Starting phenix.real_space_refine on Mon Sep 30 04:18:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh2_14718/09_2024/7zh2_14718.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh2_14718/09_2024/7zh2_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh2_14718/09_2024/7zh2_14718.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh2_14718/09_2024/7zh2_14718.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh2_14718/09_2024/7zh2_14718.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh2_14718/09_2024/7zh2_14718.cif" } resolution = 2.71 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 27 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 dihedrals: 27 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 dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 14.61, per 1000 atoms: 0.60 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: 6.41 Conformation dependent library (CDL) restraints added in 3.2 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: 3.76 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: 12.42 Time building geometry restraints manager: 7.30 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: 14033 17.96 - 35.91: 1002 35.91 - 53.87: 179 53.87 - 71.83: 52 71.83 - 89.78: 23 Dihedral angle restraints: 15289 sinusoidal: 6358 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 15286 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 1105 or resid 1301 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 1105 or resid 1301 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: 0.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.970 Check model and map are aligned: 0.180 Set scattering table: 0.240 Process input model: 58.970 Find NCS groups from input model: 1.380 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 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 0.065 24971 Z= 0.219 Angle : 0.622 12.049 33933 Z= 0.361 Chirality : 0.045 0.241 3917 Planarity : 0.004 0.106 4352 Dihedral : 13.216 89.781 9433 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 2.41 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (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 TRP 0.008 0.001 TRP B 423 HIS 0.007 0.001 HIS A1065 PHE 0.027 0.001 PHE A 334 TYR 0.009 0.001 TYR C 491 ARG 0.010 0.000 ARG A 495 *********************** 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 fitting. rotamer outliers: 8 poor density : 343 time to evaluate : 2.679 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: 1.4933 time to fit residues: 586.8208 Evaluate side-chains 257 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 253 time to evaluate : 2.914 ------------------------------------------------------------------------------- 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 258 optimal weight: 10.0000 chunk 231 optimal weight: 9.9990 chunk 128 optimal weight: 6.9990 chunk 79 optimal weight: 9.9990 chunk 156 optimal weight: 7.9990 chunk 123 optimal weight: 0.2980 chunk 239 optimal weight: 0.8980 chunk 92 optimal weight: 6.9990 chunk 145 optimal weight: 9.9990 chunk 178 optimal weight: 30.0000 chunk 277 optimal weight: 1.9990 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 ASN A 479 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 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: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 24971 Z= 0.269 Angle : 0.650 7.727 33933 Z= 0.358 Chirality : 0.049 0.223 3917 Planarity : 0.005 0.068 4352 Dihedral : 7.268 77.515 4034 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.44 % Favored : 95.49 % Rotamer: Outliers : 2.16 % Allowed : 6.14 % Favored : 91.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.14), residues: 3018 helix: 1.23 (0.20), residues: 708 sheet: 0.86 (0.21), residues: 567 loop : -1.53 (0.12), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 423 HIS 0.008 0.002 HIS A1065 PHE 0.037 0.002 PHE A 334 TYR 0.024 0.002 TYR B 352 ARG 0.006 0.001 ARG C 426 *********************** 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 324 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 267 time to evaluate : 2.770 Fit side-chains revert: symmetry clash REVERT: A 319 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.8183 (mp) REVERT: A 449 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.7748 (mtt90) REVERT: A 544 ARG cc_start: 0.6795 (OUTLIER) cc_final: 0.6557 (mtp85) REVERT: A 713 MET cc_start: 0.8608 (ptm) cc_final: 0.8142 (ptm) REVERT: A 1054 GLU cc_start: 0.6825 (OUTLIER) cc_final: 0.6392 (pm20) REVERT: A 1103 PHE cc_start: 0.6054 (p90) cc_final: 0.5606 (p90) REVERT: B 306 ARG cc_start: 0.7495 (OUTLIER) cc_final: 0.6910 (mtt90) REVERT: B 484 TYR cc_start: 0.7839 (m-80) cc_final: 0.7591 (m-80) REVERT: B 758 ARG cc_start: 0.7767 (ttm170) cc_final: 0.7397 (ttp80) REVERT: B 762 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7586 (mt-10) REVERT: B 790 ASP cc_start: 0.6799 (t0) cc_final: 0.6239 (t70) REVERT: B 884 MET cc_start: 0.7751 (tpt) cc_final: 0.7362 (tpt) REVERT: C 32 GLN cc_start: 0.7260 (mm110) cc_final: 0.6858 (mm110) REVERT: C 54 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8185 (tp) REVERT: C 449 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7157 (mtp180) REVERT: C 786 GLN cc_start: 0.6862 (mt0) cc_final: 0.6594 (mm-40) REVERT: C 809 THR cc_start: 0.7398 (m) cc_final: 0.6994 (p) REVERT: C 911 LYS cc_start: 0.7780 (OUTLIER) cc_final: 0.7330 (tmtt) outliers start: 57 outliers final: 28 residues processed: 296 average time/residue: 1.5723 time to fit residues: 529.0239 Evaluate side-chains 282 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 245 time to evaluate : 2.610 ------------------------------------------------------------------------------- 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 816 MET 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 333 LYS Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 647 GLU 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 154 optimal weight: 7.9990 chunk 86 optimal weight: 9.9990 chunk 231 optimal weight: 9.9990 chunk 189 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 278 optimal weight: 5.9990 chunk 300 optimal weight: 1.9990 chunk 247 optimal weight: 0.9990 chunk 276 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 chunk 223 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 GLN A 889 ASN A 908 GLN A1088 GLN B 70 HIS B 827 ASN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 ASN B 992 GLN C 96 ASN C 201 GLN C 301 GLN C 445 HIS C 479 ASN C 546 GLN C 769 GLN C 917 GLN C1053 GLN C1095 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 24971 Z= 0.298 Angle : 0.682 13.916 33933 Z= 0.373 Chirality : 0.050 0.300 3917 Planarity : 0.005 0.055 4352 Dihedral : 7.203 67.398 4029 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.64 % Favored : 95.29 % Rotamer: Outliers : 2.80 % Allowed : 7.58 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.14), residues: 3018 helix: 1.20 (0.19), residues: 717 sheet: 0.78 (0.21), residues: 564 loop : -1.63 (0.12), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 423 HIS 0.008 0.002 HIS A1065 PHE 0.028 0.002 PHE A 334 TYR 0.023 0.002 TYR A 367 ARG 0.005 0.001 ARG C 48 *********************** 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 327 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 253 time to evaluate : 3.046 Fit side-chains revert: symmetry clash REVERT: A 319 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.8233 (mp) REVERT: A 544 ARG cc_start: 0.6875 (OUTLIER) cc_final: 0.6642 (mtp85) REVERT: A 589 ASN cc_start: 0.6456 (OUTLIER) cc_final: 0.5842 (p0) REVERT: A 593 GLU cc_start: 0.6846 (OUTLIER) cc_final: 0.6563 (tt0) REVERT: A 730 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6967 (pm20) REVERT: A 1053 GLN cc_start: 0.6793 (OUTLIER) cc_final: 0.6422 (mt0) REVERT: A 1054 GLU cc_start: 0.6851 (OUTLIER) cc_final: 0.6440 (pm20) REVERT: B 306 ARG cc_start: 0.7485 (OUTLIER) cc_final: 0.6881 (mtt90) REVERT: B 484 TYR cc_start: 0.7840 (m-80) cc_final: 0.7544 (m-80) REVERT: B 758 ARG cc_start: 0.7743 (ttm170) cc_final: 0.7410 (ttp80) REVERT: B 762 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7589 (mt-10) REVERT: B 884 MET cc_start: 0.7794 (tpt) cc_final: 0.7394 (tpt) REVERT: C 32 GLN cc_start: 0.7204 (mm110) cc_final: 0.6828 (mm110) REVERT: C 54 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8176 (tp) REVERT: C 449 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7174 (mtp180) REVERT: C 624 THR cc_start: 0.5670 (OUTLIER) cc_final: 0.5316 (t) REVERT: C 786 GLN cc_start: 0.6903 (mt0) cc_final: 0.6610 (mm-40) REVERT: C 809 THR cc_start: 0.7507 (m) cc_final: 0.7165 (p) REVERT: C 917 GLN cc_start: 0.7387 (tt0) cc_final: 0.6907 (tt0) outliers start: 74 outliers final: 29 residues processed: 297 average time/residue: 1.5435 time to fit residues: 520.5600 Evaluate side-chains 285 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 244 time to evaluate : 2.691 ------------------------------------------------------------------------------- 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 359 THR Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 544 ARG 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 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 54 LEU Chi-restraints excluded: chain B residue 306 ARG Chi-restraints excluded: chain B residue 468 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 102 VAL 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 693 THR Chi-restraints excluded: chain C residue 863 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 275 optimal weight: 3.9990 chunk 209 optimal weight: 8.9990 chunk 144 optimal weight: 0.0010 chunk 30 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 186 optimal weight: 5.9990 chunk 279 optimal weight: 4.9990 chunk 295 optimal weight: 1.9990 chunk 145 optimal weight: 0.6980 chunk 264 optimal weight: 9.9990 chunk 79 optimal weight: 0.9980 overall best weight: 1.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 627 ASN ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 GLN A 915 GLN A1088 GLN B 827 ASN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN C 96 ASN C 112 GLN C 546 GLN C 901 ASN C1053 GLN C1095 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 24971 Z= 0.167 Angle : 0.549 10.542 33933 Z= 0.299 Chirality : 0.045 0.212 3917 Planarity : 0.004 0.067 4352 Dihedral : 6.392 55.330 4029 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.27 % Favored : 95.69 % Rotamer: Outliers : 2.16 % Allowed : 8.83 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.14), residues: 3018 helix: 1.60 (0.20), residues: 708 sheet: 0.79 (0.21), residues: 546 loop : -1.52 (0.13), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 423 HIS 0.007 0.001 HIS A1065 PHE 0.012 0.001 PHE A 334 TYR 0.019 0.001 TYR C 352 ARG 0.003 0.000 ARG B 99 *********************** 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 329 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 272 time to evaluate : 2.647 Fit side-chains revert: symmetry clash REVERT: A 277 ASP cc_start: 0.8085 (t0) cc_final: 0.7808 (t0) REVERT: A 544 ARG cc_start: 0.6902 (OUTLIER) cc_final: 0.6684 (mtp85) REVERT: A 730 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6879 (pm20) REVERT: A 911 LYS cc_start: 0.7585 (ttpp) cc_final: 0.7146 (mmtm) REVERT: A 1054 GLU cc_start: 0.6807 (OUTLIER) cc_final: 0.6476 (pm20) REVERT: A 1088 GLN cc_start: 0.6859 (pt0) cc_final: 0.6637 (pt0) REVERT: B 306 ARG cc_start: 0.7494 (OUTLIER) cc_final: 0.6933 (mtt90) REVERT: B 484 TYR cc_start: 0.7757 (m-80) cc_final: 0.7513 (m-80) REVERT: B 758 ARG cc_start: 0.7747 (ttm170) cc_final: 0.7353 (ttp-110) REVERT: B 762 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7415 (mt-10) REVERT: B 790 ASP cc_start: 0.6863 (t0) cc_final: 0.6214 (t70) REVERT: B 884 MET cc_start: 0.7774 (tpt) cc_final: 0.7324 (tpt) REVERT: B 1098 THR cc_start: 0.5742 (m) cc_final: 0.5393 (p) REVERT: C 54 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8154 (tp) REVERT: C 107 MET cc_start: 0.8120 (mmm) cc_final: 0.7703 (mmt) REVERT: C 449 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7146 (mtp180) REVERT: C 624 THR cc_start: 0.5660 (OUTLIER) cc_final: 0.5302 (t) REVERT: C 647 GLU cc_start: 0.6305 (tp30) cc_final: 0.5861 (tm-30) outliers start: 57 outliers final: 24 residues processed: 306 average time/residue: 1.4368 time to fit residues: 502.7301 Evaluate side-chains 283 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 251 time to evaluate : 2.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 544 ARG 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 769 GLN 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 A residue 1098 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 306 ARG Chi-restraints excluded: chain B residue 426 ARG 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 1054 GLU 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 260 THR Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 693 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 246 optimal weight: 7.9990 chunk 167 optimal weight: 9.9990 chunk 4 optimal weight: 0.9990 chunk 220 optimal weight: 10.0000 chunk 122 optimal weight: 6.9990 chunk 252 optimal weight: 10.0000 chunk 204 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 151 optimal weight: 7.9990 chunk 265 optimal weight: 9.9990 chunk 74 optimal weight: 0.8980 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN A 505 ASN A 889 ASN A 908 GLN A 915 GLN B 445 HIS B 827 ASN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN C 32 GLN C 74 HIS C 96 ASN C 546 GLN C 626 ASN 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: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 24971 Z= 0.356 Angle : 0.725 12.489 33933 Z= 0.396 Chirality : 0.051 0.252 3917 Planarity : 0.006 0.068 4352 Dihedral : 7.001 53.677 4026 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.40 % Favored : 94.57 % Rotamer: Outliers : 3.22 % Allowed : 9.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.14), residues: 3018 helix: 1.08 (0.19), residues: 723 sheet: 0.70 (0.21), residues: 564 loop : -1.68 (0.12), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 423 HIS 0.009 0.002 HIS C1065 PHE 0.020 0.003 PHE A1091 TYR 0.023 0.003 TYR B 352 ARG 0.007 0.001 ARG B 982 *********************** 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 334 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 249 time to evaluate : 2.784 Fit side-chains revert: symmetry clash REVERT: A 31 THR cc_start: 0.7035 (OUTLIER) cc_final: 0.6807 (t) REVERT: A 132 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.6686 (mm) REVERT: A 433 THR cc_start: 0.6614 (OUTLIER) cc_final: 0.6357 (t) REVERT: A 544 ARG cc_start: 0.6833 (OUTLIER) cc_final: 0.6611 (mtp85) REVERT: A 589 ASN cc_start: 0.6466 (OUTLIER) cc_final: 0.5880 (p0) REVERT: A 593 GLU cc_start: 0.6847 (OUTLIER) cc_final: 0.6558 (tt0) REVERT: A 730 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6982 (pm20) REVERT: A 1053 GLN cc_start: 0.6909 (OUTLIER) cc_final: 0.6504 (mt0) REVERT: A 1054 GLU cc_start: 0.6846 (OUTLIER) cc_final: 0.6459 (pm20) REVERT: B 758 ARG cc_start: 0.7737 (ttm170) cc_final: 0.7412 (ttp80) REVERT: B 762 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7633 (mt-10) REVERT: B 769 GLN cc_start: 0.7334 (OUTLIER) cc_final: 0.7056 (tt0) REVERT: B 790 ASP cc_start: 0.7027 (t0) cc_final: 0.6394 (t70) REVERT: B 884 MET cc_start: 0.7807 (tpt) cc_final: 0.7478 (tpt) REVERT: B 1098 THR cc_start: 0.5934 (m) cc_final: 0.5567 (p) REVERT: B 1103 PHE cc_start: 0.7504 (p90) cc_final: 0.7247 (p90) REVERT: C 54 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8165 (tp) REVERT: C 449 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7172 (mtp180) REVERT: C 624 THR cc_start: 0.6332 (OUTLIER) cc_final: 0.5954 (t) REVERT: C 707 GLU cc_start: 0.7996 (tt0) cc_final: 0.7783 (tt0) REVERT: C 894 THR cc_start: 0.7826 (OUTLIER) cc_final: 0.7589 (p) outliers start: 85 outliers final: 40 residues processed: 307 average time/residue: 1.4526 time to fit residues: 509.1933 Evaluate side-chains 295 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 240 time to evaluate : 2.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 544 ARG 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 679 MET Chi-restraints excluded: chain A residue 730 GLU Chi-restraints excluded: chain A residue 816 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 1058 THR 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 468 THR 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 1054 GLU 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 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 809 THR Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 894 THR Chi-restraints excluded: chain C residue 898 LEU Chi-restraints excluded: chain C residue 916 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 99 optimal weight: 6.9990 chunk 266 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 173 optimal weight: 0.6980 chunk 73 optimal weight: 9.9990 chunk 296 optimal weight: 3.9990 chunk 245 optimal weight: 4.9990 chunk 137 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 155 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** B 992 GLN C 32 GLN C 96 ASN C 546 GLN C 627 ASN ** C 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1053 GLN C1065 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 24971 Z= 0.205 Angle : 0.582 10.757 33933 Z= 0.318 Chirality : 0.046 0.207 3917 Planarity : 0.004 0.055 4352 Dihedral : 6.370 54.777 4026 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.24 % Favored : 95.73 % Rotamer: Outliers : 2.50 % Allowed : 10.49 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.14), residues: 3018 helix: 1.46 (0.20), residues: 708 sheet: 0.82 (0.21), residues: 564 loop : -1.64 (0.13), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 423 HIS 0.006 0.001 HIS C1065 PHE 0.015 0.002 PHE B 578 TYR 0.021 0.002 TYR A 352 ARG 0.003 0.000 ARG C 758 *********************** 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 317 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 251 time to evaluate : 2.902 Fit side-chains revert: symmetry clash REVERT: A 92 THR cc_start: 0.7567 (OUTLIER) cc_final: 0.7324 (p) REVERT: A 132 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.6698 (mm) REVERT: A 277 ASP cc_start: 0.8170 (t0) cc_final: 0.7879 (t0) REVERT: A 544 ARG cc_start: 0.6901 (OUTLIER) cc_final: 0.6674 (mtp85) REVERT: A 589 ASN cc_start: 0.6515 (OUTLIER) cc_final: 0.5926 (p0) REVERT: A 730 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6846 (pm20) REVERT: A 1053 GLN cc_start: 0.6813 (OUTLIER) cc_final: 0.6443 (mt0) REVERT: A 1054 GLU cc_start: 0.6807 (OUTLIER) cc_final: 0.6505 (pm20) REVERT: B 758 ARG cc_start: 0.7748 (ttm170) cc_final: 0.7264 (ttp-110) REVERT: B 762 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7537 (mt-10) REVERT: B 769 GLN cc_start: 0.7301 (OUTLIER) cc_final: 0.7045 (tt0) REVERT: B 884 MET cc_start: 0.7763 (tpt) cc_final: 0.7415 (tpt) REVERT: B 1098 THR cc_start: 0.5587 (m) cc_final: 0.5287 (p) REVERT: B 1103 PHE cc_start: 0.7552 (p90) cc_final: 0.7289 (p90) REVERT: C 54 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8163 (tp) REVERT: C 449 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7164 (mtp180) REVERT: C 624 THR cc_start: 0.5512 (OUTLIER) cc_final: 0.5154 (t) REVERT: C 647 GLU cc_start: 0.6541 (tp30) cc_final: 0.6066 (tm-30) REVERT: C 707 GLU cc_start: 0.8035 (tt0) cc_final: 0.7802 (tt0) REVERT: C 917 GLN cc_start: 0.7617 (tt0) cc_final: 0.7365 (tt0) outliers start: 66 outliers final: 36 residues processed: 295 average time/residue: 1.4608 time to fit residues: 493.2964 Evaluate side-chains 297 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 249 time to evaluate : 2.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 544 ARG Chi-restraints excluded: chain A residue 589 ASN 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 769 GLN 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 150 THR Chi-restraints excluded: chain B residue 426 ARG Chi-restraints excluded: chain B residue 447 LYS 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 769 GLN 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 918 GLU Chi-restraints excluded: chain B residue 1054 GLU 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 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 898 LEU Chi-restraints excluded: chain C residue 916 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 285 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 168 optimal weight: 5.9990 chunk 216 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 249 optimal weight: 3.9990 chunk 165 optimal weight: 8.9990 chunk 294 optimal weight: 6.9990 chunk 184 optimal weight: 5.9990 chunk 179 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** B 992 GLN C 32 GLN C 96 ASN C 546 GLN ** C 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1053 GLN C1065 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 24971 Z= 0.219 Angle : 0.593 10.540 33933 Z= 0.324 Chirality : 0.046 0.205 3917 Planarity : 0.005 0.055 4352 Dihedral : 6.306 55.130 4026 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.00 % Favored : 94.93 % Rotamer: Outliers : 2.69 % Allowed : 10.57 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.14), residues: 3018 helix: 1.47 (0.20), residues: 711 sheet: 0.72 (0.21), residues: 546 loop : -1.59 (0.13), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 423 HIS 0.006 0.001 HIS C1065 PHE 0.014 0.002 PHE B 578 TYR 0.021 0.002 TYR A 352 ARG 0.004 0.001 ARG C 758 *********************** 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 318 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 247 time to evaluate : 2.805 Fit side-chains revert: symmetry clash REVERT: A 72 ILE cc_start: 0.2823 (OUTLIER) cc_final: 0.1962 (tt) REVERT: A 132 LEU cc_start: 0.7442 (OUTLIER) cc_final: 0.6698 (mm) REVERT: A 277 ASP cc_start: 0.8155 (t0) cc_final: 0.7904 (t0) REVERT: A 544 ARG cc_start: 0.6907 (OUTLIER) cc_final: 0.6667 (mtp85) REVERT: A 589 ASN cc_start: 0.6514 (OUTLIER) cc_final: 0.5931 (p0) REVERT: A 593 GLU cc_start: 0.6906 (OUTLIER) cc_final: 0.6627 (tt0) REVERT: A 730 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6933 (pm20) REVERT: A 911 LYS cc_start: 0.7571 (ttpp) cc_final: 0.7273 (mppt) REVERT: A 1053 GLN cc_start: 0.6832 (OUTLIER) cc_final: 0.6450 (mt0) REVERT: A 1054 GLU cc_start: 0.6807 (OUTLIER) cc_final: 0.6519 (pm20) REVERT: B 285 GLU cc_start: 0.7374 (tp30) cc_final: 0.7056 (tp30) REVERT: B 758 ARG cc_start: 0.7747 (ttm170) cc_final: 0.7262 (ttp-110) REVERT: B 762 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7546 (mt-10) REVERT: B 769 GLN cc_start: 0.7333 (OUTLIER) cc_final: 0.7097 (tt0) REVERT: B 884 MET cc_start: 0.7729 (tpt) cc_final: 0.7427 (tpt) REVERT: B 1098 THR cc_start: 0.5607 (m) cc_final: 0.5314 (p) REVERT: B 1103 PHE cc_start: 0.7560 (p90) cc_final: 0.7288 (p90) REVERT: C 54 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8152 (tp) REVERT: C 164 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.8037 (mm) REVERT: C 333 LYS cc_start: 0.7835 (OUTLIER) cc_final: 0.7039 (tmtm) REVERT: C 449 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7163 (mtp180) REVERT: C 624 THR cc_start: 0.5650 (OUTLIER) cc_final: 0.5218 (t) REVERT: C 647 GLU cc_start: 0.6615 (tp30) cc_final: 0.6067 (tm-30) REVERT: C 707 GLU cc_start: 0.7982 (tt0) cc_final: 0.7730 (tt0) REVERT: C 917 GLN cc_start: 0.7661 (tt0) cc_final: 0.7433 (tt0) outliers start: 71 outliers final: 41 residues processed: 297 average time/residue: 1.5341 time to fit residues: 518.3011 Evaluate side-chains 297 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 241 time to evaluate : 2.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 544 ARG 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 632 GLN 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 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 769 GLN 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 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 823 LEU Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 898 LEU Chi-restraints excluded: chain C residue 916 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 182 optimal weight: 1.9990 chunk 117 optimal weight: 20.0000 chunk 176 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 57 optimal weight: 0.0670 chunk 187 optimal weight: 10.0000 chunk 200 optimal weight: 2.9990 chunk 145 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 231 optimal weight: 10.0000 chunk 268 optimal weight: 1.9990 overall best weight: 2.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 GLN A 915 GLN A1065 HIS B 827 ASN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN C 32 GLN C 96 ASN C 546 GLN ** C 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1053 GLN C1065 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 24971 Z= 0.207 Angle : 0.579 10.354 33933 Z= 0.316 Chirality : 0.046 0.206 3917 Planarity : 0.004 0.052 4352 Dihedral : 6.203 55.749 4026 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.80 % Favored : 95.16 % Rotamer: Outliers : 2.61 % Allowed : 10.80 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.14), residues: 3018 helix: 1.55 (0.20), residues: 708 sheet: 0.74 (0.21), residues: 546 loop : -1.59 (0.13), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 423 HIS 0.006 0.001 HIS C1065 PHE 0.014 0.002 PHE B 578 TYR 0.021 0.002 TYR A 352 ARG 0.004 0.000 ARG C 758 *********************** 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 317 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 248 time to evaluate : 2.796 Fit side-chains revert: symmetry clash REVERT: A 72 ILE cc_start: 0.2852 (OUTLIER) cc_final: 0.2019 (tt) REVERT: A 92 THR cc_start: 0.7567 (OUTLIER) cc_final: 0.7357 (p) REVERT: A 132 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.6696 (mm) REVERT: A 277 ASP cc_start: 0.8138 (t0) cc_final: 0.7870 (t0) REVERT: A 544 ARG cc_start: 0.6908 (OUTLIER) cc_final: 0.6669 (mtp85) REVERT: A 589 ASN cc_start: 0.6506 (OUTLIER) cc_final: 0.5923 (p0) REVERT: A 593 GLU cc_start: 0.6887 (OUTLIER) cc_final: 0.6611 (tt0) REVERT: A 730 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6952 (pm20) REVERT: A 1053 GLN cc_start: 0.6821 (OUTLIER) cc_final: 0.6443 (mt0) REVERT: A 1054 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.6508 (pm20) REVERT: B 285 GLU cc_start: 0.7384 (tp30) cc_final: 0.7076 (tp30) REVERT: B 758 ARG cc_start: 0.7754 (ttm170) cc_final: 0.7274 (ttp-110) REVERT: B 762 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7533 (mt-10) REVERT: B 769 GLN cc_start: 0.7321 (OUTLIER) cc_final: 0.7086 (tt0) REVERT: B 884 MET cc_start: 0.7732 (tpt) cc_final: 0.7424 (tpt) REVERT: B 1098 THR cc_start: 0.5724 (m) cc_final: 0.5465 (p) REVERT: B 1103 PHE cc_start: 0.7552 (p90) cc_final: 0.7262 (p90) REVERT: C 54 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8165 (tp) REVERT: C 164 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.8090 (mm) REVERT: C 449 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7149 (mtp180) REVERT: C 624 THR cc_start: 0.5591 (OUTLIER) cc_final: 0.5156 (t) REVERT: C 647 GLU cc_start: 0.6527 (tp30) cc_final: 0.5959 (tm-30) REVERT: C 707 GLU cc_start: 0.8004 (tt0) cc_final: 0.7568 (tt0) REVERT: C 911 LYS cc_start: 0.7841 (OUTLIER) cc_final: 0.7342 (tmtt) outliers start: 69 outliers final: 41 residues processed: 299 average time/residue: 1.4753 time to fit residues: 504.5406 Evaluate side-chains 299 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 242 time to evaluate : 4.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 544 ARG 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 769 GLN 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 1098 THR Chi-restraints excluded: chain B residue 55 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 769 GLN 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 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 85 ASP 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 898 LEU Chi-restraints excluded: chain C residue 911 LYS 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 282 optimal weight: 10.0000 chunk 257 optimal weight: 0.0470 chunk 274 optimal weight: 6.9990 chunk 165 optimal weight: 9.9990 chunk 119 optimal weight: 0.0980 chunk 215 optimal weight: 3.9990 chunk 84 optimal weight: 9.9990 chunk 248 optimal weight: 7.9990 chunk 259 optimal weight: 9.9990 chunk 273 optimal weight: 0.8980 chunk 180 optimal weight: 20.0000 overall best weight: 2.4082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** B 992 GLN C 96 ASN C 546 GLN ** C 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1053 GLN C1065 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24971 Z= 0.207 Angle : 0.580 10.243 33933 Z= 0.316 Chirality : 0.046 0.206 3917 Planarity : 0.005 0.052 4352 Dihedral : 6.187 55.840 4026 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.07 % Favored : 94.90 % Rotamer: Outliers : 2.54 % Allowed : 11.14 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.14), residues: 3018 helix: 1.56 (0.20), residues: 708 sheet: 0.78 (0.21), residues: 543 loop : -1.59 (0.13), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 423 HIS 0.007 0.001 HIS C1065 PHE 0.014 0.002 PHE B 578 TYR 0.021 0.002 TYR A 352 ARG 0.003 0.000 ARG C 758 *********************** 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 fitting. rotamer outliers: 67 poor density : 245 time to evaluate : 2.810 Fit side-chains revert: symmetry clash REVERT: A 72 ILE cc_start: 0.2857 (OUTLIER) cc_final: 0.2036 (tt) REVERT: A 92 THR cc_start: 0.7578 (OUTLIER) cc_final: 0.7378 (p) REVERT: A 132 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.6691 (mm) REVERT: A 277 ASP cc_start: 0.8138 (t0) cc_final: 0.7864 (t0) REVERT: A 544 ARG cc_start: 0.6904 (OUTLIER) cc_final: 0.6668 (mtp85) REVERT: A 589 ASN cc_start: 0.6504 (OUTLIER) cc_final: 0.5923 (p0) REVERT: A 593 GLU cc_start: 0.6884 (OUTLIER) cc_final: 0.6616 (tt0) REVERT: A 730 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6899 (pm20) REVERT: A 911 LYS cc_start: 0.7568 (ttpp) cc_final: 0.7174 (mmtm) REVERT: A 1053 GLN cc_start: 0.6825 (OUTLIER) cc_final: 0.6446 (mt0) REVERT: A 1054 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.6507 (pm20) REVERT: B 285 GLU cc_start: 0.7384 (tp30) cc_final: 0.7077 (tp30) REVERT: B 758 ARG cc_start: 0.7755 (ttm170) cc_final: 0.7274 (ttp-110) REVERT: B 762 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7532 (mt-10) REVERT: B 769 GLN cc_start: 0.7320 (OUTLIER) cc_final: 0.7084 (tt0) REVERT: B 884 MET cc_start: 0.7736 (tpt) cc_final: 0.7442 (tpt) REVERT: B 1098 THR cc_start: 0.5724 (m) cc_final: 0.5472 (p) REVERT: B 1103 PHE cc_start: 0.7561 (p90) cc_final: 0.7267 (p90) REVERT: C 54 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8163 (tp) REVERT: C 164 ILE cc_start: 0.8341 (OUTLIER) cc_final: 0.8091 (mm) REVERT: C 449 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7149 (mtp180) REVERT: C 624 THR cc_start: 0.5648 (OUTLIER) cc_final: 0.5210 (t) REVERT: C 647 GLU cc_start: 0.6526 (tp30) cc_final: 0.5957 (tm-30) REVERT: C 707 GLU cc_start: 0.8005 (tt0) cc_final: 0.7567 (tt0) REVERT: C 911 LYS cc_start: 0.7834 (OUTLIER) cc_final: 0.7332 (tmtt) REVERT: C 1085 PHE cc_start: 0.7095 (m-80) cc_final: 0.6712 (m-80) outliers start: 67 outliers final: 45 residues processed: 291 average time/residue: 1.6006 time to fit residues: 531.0651 Evaluate side-chains 304 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 243 time to evaluate : 2.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 544 ARG 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 769 GLN 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 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 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 769 GLN 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 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 85 ASP 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 769 GLN Chi-restraints excluded: chain C residue 776 LEU 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 898 LEU Chi-restraints excluded: chain C residue 911 LYS 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 290 optimal weight: 9.9990 chunk 177 optimal weight: 6.9990 chunk 137 optimal weight: 10.0000 chunk 202 optimal weight: 6.9990 chunk 304 optimal weight: 10.0000 chunk 280 optimal weight: 2.9990 chunk 242 optimal weight: 8.9990 chunk 25 optimal weight: 0.9980 chunk 187 optimal weight: 10.0000 chunk 148 optimal weight: 6.9990 chunk 192 optimal weight: 5.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 889 ASN A 908 GLN A 915 GLN B 827 ASN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN C 96 ASN C 435 ASN C 546 GLN ** C 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1053 GLN C1065 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 24971 Z= 0.344 Angle : 0.703 11.160 33933 Z= 0.384 Chirality : 0.050 0.235 3917 Planarity : 0.005 0.054 4352 Dihedral : 6.777 53.091 4026 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.50 % Allowed : 11.14 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.14), residues: 3018 helix: 1.13 (0.19), residues: 723 sheet: 0.67 (0.21), residues: 570 loop : -1.68 (0.13), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 423 HIS 0.009 0.002 HIS C1065 PHE 0.019 0.002 PHE B1092 TYR 0.024 0.002 TYR B 352 ARG 0.008 0.001 ARG B 982 ********************** 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 309 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 243 time to evaluate : 2.550 Fit side-chains revert: symmetry clash REVERT: A 132 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.6655 (mm) REVERT: A 544 ARG cc_start: 0.6924 (OUTLIER) cc_final: 0.6695 (mtp85) REVERT: A 589 ASN cc_start: 0.6473 (OUTLIER) cc_final: 0.5891 (p0) REVERT: A 593 GLU cc_start: 0.6846 (OUTLIER) cc_final: 0.6568 (tt0) REVERT: A 730 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6979 (pm20) REVERT: A 1053 GLN cc_start: 0.6943 (OUTLIER) cc_final: 0.6548 (mt0) REVERT: A 1054 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.6470 (pm20) REVERT: B 274 ASP cc_start: 0.8025 (OUTLIER) cc_final: 0.7658 (m-30) REVERT: B 762 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7590 (mt-10) REVERT: B 769 GLN cc_start: 0.7326 (OUTLIER) cc_final: 0.7050 (tt0) REVERT: B 884 MET cc_start: 0.7756 (tpt) cc_final: 0.7449 (tpt) REVERT: B 984 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7707 (tm-30) REVERT: B 1098 THR cc_start: 0.5805 (m) cc_final: 0.5543 (p) REVERT: B 1103 PHE cc_start: 0.7583 (p90) cc_final: 0.7297 (p90) REVERT: C 54 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8164 (tp) REVERT: C 164 ILE cc_start: 0.8290 (OUTLIER) cc_final: 0.8050 (mm) REVERT: C 449 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7173 (mtp180) REVERT: C 624 THR cc_start: 0.5734 (OUTLIER) cc_final: 0.5299 (t) REVERT: C 707 GLU cc_start: 0.8010 (tt0) cc_final: 0.7691 (tt0) REVERT: C 911 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7374 (tmtt) outliers start: 66 outliers final: 43 residues processed: 288 average time/residue: 1.5192 time to fit residues: 498.7228 Evaluate side-chains 299 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 240 time to evaluate : 2.656 ------------------------------------------------------------------------------- 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 332 THR Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 544 ARG 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 769 GLN 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 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 447 LYS 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 898 LEU Chi-restraints excluded: chain B residue 904 GLN Chi-restraints excluded: chain B residue 984 GLN Chi-restraints excluded: chain B residue 1054 GLU 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 769 GLN Chi-restraints excluded: chain C residue 776 LEU 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 898 LEU Chi-restraints excluded: chain C residue 911 LYS Chi-restraints excluded: chain C residue 916 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 8.9990 chunk 74 optimal weight: 0.7980 chunk 223 optimal weight: 10.0000 chunk 35 optimal weight: 0.0970 chunk 67 optimal weight: 5.9990 chunk 243 optimal weight: 10.0000 chunk 101 optimal weight: 0.5980 chunk 249 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 213 optimal weight: 8.9990 overall best weight: 1.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 786 GLN ** 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** B 992 GLN C 32 GLN C 96 ASN C 546 GLN C 769 GLN ** C 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1053 GLN C1065 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.132656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.105386 restraints weight = 28482.902| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.67 r_work: 0.2938 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 24971 Z= 0.152 Angle : 0.530 11.722 33933 Z= 0.288 Chirality : 0.044 0.224 3917 Planarity : 0.004 0.048 4352 Dihedral : 5.940 57.623 4026 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.04 % Favored : 95.92 % Rotamer: Outliers : 2.12 % Allowed : 11.89 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.14), residues: 3018 helix: 1.68 (0.20), residues: 708 sheet: 0.83 (0.21), residues: 543 loop : -1.54 (0.13), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 423 HIS 0.006 0.001 HIS C1065 PHE 0.013 0.001 PHE B 799 TYR 0.021 0.001 TYR A 352 ARG 0.003 0.000 ARG C 758 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8558.64 seconds wall clock time: 150 minutes 42.09 seconds (9042.09 seconds total)