2.30082 / 1.61 ( 90) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 249 time to evaluate : 1.071 Fit side-chains revert: symmetry clash REVERT: A 31 THR cc_start: 0.6943 (OUTLIER) cc_final: 0.6610 (t) REVERT: A 132 LEU cc_start: 0.7424 (OUTLIER) cc_final: 0.6527 (mm) REVERT: A 589 ASN cc_start: 0.6771 (OUTLIER) cc_final: 0.6254 (p0) REVERT: A 593 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6862 (tt0) REVERT: A 632 GLN cc_start: 0.7471 (tp40) cc_final: 0.7086 (mt0) REVERT: A 730 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7236 (pm20) REVERT: A 1053 GLN cc_start: 0.6886 (OUTLIER) cc_final: 0.6516 (mt0) REVERT: A 1054 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6907 (pm20) REVERT: B 274 ASP cc_start: 0.8444 (OUTLIER) cc_final: 0.8077 (m-30) REVERT: B 285 GLU cc_start: 0.8037 (tp30) cc_final: 0.7809 (tp30) REVERT: B 762 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8389 (mt-10) REVERT: B 790 ASP cc_start: 0.7104 (t0) cc_final: 0.6487 (t70) REVERT: B 972 GLU cc_start: 0.7828 (tt0) cc_final: 0.7622 (tt0) REVERT: B 984 GLN cc_start: 0.8455 (tm-30) cc_final: 0.8043 (pp30) REVERT: B 1091 PHE cc_start: 0.7782 (t80) cc_final: 0.7565 (t80) REVERT: B 1095 GLN cc_start: 0.6257 (mm-40) cc_final: 0.6026 (mp10) REVERT: B 1098 THR cc_start: 0.5705 (m) cc_final: 0.5182 (p) REVERT: C 32 GLN cc_start: 0.7435 (mm110) cc_final: 0.7152 (mm110) REVERT: C 54 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8350 (tp) REVERT: C 164 ILE cc_start: 0.8354 (OUTLIER) cc_final: 0.8120 (mm) REVERT: C 449 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.7849 (mtp180) REVERT: C 624 THR cc_start: 0.6151 (OUTLIER) cc_final: 0.5796 (t) REVERT: C 707 GLU cc_start: 0.8442 (tt0) cc_final: 0.8144 (tt0) REVERT: C 882 MET cc_start: 0.8250 (OUTLIER) cc_final: 0.7955 (mtm) REVERT: C 894 THR cc_start: 0.7915 (OUTLIER) cc_final: 0.7613 (p) REVERT: C 917 GLN cc_start: 0.7501 (tt0) cc_final: 0.7091 (tt0) outliers start: 74 outliers final: 43 residues processed: 303 average time/residue: 0.6902 time to fit residues: 239.2687 Evaluate side-chains 299 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 241 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 589 ASN Chi-restraints excluded: chain A residue 593 GLU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 730 GLU Chi-restraints excluded: chain A residue 816 MET Chi-restraints excluded: chain A residue 939 GLN Chi-restraints excluded: chain A residue 1053 GLN Chi-restraints excluded: chain A residue 1054 GLU Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain B residue 426 ARG Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 762 GLU Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 904 GLN Chi-restraints excluded: chain B residue 1054 GLU Chi-restraints excluded: chain B residue 1086 ILE Chi-restraints excluded: chain B residue 1093 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 159 CYS Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 333 LYS Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 632 GLN Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 823 LEU Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 882 MET Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 894 THR Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain C residue 934 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 12 optimal weight: 7.9990 chunk 186 optimal weight: 8.9990 chunk 271 optimal weight: 5.9990 chunk 83 optimal weight: 0.0470 chunk 204 optimal weight: 10.0000 chunk 280 optimal weight: 9.9990 chunk 127 optimal weight: 4.9990 chunk 150 optimal weight: 9.9990 chunk 101 optimal weight: 8.9990 chunk 37 optimal weight: 0.9980 chunk 286 optimal weight: 10.0000 overall best weight: 4.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 889 ASN A 908 GLN A 915 GLN A1040 HIS B 827 ASN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN C 546 GLN ** C 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1065 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.129061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.101957 restraints weight = 28378.561| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.62 r_work: 0.2886 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 25040 Z= 0.201 Angle : 0.687 11.238 34104 Z= 0.371 Chirality : 0.049 0.234 3917 Planarity : 0.005 0.052 4352 Dihedral : 6.400 51.673 3333 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.46 % Allowed : 11.48 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.14), residues: 3018 helix: 1.08 (0.19), residues: 714 sheet: 0.52 (0.20), residues: 615 loop : -1.75 (0.13), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 758 TYR 0.023 0.002 TYR A 352 PHE 0.022 0.002 PHE B 799 TRP 0.013 0.002 TRP B 423 HIS 0.007 0.002 HIS B1046 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.20 (24971) covalent geometry : angle 0.67379 / 0.37 (33933) SS BOND : bond 0.00643 / 0.37 ( 36) SS BOND : angle 1.96318 / 1.47 ( 72) hydrogen bonds : bond 0.08013 / 5.17 ( 977) hydrogen bonds : angle 5.67853 / 3.91 ( 2856) link_BETA1-4 : bond 0.00587 / 0.29 ( 3) link_BETA1-4 : angle 1.61259 / 0.94 ( 9) link_NAG-ASN : bond 0.00422 / 0.24 ( 30) link_NAG-ASN : angle 2.10923 / 1.45 ( 90) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 247 time to evaluate : 0.984 Fit side-chains revert: symmetry clash REVERT: A 132 LEU cc_start: 0.7380 (OUTLIER) cc_final: 0.6474 (mm) REVERT: A 593 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6834 (tt0) REVERT: A 632 GLN cc_start: 0.7412 (tp40) cc_final: 0.7046 (mt0) REVERT: A 730 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.7223 (pm20) REVERT: A 1053 GLN cc_start: 0.6811 (OUTLIER) cc_final: 0.6445 (mt0) REVERT: A 1054 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6888 (pm20) REVERT: B 274 ASP cc_start: 0.8419 (OUTLIER) cc_final: 0.8067 (m-30) REVERT: B 285 GLU cc_start: 0.8022 (tp30) cc_final: 0.7818 (tp30) REVERT: B 762 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8350 (mt-10) REVERT: B 790 ASP cc_start: 0.7173 (t0) cc_final: 0.6550 (t70) REVERT: B 884 MET cc_start: 0.8105 (tpt) cc_final: 0.7794 (tpt) REVERT: B 972 GLU cc_start: 0.7711 (tt0) cc_final: 0.7487 (tt0) REVERT: B 984 GLN cc_start: 0.8449 (tm-30) cc_final: 0.8056 (pp30) REVERT: B 1098 THR cc_start: 0.5334 (m) cc_final: 0.4841 (p) REVERT: C 32 GLN cc_start: 0.7431 (mm110) cc_final: 0.7181 (mm110) REVERT: C 54 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8375 (tp) REVERT: C 164 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.8091 (mm) REVERT: C 449 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.7839 (mtp180) REVERT: C 624 THR cc_start: 0.5911 (OUTLIER) cc_final: 0.5571 (t) REVERT: C 647 GLU cc_start: 0.7051 (tp30) cc_final: 0.6397 (tm-30) REVERT: C 707 GLU cc_start: 0.8469 (tt0) cc_final: 0.8167 (tt0) REVERT: C 882 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7886 (mtm) REVERT: C 894 THR cc_start: 0.7889 (OUTLIER) cc_final: 0.7592 (p) REVERT: C 917 GLN cc_start: 0.7420 (tt0) cc_final: 0.7016 (tt0) outliers start: 65 outliers final: 40 residues processed: 295 average time/residue: 0.6640 time to fit residues: 223.9445 Evaluate side-chains 297 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 244 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 593 GLU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 730 GLU Chi-restraints excluded: chain A residue 816 MET Chi-restraints excluded: chain A residue 939 GLN Chi-restraints excluded: chain A residue 1053 GLN Chi-restraints excluded: chain A residue 1054 GLU Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain B residue 426 ARG Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 762 GLU Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 904 GLN Chi-restraints excluded: chain B residue 911 LYS Chi-restraints excluded: chain B residue 1054 GLU Chi-restraints excluded: chain B residue 1086 ILE Chi-restraints excluded: chain B residue 1093 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 159 CYS Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 333 LYS Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 632 GLN Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 769 GLN Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 823 LEU Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 882 MET Chi-restraints excluded: chain C residue 894 THR Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain C residue 934 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 303 optimal weight: 9.9990 chunk 173 optimal weight: 0.9980 chunk 55 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 chunk 219 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 chunk 194 optimal weight: 9.9990 chunk 277 optimal weight: 6.9990 chunk 253 optimal weight: 0.7980 chunk 112 optimal weight: 20.0000 chunk 280 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 889 ASN A 908 GLN A 915 GLN A1040 HIS B 347 ASN B 827 ASN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN C 546 GLN C 769 GLN ** C 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1065 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.131772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.104458 restraints weight = 28442.521| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.67 r_work: 0.2923 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25040 Z= 0.127 Angle : 0.567 11.130 34104 Z= 0.303 Chirality : 0.044 0.207 3917 Planarity : 0.004 0.051 4352 Dihedral : 5.920 53.241 3333 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.67 % Favored : 95.29 % Rotamer: Outliers : 1.74 % Allowed : 12.39 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.14), residues: 3018 helix: 1.50 (0.20), residues: 711 sheet: 0.79 (0.21), residues: 543 loop : -1.62 (0.13), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 758 TYR 0.020 0.001 TYR A 352 PHE 0.021 0.001 PHE B 799 TRP 0.012 0.001 TRP B 423 HIS 0.005 0.001 HIS C1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.13 (24971) covalent geometry : angle 0.55515 / 0.30 (33933) SS BOND : bond 0.00410 / 0.25 ( 36) SS BOND : angle 1.51828 / 1.14 ( 72) hydrogen bonds : bond 0.06280 / 4.04 ( 977) hydrogen bonds : angle 5.35628 / 3.68 ( 2856) link_BETA1-4 : bond 0.00363 / 0.18 ( 3) link_BETA1-4 : angle 1.46504 / 0.86 ( 9) link_NAG-ASN : bond 0.00263 / 0.14 ( 30) link_NAG-ASN : angle 1.85799 / 1.25 ( 90) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 251 time to evaluate : 0.844 Fit side-chains revert: symmetry clash REVERT: A 72 ILE cc_start: 0.1955 (OUTLIER) cc_final: 0.1340 (tt) REVERT: A 132 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.6491 (mm) REVERT: A 632 GLN cc_start: 0.7413 (tp40) cc_final: 0.7044 (mt0) REVERT: A 730 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7133 (pm20) REVERT: A 889 ASN cc_start: 0.8507 (OUTLIER) cc_final: 0.8261 (t0) REVERT: A 911 LYS cc_start: 0.7828 (ttpp) cc_final: 0.7015 (mmtm) REVERT: A 1054 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6843 (pm20) REVERT: A 1088 GLN cc_start: 0.7237 (pt0) cc_final: 0.6993 (pt0) REVERT: B 274 ASP cc_start: 0.8378 (OUTLIER) cc_final: 0.8041 (m-30) REVERT: B 285 GLU cc_start: 0.8065 (tp30) cc_final: 0.7849 (tp30) REVERT: B 758 ARG cc_start: 0.8295 (ttm170) cc_final: 0.7852 (ttp-110) REVERT: B 762 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8199 (mt-10) REVERT: B 884 MET cc_start: 0.8084 (tpt) cc_final: 0.7678 (tpt) REVERT: B 1098 THR cc_start: 0.5266 (m) cc_final: 0.4807 (p) REVERT: C 32 GLN cc_start: 0.7464 (mm110) cc_final: 0.7210 (mm110) REVERT: C 54 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8376 (tp) REVERT: C 107 MET cc_start: 0.8295 (mmm) cc_final: 0.8039 (mmt) REVERT: C 117 ILE cc_start: 0.8635 (pt) cc_final: 0.8409 (pp) REVERT: C 449 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.7841 (mtp180) REVERT: C 624 THR cc_start: 0.6033 (OUTLIER) cc_final: 0.5676 (t) REVERT: C 647 GLU cc_start: 0.7034 (tp30) cc_final: 0.6360 (tm-30) REVERT: C 707 GLU cc_start: 0.8419 (tt0) cc_final: 0.8022 (tt0) REVERT: C 882 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7887 (mtm) REVERT: C 1085 PHE cc_start: 0.7034 (m-80) cc_final: 0.6635 (m-80) outliers start: 46 outliers final: 25 residues processed: 282 average time/residue: 0.6907 time to fit residues: 222.5538 Evaluate side-chains 280 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 244 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 730 GLU Chi-restraints excluded: chain A residue 816 MET Chi-restraints excluded: chain A residue 889 ASN Chi-restraints excluded: chain A residue 939 GLN Chi-restraints excluded: chain A residue 1054 GLU Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain B residue 426 ARG Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 762 GLU Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 904 GLN Chi-restraints excluded: chain B residue 911 LYS Chi-restraints excluded: chain B residue 1093 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 159 CYS Chi-restraints excluded: chain C residue 333 LYS Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 632 GLN Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 882 MET Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain C residue 934 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 82 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 76 optimal weight: 6.9990 chunk 204 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 135 optimal weight: 9.9990 chunk 254 optimal weight: 4.9990 chunk 283 optimal weight: 9.9990 chunk 276 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 889 ASN A 908 GLN A 915 GLN A 917 GLN A1040 HIS B 347 ASN B 827 ASN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN C 301 GLN C 546 GLN ** C 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1040 HIS C1053 GLN C1065 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.127755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.100300 restraints weight = 28445.869| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.66 r_work: 0.2877 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 25040 Z= 0.282 Angle : 0.804 11.543 34104 Z= 0.433 Chirality : 0.054 0.253 3917 Planarity : 0.006 0.055 4352 Dihedral : 6.684 59.034 3333 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.23 % Allowed : 12.23 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.14), residues: 3018 helix: 0.77 (0.19), residues: 744 sheet: 0.47 (0.20), residues: 621 loop : -1.74 (0.13), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 982 TYR 0.026 0.003 TYR A 352 PHE 0.025 0.003 PHE B 799 TRP 0.015 0.002 TRP B 423 HIS 0.011 0.002 HIS C1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00666 / 0.28 (24971) covalent geometry : angle 0.79023 / 0.43 (33933) SS BOND : bond 0.00886 / 0.51 ( 36) SS BOND : angle 2.29782 / 1.69 ( 72) hydrogen bonds : bond 0.09206 / 5.95 ( 977) hydrogen bonds : angle 5.83359 / 4.03 ( 2856) link_BETA1-4 : bond 0.00778 / 0.39 ( 3) link_BETA1-4 : angle 1.62561 / 0.96 ( 9) link_NAG-ASN : bond 0.00584 / 0.34 ( 30) link_NAG-ASN : angle 2.26450 / 1.57 ( 90) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8531.32 seconds wall clock time: 145 minutes 57.45 seconds (8757.45 seconds total)