Starting phenix.real_space_refine on Sat Mar 7 06:07:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xo8_33340/03_2026/7xo8_33340.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xo8_33340/03_2026/7xo8_33340.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xo8_33340/03_2026/7xo8_33340.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xo8_33340/03_2026/7xo8_33340.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xo8_33340/03_2026/7xo8_33340.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xo8_33340/03_2026/7xo8_33340.map" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 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: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 S 192 5.16 5 Cl 3 4.86 5 C 25008 2.51 5 N 6444 2.21 5 O 7476 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 175 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39126 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 8001 Classifications: {'peptide': 1026} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 56, 'TRANS': 969} Chain breaks: 7 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 8001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 8001 Classifications: {'peptide': 1026} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 56, 'TRANS': 969} Chain breaks: 7 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "C" Number of atoms: 8001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 8001 Classifications: {'peptide': 1026} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 56, 'TRANS': 969} Chain breaks: 7 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "D" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain: "F" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain: "E" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' CL': 1, ' ZN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' CL': 1, ' ZN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' CL': 1, ' ZN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 8.06, per 1000 atoms: 0.21 Number of scatterers: 39126 At special positions: 0 Unit cell: (160.68, 154.912, 240.608, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 Cl 3 17.00 S 192 16.00 O 7476 8.00 N 6444 7.00 C 25008 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=1.46 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.09 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " 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 NAG-ASN " NAG A1301 " - " ASN A1074 " " NAG A1302 " - " ASN A1098 " " NAG A1303 " - " ASN A 801 " " NAG A1304 " - " ASN A 709 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 603 " " NAG A1308 " - " ASN A1134 " " NAG A1309 " - " ASN A 61 " " NAG A1310 " - " ASN A 122 " " NAG A1311 " - " ASN A 331 " " NAG B1301 " - " ASN B1074 " " NAG B1302 " - " ASN B1098 " " NAG B1303 " - " ASN B 801 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B1134 " " NAG B1307 " - " ASN B 61 " " NAG B1308 " - " ASN B 122 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B 657 " " NAG B1311 " - " ASN B 331 " " NAG C1301 " - " ASN C1074 " " NAG C1302 " - " ASN C1098 " " NAG C1303 " - " ASN C 801 " " NAG C1304 " - " ASN C 709 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C1134 " " NAG C1308 " - " ASN C 61 " " NAG C1309 " - " ASN C 122 " " NAG C1310 " - " ASN C 331 " " NAG C1311 " - " ASN C 657 " " NAG D 903 " - " ASN D 546 " " NAG D 904 " - " ASN D 90 " " NAG E 903 " - " ASN E 546 " " NAG E 904 " - " ASN E 90 " " NAG F 903 " - " ASN F 546 " " NAG F 904 " - " ASN F 90 " Time building additional restraints: 3.04 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 902 " pdb="ZN ZN D 902 " - pdb=" NE2 HIS D 374 " pdb=" ZN E 902 " pdb="ZN ZN E 902 " - pdb=" NE2 HIS E 374 " pdb=" ZN F 902 " pdb="ZN ZN F 902 " - pdb=" NE2 HIS F 374 " 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9144 Finding SS restraints... Secondary structure from input PDB file: 155 helices and 51 sheets defined 39.8% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 366 through 370 removed outlier: 4.101A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 390 removed outlier: 3.607A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.356A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.775A pdb=" N ASP A 420 " --> pdb=" O GLY A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.883A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.502A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 778 removed outlier: 3.865A pdb=" N LYS A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG A 765 " --> pdb=" O THR A 761 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 868 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.693A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 removed outlier: 4.013A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.064A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N VAL A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.628A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 988 Processing helix chain 'A' and resid 989 through 1033 removed outlier: 3.504A pdb=" N LEU A1004 " --> pdb=" O ARG A1000 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR A1006 " --> pdb=" O GLN A1002 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.813A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 370 Processing helix chain 'B' and resid 385 through 390 removed outlier: 3.607A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.356A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.775A pdb=" N ASP B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.884A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.502A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 778 removed outlier: 3.866A pdb=" N LYS B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG B 765 " --> pdb=" O THR B 761 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 868 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.692A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 removed outlier: 4.013A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.064A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.628A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 988 Processing helix chain 'B' and resid 989 through 1033 removed outlier: 3.504A pdb=" N LEU B1004 " --> pdb=" O ARG B1000 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR B1006 " --> pdb=" O GLN B1002 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 366 through 370 Processing helix chain 'C' and resid 385 through 390 removed outlier: 3.605A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.356A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.776A pdb=" N ASP C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.832A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.716A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 778 removed outlier: 3.843A pdb=" N LYS C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG C 765 " --> pdb=" O THR C 761 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 868 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.687A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.741A pdb=" N ILE C 923 " --> pdb=" O ASN C 919 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER C 940 " --> pdb=" O ASP C 936 " (cutoff:3.500A) Processing helix chain 'C' and resid 943 through 947 removed outlier: 4.503A pdb=" N LYS C 947 " --> pdb=" O ALA C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 949 through 959 Processing helix chain 'C' and resid 960 through 965 Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.718A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 988 Processing helix chain 'C' and resid 989 through 1033 removed outlier: 3.618A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing helix chain 'D' and resid 20 through 53 removed outlier: 3.652A pdb=" N GLN D 24 " --> pdb=" O THR D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.617A pdb=" N GLN D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 108 removed outlier: 4.002A pdb=" N SER D 106 " --> pdb=" O ASN D 103 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU D 108 " --> pdb=" O SER D 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 108' Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 147 through 155 Processing helix chain 'D' and resid 157 through 194 removed outlier: 3.615A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LYS D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLN D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 3.647A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 218 through 252 removed outlier: 3.957A pdb=" N LEU D 222 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 4.751A pdb=" N ASN D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 293 through 299 Processing helix chain 'D' and resid 303 through 319 removed outlier: 3.503A pdb=" N GLY D 319 " --> pdb=" O PHE D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 331 removed outlier: 3.866A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.671A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.920A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 444 Processing helix chain 'D' and resid 449 through 466 Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 485 Processing helix chain 'D' and resid 499 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 531 removed outlier: 3.542A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN D 531 " --> pdb=" O GLU D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.743A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 574 removed outlier: 3.598A pdb=" N VAL D 573 " --> pdb=" O ALA D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 599 Processing helix chain 'F' and resid 20 through 53 removed outlier: 3.653A pdb=" N GLN F 24 " --> pdb=" O THR F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 81 Processing helix chain 'F' and resid 90 through 102 removed outlier: 3.617A pdb=" N GLN F 102 " --> pdb=" O GLN F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 108 removed outlier: 4.001A pdb=" N SER F 106 " --> pdb=" O ASN F 103 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL F 107 " --> pdb=" O GLY F 104 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU F 108 " --> pdb=" O SER F 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 103 through 108' Processing helix chain 'F' and resid 109 through 129 Processing helix chain 'F' and resid 147 through 155 Processing helix chain 'F' and resid 157 through 194 removed outlier: 3.616A pdb=" N ARG F 169 " --> pdb=" O TRP F 165 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LYS F 174 " --> pdb=" O SER F 170 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLN F 175 " --> pdb=" O GLU F 171 " (cutoff:3.500A) Proline residue: F 178 - end of helix removed outlier: 3.649A pdb=" N GLU F 182 " --> pdb=" O PRO F 178 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL F 185 " --> pdb=" O GLU F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 205 Processing helix chain 'F' and resid 206 through 208 No H-bonds generated for 'chain 'F' and resid 206 through 208' Processing helix chain 'F' and resid 218 through 252 removed outlier: 3.957A pdb=" N LEU F 222 " --> pdb=" O SER F 218 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ILE F 223 " --> pdb=" O ARG F 219 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU F 224 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU F 232 " --> pdb=" O HIS F 228 " (cutoff:3.500A) Proline residue: F 235 - end of helix removed outlier: 4.751A pdb=" N ASN F 250 " --> pdb=" O ALA F 246 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA F 251 " --> pdb=" O LYS F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 267 No H-bonds generated for 'chain 'F' and resid 265 through 267' Processing helix chain 'F' and resid 275 through 279 Processing helix chain 'F' and resid 293 through 299 Processing helix chain 'F' and resid 303 through 319 removed outlier: 3.504A pdb=" N GLY F 319 " --> pdb=" O PHE F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 331 removed outlier: 3.868A pdb=" N TRP F 328 " --> pdb=" O THR F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 385 removed outlier: 3.671A pdb=" N TYR F 385 " --> pdb=" O TYR F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 393 Processing helix chain 'F' and resid 399 through 413 removed outlier: 3.920A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER F 409 " --> pdb=" O GLY F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 421 Processing helix chain 'F' and resid 431 through 444 Processing helix chain 'F' and resid 449 through 466 Processing helix chain 'F' and resid 469 through 471 No H-bonds generated for 'chain 'F' and resid 469 through 471' Processing helix chain 'F' and resid 472 through 485 Processing helix chain 'F' and resid 499 through 502 Processing helix chain 'F' and resid 503 through 508 Processing helix chain 'F' and resid 513 through 531 removed outlier: 3.541A pdb=" N THR F 519 " --> pdb=" O TYR F 515 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N PHE F 523 " --> pdb=" O THR F 519 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN F 531 " --> pdb=" O GLU F 527 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 542 Processing helix chain 'F' and resid 547 through 559 removed outlier: 3.743A pdb=" N MET F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 574 removed outlier: 3.595A pdb=" N VAL F 573 " --> pdb=" O ALA F 569 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 588 Processing helix chain 'F' and resid 588 through 599 Processing helix chain 'E' and resid 20 through 53 removed outlier: 3.652A pdb=" N GLN E 24 " --> pdb=" O THR E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 81 Processing helix chain 'E' and resid 90 through 102 removed outlier: 3.616A pdb=" N GLN E 102 " --> pdb=" O GLN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 108 removed outlier: 4.001A pdb=" N SER E 106 " --> pdb=" O ASN E 103 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL E 107 " --> pdb=" O GLY E 104 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU E 108 " --> pdb=" O SER E 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 103 through 108' Processing helix chain 'E' and resid 109 through 129 Processing helix chain 'E' and resid 147 through 155 Processing helix chain 'E' and resid 157 through 194 removed outlier: 3.616A pdb=" N ARG E 169 " --> pdb=" O TRP E 165 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LYS E 174 " --> pdb=" O SER E 170 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN E 175 " --> pdb=" O GLU E 171 " (cutoff:3.500A) Proline residue: E 178 - end of helix removed outlier: 3.647A pdb=" N GLU E 182 " --> pdb=" O PRO E 178 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL E 185 " --> pdb=" O GLU E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 205 Processing helix chain 'E' and resid 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'E' and resid 218 through 252 removed outlier: 3.957A pdb=" N LEU E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU E 232 " --> pdb=" O HIS E 228 " (cutoff:3.500A) Proline residue: E 235 - end of helix removed outlier: 4.751A pdb=" N ASN E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA E 251 " --> pdb=" O LYS E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 267 No H-bonds generated for 'chain 'E' and resid 265 through 267' Processing helix chain 'E' and resid 275 through 279 Processing helix chain 'E' and resid 293 through 299 Processing helix chain 'E' and resid 303 through 319 removed outlier: 3.504A pdb=" N GLY E 319 " --> pdb=" O PHE E 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 331 removed outlier: 3.867A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.671A pdb=" N TYR E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 393 Processing helix chain 'E' and resid 399 through 413 removed outlier: 3.920A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER E 409 " --> pdb=" O GLY E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 Processing helix chain 'E' and resid 431 through 444 Processing helix chain 'E' and resid 449 through 466 Processing helix chain 'E' and resid 469 through 471 No H-bonds generated for 'chain 'E' and resid 469 through 471' Processing helix chain 'E' and resid 472 through 485 Processing helix chain 'E' and resid 499 through 502 Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 513 through 531 removed outlier: 3.542A pdb=" N THR E 519 " --> pdb=" O TYR E 515 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN E 531 " --> pdb=" O GLU E 527 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 Processing helix chain 'E' and resid 547 through 559 removed outlier: 3.742A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 574 removed outlier: 3.598A pdb=" N VAL E 573 " --> pdb=" O ALA E 569 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 588 Processing helix chain 'E' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.644A pdb=" N SER A 31 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.607A pdb=" N HIS A 49 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 276 " --> pdb=" O VAL A 289 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 94 removed outlier: 3.799A pdb=" N LEU A 229 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 171 through 172 removed outlier: 4.338A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.757A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA A 609 " --> pdb=" O ILE A 598 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE A 643 " --> pdb=" O LEU A 650 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 356 removed outlier: 3.539A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.601A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 539 through 543 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.086A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 712 through 714 removed outlier: 3.639A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 717 through 728 removed outlier: 3.767A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB6, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.644A pdb=" N SER B 31 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.562A pdb=" N LEU B 276 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 90 through 94 removed outlier: 3.798A pdb=" N LEU B 229 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 171 through 172 removed outlier: 4.337A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 314 removed outlier: 3.757A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA B 609 " --> pdb=" O ILE B 598 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE B 643 " --> pdb=" O LEU B 650 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 325 through 326 Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 356 removed outlier: 3.539A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC5, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.601A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.085A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER B 673 " --> pdb=" O ILE B 693 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 712 through 714 removed outlier: 3.639A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 717 through 728 removed outlier: 3.767A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD1, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD2, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.764A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.514A pdb=" N LEU C 276 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 90 through 94 removed outlier: 4.265A pdb=" N LEU C 189 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 229 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 128 through 132 removed outlier: 4.114A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 311 through 316 removed outlier: 3.614A pdb=" N THR C 315 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE C 643 " --> pdb=" O LEU C 650 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 354 through 356 removed outlier: 3.540A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD9, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.603A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 539 through 543 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.047A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER C 673 " --> pdb=" O ILE C 693 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 712 through 714 removed outlier: 3.751A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 717 through 728 removed outlier: 3.725A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 733 through 736 removed outlier: 3.850A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE7, first strand: chain 'D' and resid 131 through 132 removed outlier: 3.644A pdb=" N VAL D 132 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU D 142 " --> pdb=" O VAL D 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.074A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.026A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 131 through 132 removed outlier: 3.645A pdb=" N VAL F 132 " --> pdb=" O LEU F 142 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU F 142 " --> pdb=" O VAL F 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'F' and resid 262 through 263 removed outlier: 6.073A pdb=" N LEU F 262 " --> pdb=" O VAL F 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'F' and resid 347 through 352 removed outlier: 6.026A pdb=" N ASP F 355 " --> pdb=" O LEU F 351 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 131 through 132 removed outlier: 3.644A pdb=" N VAL E 132 " --> pdb=" O LEU E 142 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU E 142 " --> pdb=" O VAL E 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'E' and resid 262 through 263 removed outlier: 6.074A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'E' and resid 347 through 352 removed outlier: 6.026A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 1623 hydrogen bonds defined for protein. 4521 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: 9.24 Time building geometry restraints manager: 3.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 6687 1.32 - 1.45: 11258 1.45 - 1.58: 21880 1.58 - 1.70: 0 1.70 - 1.83: 279 Bond restraints: 40104 Sorted by residual: bond pdb=" C PRO B 337 " pdb=" N PHE B 338 " ideal model delta sigma weight residual 1.335 1.262 0.073 1.34e-02 5.57e+03 2.96e+01 bond pdb=" N THR C 208 " pdb=" CA THR C 208 " ideal model delta sigma weight residual 1.453 1.488 -0.035 8.30e-03 1.45e+04 1.78e+01 bond pdb=" N PRO C 295 " pdb=" CA PRO C 295 " ideal model delta sigma weight residual 1.469 1.416 0.053 1.28e-02 6.10e+03 1.70e+01 bond pdb=" N THR C 333 " pdb=" CA THR C 333 " ideal model delta sigma weight residual 1.453 1.501 -0.049 1.18e-02 7.18e+03 1.69e+01 bond pdb=" N LEU A 517 " pdb=" CA LEU A 517 " ideal model delta sigma weight residual 1.455 1.505 -0.050 1.25e-02 6.40e+03 1.61e+01 ... (remaining 40099 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 53782 2.84 - 5.67: 679 5.67 - 8.51: 79 8.51 - 11.35: 15 11.35 - 14.19: 3 Bond angle restraints: 54558 Sorted by residual: angle pdb=" N SER C 530 " pdb=" CA SER C 530 " pdb=" C SER C 530 " ideal model delta sigma weight residual 108.23 122.42 -14.19 1.38e+00 5.25e-01 1.06e+02 angle pdb=" N PRO C 330 " pdb=" CA PRO C 330 " pdb=" C PRO C 330 " ideal model delta sigma weight residual 111.33 122.30 -10.97 1.43e+00 4.89e-01 5.88e+01 angle pdb=" CA PHE A 329 " pdb=" C PHE A 329 " pdb=" N PRO A 330 " ideal model delta sigma weight residual 117.71 124.59 -6.88 9.20e-01 1.18e+00 5.59e+01 angle pdb=" N GLU A 340 " pdb=" CA GLU A 340 " pdb=" C GLU A 340 " ideal model delta sigma weight residual 114.39 103.95 10.44 1.45e+00 4.76e-01 5.18e+01 angle pdb=" CA PHE C 329 " pdb=" C PHE C 329 " pdb=" O PHE C 329 " ideal model delta sigma weight residual 120.41 111.98 8.43 1.19e+00 7.06e-01 5.02e+01 ... (remaining 54553 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.65: 22749 21.65 - 43.29: 1262 43.29 - 64.94: 185 64.94 - 86.59: 49 86.59 - 108.23: 16 Dihedral angle restraints: 24261 sinusoidal: 10056 harmonic: 14205 Sorted by residual: dihedral pdb=" C THR C 523 " pdb=" N THR C 523 " pdb=" CA THR C 523 " pdb=" CB THR C 523 " ideal model delta harmonic sigma weight residual -122.00 -149.28 27.28 0 2.50e+00 1.60e-01 1.19e+02 dihedral pdb=" CB CYS C 131 " pdb=" SG CYS C 131 " pdb=" SG CYS C 166 " pdb=" CB CYS C 166 " ideal model delta sinusoidal sigma weight residual -86.00 -172.49 86.49 1 1.00e+01 1.00e-02 9.01e+01 dihedral pdb=" N THR C 523 " pdb=" C THR C 523 " pdb=" CA THR C 523 " pdb=" CB THR C 523 " ideal model delta harmonic sigma weight residual 123.40 146.10 -22.70 0 2.50e+00 1.60e-01 8.25e+01 ... (remaining 24258 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.313: 6088 0.313 - 0.625: 21 0.625 - 0.938: 3 0.938 - 1.251: 2 1.251 - 1.563: 3 Chirality restraints: 6117 Sorted by residual: chirality pdb=" C1 NAG C1302 " pdb=" ND2 ASN C1098 " pdb=" C2 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.40 -0.84 -1.56 2.00e-01 2.50e+01 6.11e+01 chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -0.86 -1.54 2.00e-01 2.50e+01 5.95e+01 chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -0.97 -1.43 2.00e-01 2.50e+01 5.15e+01 ... (remaining 6114 not shown) Planarity restraints: 7044 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1308 " -0.346 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG B1308 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG B1308 " -0.109 2.00e-02 2.50e+03 pdb=" N2 NAG B1308 " 0.533 2.00e-02 2.50e+03 pdb=" O7 NAG B1308 " -0.159 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1311 " 0.343 2.00e-02 2.50e+03 2.97e-01 1.10e+03 pdb=" C7 NAG C1311 " -0.079 2.00e-02 2.50e+03 pdb=" C8 NAG C1311 " 0.082 2.00e-02 2.50e+03 pdb=" N2 NAG C1311 " -0.527 2.00e-02 2.50e+03 pdb=" O7 NAG C1311 " 0.180 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1306 " 0.319 2.00e-02 2.50e+03 2.71e-01 9.17e+02 pdb=" C7 NAG A1306 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG A1306 " 0.182 2.00e-02 2.50e+03 pdb=" N2 NAG A1306 " -0.472 2.00e-02 2.50e+03 pdb=" O7 NAG A1306 " 0.051 2.00e-02 2.50e+03 ... (remaining 7041 not shown) Histogram of nonbonded interaction distances: 1.27 - 2.00: 7 2.00 - 2.72: 1920 2.72 - 3.45: 56090 3.45 - 4.17: 92360 4.17 - 4.90: 164857 Nonbonded interactions: 315234 Sorted by model distance: nonbonded pdb=" OG SER B 530 " pdb=" NE2 GLN B 580 " model vdw 1.275 3.120 nonbonded pdb=" OE1 GLU A 169 " pdb=" NH2 ARG B 357 " model vdw 1.298 3.120 nonbonded pdb=" CG2 THR B 323 " pdb=" OE1 GLU B 324 " model vdw 1.466 3.460 nonbonded pdb=" OD1 ASN C 360 " pdb=" OG1 THR C 523 " model vdw 1.747 3.040 nonbonded pdb=" CB SER B 530 " pdb=" NE2 GLN B 580 " model vdw 1.758 3.520 ... (remaining 315229 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.700 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 39.400 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.080 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:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4584 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 : 0.005 0.571 40176 Z= 0.285 Angle : 0.897 69.211 54735 Z= 0.489 Chirality : 0.069 1.563 6117 Planarity : 0.013 0.299 7005 Dihedral : 13.521 108.234 15027 Min Nonbonded Distance : 1.275 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.56 % Favored : 96.28 % Rotamer: Outliers : 0.45 % Allowed : 9.72 % Favored : 89.83 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.72 (0.11), residues: 4809 helix: -0.56 (0.11), residues: 1750 sheet: -1.76 (0.18), residues: 628 loop : -2.85 (0.11), residues: 2431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG A 328 TYR 0.023 0.001 TYR A 279 PHE 0.027 0.001 PHE C 329 TRP 0.006 0.001 TRP F 165 HIS 0.002 0.000 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00374 (40104) covalent geometry : angle 0.71432 (54558) SS BOND : bond 0.10494 ( 30) SS BOND : angle 11.96786 ( 60) hydrogen bonds : bond 0.16398 ( 1623) hydrogen bonds : angle 5.83521 ( 4521) metal coordination : bond 0.15567 ( 3) link_NAG-ASN : bond 0.02132 ( 39) link_NAG-ASN : angle 8.07226 ( 117) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 899 residues out of total 4269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 880 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 ILE cc_start: 0.4954 (OUTLIER) cc_final: 0.4657 (pt) REVERT: A 324 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7610 (mp0) REVERT: A 327 VAL cc_start: 0.8676 (t) cc_final: 0.8341 (p) REVERT: A 328 ARG cc_start: 0.7472 (mmm160) cc_final: 0.7092 (mtp85) REVERT: A 534 VAL cc_start: 0.8634 (t) cc_final: 0.8418 (m) REVERT: A 587 ILE cc_start: 0.7725 (mt) cc_final: 0.7448 (mt) REVERT: A 658 ASN cc_start: 0.7525 (p0) cc_final: 0.6387 (p0) REVERT: A 692 ILE cc_start: 0.8364 (mm) cc_final: 0.8163 (mt) REVERT: A 820 ASP cc_start: 0.7374 (t0) cc_final: 0.7073 (t0) REVERT: A 1073 LYS cc_start: 0.7519 (mtpp) cc_final: 0.7242 (mtpp) REVERT: A 1084 ASP cc_start: 0.7029 (m-30) cc_final: 0.6594 (t0) REVERT: A 1117 THR cc_start: 0.8027 (m) cc_final: 0.7799 (m) REVERT: B 190 ARG cc_start: 0.4855 (mtt180) cc_final: 0.3324 (mtt-85) REVERT: B 539 VAL cc_start: 0.6917 (m) cc_final: 0.6674 (m) REVERT: B 737 ASP cc_start: 0.6655 (t0) cc_final: 0.6450 (t0) REVERT: B 753 LEU cc_start: 0.7458 (tp) cc_final: 0.7200 (tp) REVERT: B 762 GLN cc_start: 0.7074 (tt0) cc_final: 0.6838 (tt0) REVERT: B 819 GLU cc_start: 0.6858 (mt-10) cc_final: 0.6574 (mt-10) REVERT: B 858 LEU cc_start: 0.8027 (mp) cc_final: 0.7790 (mp) REVERT: B 1038 LYS cc_start: 0.7815 (mmmm) cc_final: 0.7403 (mmmm) REVERT: C 227 VAL cc_start: 0.7957 (m) cc_final: 0.7720 (t) REVERT: C 295 PRO cc_start: 0.8500 (Cg_exo) cc_final: 0.8119 (Cg_endo) REVERT: C 542 ASN cc_start: 0.7421 (t0) cc_final: 0.7114 (t0) REVERT: C 572 THR cc_start: 0.8058 (m) cc_final: 0.7830 (t) REVERT: C 587 ILE cc_start: 0.8513 (mp) cc_final: 0.8056 (mm) REVERT: C 655 TYR cc_start: 0.6571 (t80) cc_final: 0.6138 (t80) REVERT: C 692 ILE cc_start: 0.8657 (mm) cc_final: 0.8413 (mt) REVERT: C 737 ASP cc_start: 0.7068 (t0) cc_final: 0.6800 (t70) REVERT: C 1017 GLU cc_start: 0.6605 (tp30) cc_final: 0.6175 (tp30) REVERT: C 1108 ASN cc_start: 0.7327 (m-40) cc_final: 0.7125 (m-40) REVERT: D 355 ASP cc_start: 0.4204 (t0) cc_final: 0.3991 (t0) REVERT: F 117 ASN cc_start: 0.5784 (m-40) cc_final: 0.5280 (m-40) REVERT: F 119 ILE cc_start: 0.3092 (mt) cc_final: 0.2486 (tt) REVERT: F 558 LEU cc_start: 0.5242 (mt) cc_final: 0.4303 (mt) outliers start: 19 outliers final: 8 residues processed: 893 average time/residue: 0.2334 time to fit residues: 344.1438 Evaluate side-chains 745 residues out of total 4269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 735 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 534 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 6.9990 chunk 455 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.6980 chunk 470 optimal weight: 10.0000 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 188 ASN A 314 GLN A 439 ASN A 474 GLN A 481 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN A 755 GLN A 928 ASN A 935 GLN A 955 ASN A 957 GLN A 965 GLN A 978 ASN A1088 HIS B 125 ASN B 164 ASN B 188 ASN B 439 ASN B 474 GLN B 481 ASN B 658 ASN B 755 GLN B 804 GLN B 955 ASN B 978 ASN B1011 GLN B1135 ASN C 52 GLN C 125 ASN C 314 GLN C 317 ASN C 439 ASN C 481 ASN C 607 GLN C 774 GLN C 784 GLN C 925 ASN C 955 ASN C 965 GLN C1083 HIS C1135 ASN D 51 ASN D 239 HIS ** D 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 508 ASN ** D 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 578 ASN F 51 ASN F 81 GLN F 121 ASN F 300 GLN F 305 GLN F 322 ASN F 330 ASN F 345 HIS F 508 ASN F 524 GLN F 578 ASN E 51 ASN E 81 GLN E 101 GLN E 300 GLN E 505 HIS E 578 ASN Total number of N/Q/H flips: 64 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.236311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.175554 restraints weight = 70738.686| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 3.59 r_work: 0.3722 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 40176 Z= 0.267 Angle : 0.800 15.891 54735 Z= 0.400 Chirality : 0.052 0.431 6117 Planarity : 0.005 0.075 7005 Dihedral : 6.336 91.989 6053 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.85 % Favored : 95.11 % Rotamer: Outliers : 3.51 % Allowed : 14.38 % Favored : 82.11 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.11), residues: 4809 helix: 0.19 (0.12), residues: 1757 sheet: -1.46 (0.19), residues: 629 loop : -2.25 (0.11), residues: 2423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 514 TYR 0.022 0.002 TYR C 508 PHE 0.044 0.003 PHE B 275 TRP 0.035 0.002 TRP D 461 HIS 0.016 0.002 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00590 (40104) covalent geometry : angle 0.78272 (54558) SS BOND : bond 0.01832 ( 30) SS BOND : angle 2.49759 ( 60) hydrogen bonds : bond 0.04701 ( 1623) hydrogen bonds : angle 5.04611 ( 4521) metal coordination : bond 0.00865 ( 3) link_NAG-ASN : bond 0.00657 ( 39) link_NAG-ASN : angle 3.24631 ( 117) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1033 residues out of total 4269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 884 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.7376 (m-40) cc_final: 0.6210 (t0) REVERT: A 271 GLN cc_start: 0.8145 (mm-40) cc_final: 0.7768 (mm-40) REVERT: A 298 GLU cc_start: 0.7800 (tt0) cc_final: 0.7491 (tt0) REVERT: A 304 LYS cc_start: 0.8233 (mttt) cc_final: 0.7990 (ttmm) REVERT: A 324 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8143 (mt-10) REVERT: A 327 VAL cc_start: 0.8551 (t) cc_final: 0.8328 (p) REVERT: A 436 TRP cc_start: 0.7191 (p90) cc_final: 0.6618 (p90) REVERT: A 498 ARG cc_start: 0.8124 (mtt-85) cc_final: 0.7894 (mpt180) REVERT: A 534 VAL cc_start: 0.8828 (t) cc_final: 0.8575 (p) REVERT: A 537 LYS cc_start: 0.8549 (mtpt) cc_final: 0.8334 (mtmt) REVERT: A 543 PHE cc_start: 0.7257 (m-10) cc_final: 0.6912 (m-80) REVERT: A 576 VAL cc_start: 0.8504 (p) cc_final: 0.8222 (m) REVERT: A 619 GLU cc_start: 0.6663 (pm20) cc_final: 0.5379 (mp0) REVERT: A 663 ASP cc_start: 0.7744 (t0) cc_final: 0.7447 (t0) REVERT: A 704 SER cc_start: 0.8516 (t) cc_final: 0.8303 (p) REVERT: A 737 ASP cc_start: 0.7376 (t0) cc_final: 0.7125 (t0) REVERT: A 739 THR cc_start: 0.8160 (OUTLIER) cc_final: 0.7927 (p) REVERT: A 774 GLN cc_start: 0.8273 (mm-40) cc_final: 0.8050 (mp10) REVERT: A 787 GLN cc_start: 0.8689 (mt0) cc_final: 0.8421 (mt0) REVERT: A 820 ASP cc_start: 0.8342 (t0) cc_final: 0.7770 (t0) REVERT: A 824 ASN cc_start: 0.8604 (m-40) cc_final: 0.7920 (m-40) REVERT: A 933 LYS cc_start: 0.8535 (ttmt) cc_final: 0.8325 (ttpp) REVERT: A 957 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8343 (tt0) REVERT: A 965 GLN cc_start: 0.8239 (tt0) cc_final: 0.7818 (tt0) REVERT: A 969 LYS cc_start: 0.8383 (mttm) cc_final: 0.7835 (mtmt) REVERT: A 995 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7455 (ttm-80) REVERT: A 1002 GLN cc_start: 0.8030 (tt0) cc_final: 0.7790 (tt0) REVERT: A 1045 LYS cc_start: 0.8427 (tmtt) cc_final: 0.8206 (tmtt) REVERT: A 1084 ASP cc_start: 0.8460 (m-30) cc_final: 0.7528 (t0) REVERT: A 1127 ASP cc_start: 0.7768 (t0) cc_final: 0.7422 (t0) REVERT: A 1130 ILE cc_start: 0.8716 (pt) cc_final: 0.8514 (mt) REVERT: B 279 TYR cc_start: 0.7518 (m-80) cc_final: 0.7279 (m-80) REVERT: B 304 LYS cc_start: 0.8510 (mtpp) cc_final: 0.8240 (ttmm) REVERT: B 306 PHE cc_start: 0.8614 (OUTLIER) cc_final: 0.8412 (t80) REVERT: B 317 ASN cc_start: 0.8308 (m110) cc_final: 0.7987 (m-40) REVERT: B 583 GLU cc_start: 0.7832 (tp30) cc_final: 0.7437 (tp30) REVERT: B 604 THR cc_start: 0.8673 (m) cc_final: 0.8461 (t) REVERT: B 654 GLU cc_start: 0.8060 (tt0) cc_final: 0.7804 (tt0) REVERT: B 658 ASN cc_start: 0.8074 (OUTLIER) cc_final: 0.7368 (p0) REVERT: B 698 SER cc_start: 0.8580 (t) cc_final: 0.8295 (p) REVERT: B 703 ASN cc_start: 0.8236 (t0) cc_final: 0.8030 (t0) REVERT: B 704 SER cc_start: 0.8802 (t) cc_final: 0.8498 (p) REVERT: B 720 ILE cc_start: 0.8649 (mm) cc_final: 0.8442 (mt) REVERT: B 762 GLN cc_start: 0.8608 (tt0) cc_final: 0.8398 (tt0) REVERT: B 776 LYS cc_start: 0.8972 (tttt) cc_final: 0.8610 (ttpp) REVERT: B 796 TYR cc_start: 0.8103 (t80) cc_final: 0.7687 (t80) REVERT: B 819 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7642 (mt-10) REVERT: B 895 GLN cc_start: 0.8496 (pt0) cc_final: 0.8278 (pt0) REVERT: B 921 LYS cc_start: 0.8506 (mmmm) cc_final: 0.8263 (mmtm) REVERT: B 933 LYS cc_start: 0.8442 (ttmm) cc_final: 0.8180 (ttpp) REVERT: B 947 LYS cc_start: 0.8431 (mttt) cc_final: 0.8097 (mtpt) REVERT: B 955 ASN cc_start: 0.8115 (OUTLIER) cc_final: 0.7826 (t0) REVERT: B 962 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8379 (tp) REVERT: B 981 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7591 (mt) REVERT: B 1019 ARG cc_start: 0.7561 (ttm110) cc_final: 0.6913 (ttm110) REVERT: B 1031 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7687 (mt-10) REVERT: B 1091 ARG cc_start: 0.8297 (tpp-160) cc_final: 0.8069 (tpp80) REVERT: B 1118 ASP cc_start: 0.8013 (t70) cc_final: 0.7783 (t0) REVERT: B 1130 ILE cc_start: 0.8718 (OUTLIER) cc_final: 0.8479 (mt) REVERT: C 51 THR cc_start: 0.7248 (OUTLIER) cc_final: 0.6589 (m) REVERT: C 58 PHE cc_start: 0.7867 (m-10) cc_final: 0.7617 (m-10) REVERT: C 104 TRP cc_start: 0.6966 (m-90) cc_final: 0.5846 (m-10) REVERT: C 274 THR cc_start: 0.7898 (m) cc_final: 0.7662 (t) REVERT: C 285 ILE cc_start: 0.8692 (mt) cc_final: 0.8444 (mm) REVERT: C 306 PHE cc_start: 0.8356 (OUTLIER) cc_final: 0.7892 (t80) REVERT: C 308 VAL cc_start: 0.8791 (p) cc_final: 0.8439 (m) REVERT: C 357 ARG cc_start: 0.6460 (OUTLIER) cc_final: 0.6243 (ptm-80) REVERT: C 407 VAL cc_start: 0.7773 (m) cc_final: 0.7105 (p) REVERT: C 436 TRP cc_start: 0.6896 (p90) cc_final: 0.6499 (p-90) REVERT: C 556 ASN cc_start: 0.8091 (p0) cc_final: 0.7770 (p0) REVERT: C 559 PHE cc_start: 0.8324 (m-10) cc_final: 0.7941 (m-10) REVERT: C 586 ASP cc_start: 0.7910 (m-30) cc_final: 0.7343 (m-30) REVERT: C 587 ILE cc_start: 0.8848 (mp) cc_final: 0.8640 (mt) REVERT: C 644 GLN cc_start: 0.7811 (tp40) cc_final: 0.7570 (tp-100) REVERT: C 659 SER cc_start: 0.8095 (m) cc_final: 0.7641 (p) REVERT: C 770 ILE cc_start: 0.8736 (mm) cc_final: 0.8365 (tt) REVERT: C 788 ILE cc_start: 0.8783 (mt) cc_final: 0.8546 (mm) REVERT: C 791 THR cc_start: 0.7753 (OUTLIER) cc_final: 0.7505 (p) REVERT: C 824 ASN cc_start: 0.8176 (m-40) cc_final: 0.7911 (m-40) REVERT: C 916 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8274 (tp) REVERT: C 984 LEU cc_start: 0.7920 (tt) cc_final: 0.7650 (tt) REVERT: C 1002 GLN cc_start: 0.8045 (tm-30) cc_final: 0.7666 (tm-30) REVERT: C 1005 GLN cc_start: 0.8623 (tp40) cc_final: 0.8143 (tp40) REVERT: C 1017 GLU cc_start: 0.8000 (tp30) cc_final: 0.7327 (tp30) REVERT: C 1051 SER cc_start: 0.8562 (t) cc_final: 0.8302 (m) REVERT: C 1084 ASP cc_start: 0.8423 (m-30) cc_final: 0.8207 (m-30) REVERT: C 1088 HIS cc_start: 0.8347 (m170) cc_final: 0.8053 (m170) REVERT: C 1092 GLU cc_start: 0.7410 (mm-30) cc_final: 0.7057 (mm-30) REVERT: C 1105 THR cc_start: 0.8388 (t) cc_final: 0.7940 (p) REVERT: C 1122 VAL cc_start: 0.8378 (t) cc_final: 0.8133 (m) REVERT: D 41 TYR cc_start: 0.6901 (t80) cc_final: 0.6427 (t80) REVERT: D 82 MET cc_start: 0.4867 (tmm) cc_final: 0.4660 (ppp) REVERT: D 123 MET cc_start: 0.6101 (tmm) cc_final: 0.5286 (ptp) REVERT: D 376 MET cc_start: 0.5557 (ttm) cc_final: 0.4817 (ttm) REVERT: D 457 GLU cc_start: 0.3695 (mm-30) cc_final: 0.3457 (mm-30) REVERT: D 474 MET cc_start: 0.4300 (ttp) cc_final: 0.4070 (ptm) REVERT: F 57 GLU cc_start: 0.6813 (mm-30) cc_final: 0.6436 (pt0) REVERT: F 72 PHE cc_start: 0.6040 (t80) cc_final: 0.5833 (t80) REVERT: F 96 GLN cc_start: 0.6164 (mt0) cc_final: 0.5901 (mt0) REVERT: F 117 ASN cc_start: 0.7396 (m-40) cc_final: 0.7182 (m-40) REVERT: F 123 MET cc_start: 0.7458 (mtt) cc_final: 0.7108 (mtt) REVERT: F 165 TRP cc_start: 0.6478 (t60) cc_final: 0.5676 (t60) REVERT: F 313 LYS cc_start: 0.8226 (ttmt) cc_final: 0.7959 (tmmt) REVERT: F 323 MET cc_start: 0.7925 (mmt) cc_final: 0.7534 (mmp) REVERT: F 332 MET cc_start: 0.1733 (tmm) cc_final: 0.1352 (tpp) REVERT: F 441 LYS cc_start: 0.5908 (OUTLIER) cc_final: 0.5501 (tttm) outliers start: 149 outliers final: 62 residues processed: 976 average time/residue: 0.2296 time to fit residues: 370.5274 Evaluate side-chains 884 residues out of total 4269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 806 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 170 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 270 MET Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 409 SER Chi-restraints excluded: chain F residue 441 LYS Chi-restraints excluded: chain E residue 86 GLN Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 300 optimal weight: 3.9990 chunk 421 optimal weight: 4.9990 chunk 342 optimal weight: 5.9990 chunk 374 optimal weight: 1.9990 chunk 471 optimal weight: 10.0000 chunk 250 optimal weight: 0.6980 chunk 339 optimal weight: 8.9990 chunk 246 optimal weight: 0.0170 chunk 178 optimal weight: 0.4980 chunk 183 optimal weight: 0.9980 chunk 154 optimal weight: 1.9990 overall best weight: 0.8420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 644 GLN A 751 ASN A 955 ASN A 957 GLN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN B 957 GLN B1011 GLN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN C 954 HIS C 955 ASN D 81 GLN ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 ASN D 505 HIS ** D 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 239 HIS F 345 HIS F 394 ASN F 505 HIS E 239 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.234979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.175922 restraints weight = 70289.525| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 3.63 r_work: 0.3685 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 40176 Z= 0.169 Angle : 0.633 15.732 54735 Z= 0.316 Chirality : 0.045 0.324 6117 Planarity : 0.004 0.064 7005 Dihedral : 5.685 99.444 6046 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.68 % Favored : 96.30 % Rotamer: Outliers : 3.06 % Allowed : 17.26 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.12), residues: 4809 helix: 0.69 (0.12), residues: 1759 sheet: -1.14 (0.19), residues: 620 loop : -1.98 (0.11), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 514 TYR 0.030 0.001 TYR C 369 PHE 0.026 0.002 PHE A 643 TRP 0.040 0.001 TRP D 349 HIS 0.009 0.001 HIS F 345 Details of bonding type rmsd covalent geometry : bond 0.00368 (40104) covalent geometry : angle 0.61113 (54558) SS BOND : bond 0.00664 ( 30) SS BOND : angle 1.85306 ( 60) hydrogen bonds : bond 0.03998 ( 1623) hydrogen bonds : angle 4.75069 ( 4521) metal coordination : bond 0.00116 ( 3) link_NAG-ASN : bond 0.00433 ( 39) link_NAG-ASN : angle 3.37758 ( 117) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 966 residues out of total 4269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 836 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.5870 (m-10) cc_final: 0.5635 (m-10) REVERT: A 206 LYS cc_start: 0.7702 (tppt) cc_final: 0.7426 (tppt) REVERT: A 271 GLN cc_start: 0.8192 (mm-40) cc_final: 0.7806 (mm-40) REVERT: A 298 GLU cc_start: 0.7764 (tt0) cc_final: 0.7529 (tt0) REVERT: A 304 LYS cc_start: 0.8389 (mttt) cc_final: 0.8157 (ttmm) REVERT: A 332 ILE cc_start: 0.7919 (OUTLIER) cc_final: 0.7702 (mm) REVERT: A 436 TRP cc_start: 0.7343 (p90) cc_final: 0.7018 (p90) REVERT: A 498 ARG cc_start: 0.8198 (mtt-85) cc_final: 0.7886 (mmt90) REVERT: A 534 VAL cc_start: 0.8749 (t) cc_final: 0.8533 (p) REVERT: A 542 ASN cc_start: 0.7932 (t0) cc_final: 0.7614 (t0) REVERT: A 543 PHE cc_start: 0.7453 (m-10) cc_final: 0.7192 (m-80) REVERT: A 576 VAL cc_start: 0.8602 (p) cc_final: 0.8290 (m) REVERT: A 619 GLU cc_start: 0.6586 (pm20) cc_final: 0.5439 (mp0) REVERT: A 654 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7859 (mt-10) REVERT: A 658 ASN cc_start: 0.8715 (OUTLIER) cc_final: 0.7694 (p0) REVERT: A 660 TYR cc_start: 0.8084 (m-80) cc_final: 0.7853 (m-80) REVERT: A 737 ASP cc_start: 0.7271 (t0) cc_final: 0.6969 (t0) REVERT: A 774 GLN cc_start: 0.8222 (mm-40) cc_final: 0.7989 (mp10) REVERT: A 787 GLN cc_start: 0.8702 (mt0) cc_final: 0.8480 (mt0) REVERT: A 824 ASN cc_start: 0.8604 (m-40) cc_final: 0.8005 (m-40) REVERT: A 825 LYS cc_start: 0.8813 (tptp) cc_final: 0.8576 (tttp) REVERT: A 864 LEU cc_start: 0.8316 (tp) cc_final: 0.8110 (tt) REVERT: A 922 LEU cc_start: 0.9096 (tp) cc_final: 0.8875 (tt) REVERT: A 957 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.8300 (tt0) REVERT: A 969 LYS cc_start: 0.8453 (mttm) cc_final: 0.7947 (mtmt) REVERT: A 981 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7605 (tp) REVERT: A 983 ARG cc_start: 0.6773 (mtm-85) cc_final: 0.6559 (mtm-85) REVERT: A 995 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7394 (ttm-80) REVERT: A 1045 LYS cc_start: 0.8336 (tmtt) cc_final: 0.8136 (tmtt) REVERT: A 1130 ILE cc_start: 0.8739 (pt) cc_final: 0.8523 (mt) REVERT: B 58 PHE cc_start: 0.8208 (m-10) cc_final: 0.7871 (m-80) REVERT: B 119 ILE cc_start: 0.7769 (tt) cc_final: 0.7406 (pt) REVERT: B 304 LYS cc_start: 0.8600 (mtpp) cc_final: 0.8367 (ttmm) REVERT: B 306 PHE cc_start: 0.8765 (OUTLIER) cc_final: 0.8242 (t80) REVERT: B 310 LYS cc_start: 0.8496 (ttpt) cc_final: 0.8296 (ttpt) REVERT: B 317 ASN cc_start: 0.8174 (m110) cc_final: 0.7713 (m-40) REVERT: B 488 CYS cc_start: 0.3150 (OUTLIER) cc_final: 0.2894 (m) REVERT: B 555 SER cc_start: 0.8142 (OUTLIER) cc_final: 0.6434 (p) REVERT: B 556 ASN cc_start: 0.8099 (p0) cc_final: 0.7794 (t0) REVERT: B 606 ASN cc_start: 0.8253 (p0) cc_final: 0.7928 (p0) REVERT: B 646 ARG cc_start: 0.8277 (mmt180) cc_final: 0.7968 (mmt180) REVERT: B 654 GLU cc_start: 0.8180 (tt0) cc_final: 0.7948 (tt0) REVERT: B 698 SER cc_start: 0.8713 (t) cc_final: 0.8396 (p) REVERT: B 699 LEU cc_start: 0.8615 (mt) cc_final: 0.8394 (mp) REVERT: B 704 SER cc_start: 0.8803 (t) cc_final: 0.8512 (p) REVERT: B 720 ILE cc_start: 0.8754 (mm) cc_final: 0.8470 (mt) REVERT: B 776 LYS cc_start: 0.8905 (tttt) cc_final: 0.8576 (ttpp) REVERT: B 797 PHE cc_start: 0.8125 (m-80) cc_final: 0.7861 (m-80) REVERT: B 814 LYS cc_start: 0.8045 (mmtm) cc_final: 0.7725 (mmtm) REVERT: B 895 GLN cc_start: 0.8345 (pt0) cc_final: 0.8116 (pt0) REVERT: B 957 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7764 (tt0) REVERT: B 1019 ARG cc_start: 0.7494 (ttm110) cc_final: 0.7002 (ttp-170) REVERT: B 1031 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7691 (mt-10) REVERT: B 1038 LYS cc_start: 0.8477 (mmmm) cc_final: 0.7986 (mmmm) REVERT: B 1091 ARG cc_start: 0.8341 (tpp-160) cc_final: 0.7918 (tpp80) REVERT: B 1118 ASP cc_start: 0.8020 (t70) cc_final: 0.7766 (t0) REVERT: C 41 LYS cc_start: 0.8149 (mttt) cc_final: 0.7937 (mttt) REVERT: C 51 THR cc_start: 0.7760 (OUTLIER) cc_final: 0.7428 (p) REVERT: C 52 GLN cc_start: 0.7667 (tt0) cc_final: 0.7363 (tm-30) REVERT: C 58 PHE cc_start: 0.8406 (m-10) cc_final: 0.8155 (m-10) REVERT: C 104 TRP cc_start: 0.7169 (m-90) cc_final: 0.5881 (m-90) REVERT: C 285 ILE cc_start: 0.8833 (mt) cc_final: 0.8538 (mm) REVERT: C 308 VAL cc_start: 0.8832 (p) cc_final: 0.8531 (m) REVERT: C 316 SER cc_start: 0.8606 (t) cc_final: 0.8102 (p) REVERT: C 357 ARG cc_start: 0.6571 (OUTLIER) cc_final: 0.6365 (ptm-80) REVERT: C 407 VAL cc_start: 0.7786 (m) cc_final: 0.7120 (p) REVERT: C 436 TRP cc_start: 0.7151 (p90) cc_final: 0.6676 (p-90) REVERT: C 513 LEU cc_start: 0.6655 (mm) cc_final: 0.6377 (mt) REVERT: C 556 ASN cc_start: 0.8057 (p0) cc_final: 0.7836 (p0) REVERT: C 558 LYS cc_start: 0.8560 (mmmt) cc_final: 0.8348 (mmmt) REVERT: C 572 THR cc_start: 0.8587 (t) cc_final: 0.8195 (p) REVERT: C 587 ILE cc_start: 0.8838 (mp) cc_final: 0.8602 (mt) REVERT: C 615 VAL cc_start: 0.7209 (OUTLIER) cc_final: 0.5964 (t) REVERT: C 644 GLN cc_start: 0.8021 (tp40) cc_final: 0.7640 (tp40) REVERT: C 737 ASP cc_start: 0.8096 (t0) cc_final: 0.7843 (t0) REVERT: C 770 ILE cc_start: 0.8677 (mm) cc_final: 0.8348 (tt) REVERT: C 788 ILE cc_start: 0.8816 (mt) cc_final: 0.8446 (mm) REVERT: C 822 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8301 (tp) REVERT: C 824 ASN cc_start: 0.8257 (m-40) cc_final: 0.7999 (m-40) REVERT: C 916 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.8046 (tp) REVERT: C 917 TYR cc_start: 0.8133 (m-10) cc_final: 0.7899 (m-10) REVERT: C 1002 GLN cc_start: 0.8103 (tm-30) cc_final: 0.7742 (tm-30) REVERT: C 1005 GLN cc_start: 0.8397 (tp40) cc_final: 0.8118 (tp40) REVERT: C 1017 GLU cc_start: 0.8093 (tp30) cc_final: 0.7840 (tp30) REVERT: C 1051 SER cc_start: 0.8565 (t) cc_final: 0.8353 (m) REVERT: C 1092 GLU cc_start: 0.7487 (mm-30) cc_final: 0.7144 (mm-30) REVERT: C 1097 SER cc_start: 0.8606 (t) cc_final: 0.8291 (p) REVERT: C 1105 THR cc_start: 0.8396 (t) cc_final: 0.8070 (p) REVERT: C 1122 VAL cc_start: 0.8497 (t) cc_final: 0.8280 (m) REVERT: D 41 TYR cc_start: 0.6776 (t80) cc_final: 0.6183 (t80) REVERT: D 123 MET cc_start: 0.6100 (tmm) cc_final: 0.5532 (ptp) REVERT: D 455 MET cc_start: 0.6215 (ppp) cc_final: 0.5831 (ppp) REVERT: D 457 GLU cc_start: 0.3887 (mm-30) cc_final: 0.3599 (mm-30) REVERT: D 474 MET cc_start: 0.4410 (ttp) cc_final: 0.3731 (mpp) REVERT: F 57 GLU cc_start: 0.6852 (mm-30) cc_final: 0.6631 (mt-10) REVERT: F 96 GLN cc_start: 0.6162 (mt0) cc_final: 0.5899 (mt0) REVERT: F 117 ASN cc_start: 0.7578 (m-40) cc_final: 0.7332 (m-40) REVERT: F 119 ILE cc_start: 0.3402 (tt) cc_final: 0.3043 (tt) REVERT: F 123 MET cc_start: 0.7395 (mtt) cc_final: 0.6939 (mtt) REVERT: F 165 TRP cc_start: 0.6466 (t60) cc_final: 0.5762 (t60) REVERT: F 244 VAL cc_start: 0.5417 (m) cc_final: 0.5176 (p) REVERT: F 323 MET cc_start: 0.7914 (mmt) cc_final: 0.7111 (mmt) REVERT: F 332 MET cc_start: 0.1704 (tmm) cc_final: 0.1480 (tpp) REVERT: F 376 MET cc_start: 0.6509 (ttp) cc_final: 0.6252 (ttm) REVERT: F 514 ARG cc_start: 0.7962 (ptt90) cc_final: 0.7761 (ptt90) REVERT: F 557 MET cc_start: 0.6589 (tmm) cc_final: 0.6277 (tmm) outliers start: 130 outliers final: 64 residues processed: 910 average time/residue: 0.2227 time to fit residues: 334.1988 Evaluate side-chains 881 residues out of total 4269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 803 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 537 LYS Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 949 GLN Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 170 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 309 LYS Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 345 HIS Chi-restraints excluded: chain F residue 373 HIS Chi-restraints excluded: chain F residue 409 SER Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 345 optimal weight: 7.9990 chunk 216 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 108 optimal weight: 0.5980 chunk 468 optimal weight: 20.0000 chunk 410 optimal weight: 0.0370 chunk 166 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 163 optimal weight: 0.5980 chunk 451 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 644 GLN A 926 GLN A 965 GLN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 345 HIS E 96 GLN E 522 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.234002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.171297 restraints weight = 70304.819| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 3.59 r_work: 0.3683 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 40176 Z= 0.142 Angle : 0.603 15.465 54735 Z= 0.299 Chirality : 0.044 0.401 6117 Planarity : 0.004 0.061 7005 Dihedral : 5.162 82.652 6041 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.83 % Favored : 96.15 % Rotamer: Outliers : 3.30 % Allowed : 18.36 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.12), residues: 4809 helix: 0.98 (0.13), residues: 1749 sheet: -1.14 (0.19), residues: 605 loop : -1.77 (0.11), residues: 2455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 328 TYR 0.026 0.001 TYR C 369 PHE 0.024 0.002 PHE B 192 TRP 0.036 0.001 TRP D 461 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00313 (40104) covalent geometry : angle 0.58342 (54558) SS BOND : bond 0.00533 ( 30) SS BOND : angle 1.76897 ( 60) hydrogen bonds : bond 0.03658 ( 1623) hydrogen bonds : angle 4.64781 ( 4521) metal coordination : bond 0.00041 ( 3) link_NAG-ASN : bond 0.00633 ( 39) link_NAG-ASN : angle 3.10697 ( 117) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 960 residues out of total 4269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 820 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.7326 (mtp85) cc_final: 0.6821 (mmm-85) REVERT: A 121 ASN cc_start: 0.7640 (m-40) cc_final: 0.6316 (t0) REVERT: A 271 GLN cc_start: 0.8169 (mm-40) cc_final: 0.7779 (mm-40) REVERT: A 277 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8436 (mt) REVERT: A 298 GLU cc_start: 0.7785 (tt0) cc_final: 0.7562 (tt0) REVERT: A 304 LYS cc_start: 0.8372 (mttt) cc_final: 0.8171 (ttmm) REVERT: A 339 ASP cc_start: 0.8676 (t70) cc_final: 0.8464 (t0) REVERT: A 436 TRP cc_start: 0.7322 (p90) cc_final: 0.7103 (p90) REVERT: A 542 ASN cc_start: 0.8055 (t0) cc_final: 0.7725 (t0) REVERT: A 543 PHE cc_start: 0.7657 (m-10) cc_final: 0.7334 (m-80) REVERT: A 615 VAL cc_start: 0.7986 (OUTLIER) cc_final: 0.7699 (p) REVERT: A 619 GLU cc_start: 0.6609 (pm20) cc_final: 0.5562 (mp0) REVERT: A 654 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7841 (mt-10) REVERT: A 658 ASN cc_start: 0.8798 (OUTLIER) cc_final: 0.8052 (p0) REVERT: A 722 VAL cc_start: 0.8862 (t) cc_final: 0.8657 (m) REVERT: A 737 ASP cc_start: 0.7229 (t0) cc_final: 0.6894 (t0) REVERT: A 774 GLN cc_start: 0.8172 (mm-40) cc_final: 0.7962 (mp10) REVERT: A 787 GLN cc_start: 0.8706 (mt0) cc_final: 0.8504 (mt0) REVERT: A 824 ASN cc_start: 0.8603 (m-40) cc_final: 0.8006 (m-40) REVERT: A 825 LYS cc_start: 0.8811 (tptp) cc_final: 0.8563 (tttp) REVERT: A 864 LEU cc_start: 0.8369 (tp) cc_final: 0.8163 (tt) REVERT: A 922 LEU cc_start: 0.9041 (tp) cc_final: 0.8815 (tt) REVERT: A 969 LYS cc_start: 0.8540 (mttm) cc_final: 0.8007 (mtmt) REVERT: A 983 ARG cc_start: 0.6748 (OUTLIER) cc_final: 0.6513 (mtm-85) REVERT: A 995 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7406 (ttm-80) REVERT: A 1045 LYS cc_start: 0.8425 (tmtt) cc_final: 0.8194 (tmtt) REVERT: A 1088 HIS cc_start: 0.8331 (m-70) cc_final: 0.7764 (m170) REVERT: A 1130 ILE cc_start: 0.8790 (pt) cc_final: 0.8557 (mt) REVERT: B 58 PHE cc_start: 0.8399 (m-10) cc_final: 0.7896 (m-80) REVERT: B 119 ILE cc_start: 0.7867 (OUTLIER) cc_final: 0.7599 (pt) REVERT: B 190 ARG cc_start: 0.6305 (mtt180) cc_final: 0.5554 (tpp80) REVERT: B 304 LYS cc_start: 0.8618 (mtpp) cc_final: 0.8390 (ttmm) REVERT: B 306 PHE cc_start: 0.8784 (OUTLIER) cc_final: 0.8159 (t80) REVERT: B 310 LYS cc_start: 0.8467 (ttpt) cc_final: 0.8134 (ttmt) REVERT: B 317 ASN cc_start: 0.8085 (m110) cc_final: 0.7560 (m-40) REVERT: B 329 PHE cc_start: 0.7814 (m-80) cc_final: 0.7547 (m-80) REVERT: B 555 SER cc_start: 0.8098 (OUTLIER) cc_final: 0.7854 (p) REVERT: B 556 ASN cc_start: 0.8236 (p0) cc_final: 0.7890 (t0) REVERT: B 606 ASN cc_start: 0.8312 (p0) cc_final: 0.8014 (p0) REVERT: B 646 ARG cc_start: 0.8372 (mmt180) cc_final: 0.8092 (mmt180) REVERT: B 654 GLU cc_start: 0.8177 (tt0) cc_final: 0.7965 (tt0) REVERT: B 656 VAL cc_start: 0.8223 (t) cc_final: 0.7857 (p) REVERT: B 658 ASN cc_start: 0.8400 (OUTLIER) cc_final: 0.8064 (p0) REVERT: B 698 SER cc_start: 0.8742 (t) cc_final: 0.8469 (p) REVERT: B 699 LEU cc_start: 0.8643 (mt) cc_final: 0.8440 (mp) REVERT: B 704 SER cc_start: 0.8778 (t) cc_final: 0.8515 (p) REVERT: B 720 ILE cc_start: 0.8719 (mm) cc_final: 0.8406 (mt) REVERT: B 741 TYR cc_start: 0.8669 (t80) cc_final: 0.8354 (t80) REVERT: B 776 LYS cc_start: 0.8778 (tttt) cc_final: 0.8426 (ttpp) REVERT: B 791 THR cc_start: 0.8105 (OUTLIER) cc_final: 0.7840 (p) REVERT: B 814 LYS cc_start: 0.7997 (mmtm) cc_final: 0.7698 (mmtm) REVERT: B 895 GLN cc_start: 0.8332 (pt0) cc_final: 0.8109 (pt0) REVERT: B 921 LYS cc_start: 0.8313 (mmmm) cc_final: 0.8083 (mmtm) REVERT: B 1019 ARG cc_start: 0.7468 (ttm110) cc_final: 0.7112 (ttp-170) REVERT: B 1031 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7648 (mt-10) REVERT: B 1118 ASP cc_start: 0.7959 (t70) cc_final: 0.7757 (t70) REVERT: C 45 SER cc_start: 0.8801 (t) cc_final: 0.8319 (p) REVERT: C 104 TRP cc_start: 0.7314 (m-90) cc_final: 0.5919 (m-90) REVERT: C 285 ILE cc_start: 0.8887 (mt) cc_final: 0.8567 (mm) REVERT: C 308 VAL cc_start: 0.8811 (p) cc_final: 0.8514 (m) REVERT: C 542 ASN cc_start: 0.7949 (t0) cc_final: 0.7581 (t0) REVERT: C 549 THR cc_start: 0.8047 (t) cc_final: 0.7782 (p) REVERT: C 572 THR cc_start: 0.8578 (t) cc_final: 0.8199 (p) REVERT: C 587 ILE cc_start: 0.8755 (mp) cc_final: 0.8525 (mt) REVERT: C 615 VAL cc_start: 0.7400 (OUTLIER) cc_final: 0.6228 (t) REVERT: C 644 GLN cc_start: 0.7929 (tp40) cc_final: 0.7587 (tp40) REVERT: C 656 VAL cc_start: 0.8552 (t) cc_final: 0.8289 (p) REVERT: C 693 ILE cc_start: 0.8417 (pt) cc_final: 0.8198 (mm) REVERT: C 737 ASP cc_start: 0.8054 (t0) cc_final: 0.7666 (t0) REVERT: C 770 ILE cc_start: 0.8685 (mm) cc_final: 0.8335 (tt) REVERT: C 788 ILE cc_start: 0.8782 (mt) cc_final: 0.8515 (mm) REVERT: C 819 GLU cc_start: 0.7385 (mt-10) cc_final: 0.7178 (mt-10) REVERT: C 824 ASN cc_start: 0.8305 (m-40) cc_final: 0.8056 (m-40) REVERT: C 916 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.8048 (tp) REVERT: C 955 ASN cc_start: 0.7995 (m-40) cc_final: 0.7652 (t0) REVERT: C 981 LEU cc_start: 0.8341 (mm) cc_final: 0.8123 (mt) REVERT: C 1002 GLN cc_start: 0.8132 (tm-30) cc_final: 0.7807 (tm-30) REVERT: C 1005 GLN cc_start: 0.8403 (tp40) cc_final: 0.8124 (tp40) REVERT: C 1048 HIS cc_start: 0.8338 (t-90) cc_final: 0.8014 (t-170) REVERT: C 1084 ASP cc_start: 0.8391 (OUTLIER) cc_final: 0.8089 (m-30) REVERT: C 1092 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7339 (mm-30) REVERT: C 1097 SER cc_start: 0.8532 (t) cc_final: 0.8197 (p) REVERT: C 1105 THR cc_start: 0.8432 (t) cc_final: 0.8075 (p) REVERT: C 1122 VAL cc_start: 0.8511 (t) cc_final: 0.8309 (m) REVERT: D 41 TYR cc_start: 0.6886 (t80) cc_final: 0.6379 (t80) REVERT: D 123 MET cc_start: 0.5912 (tmm) cc_final: 0.5304 (ptp) REVERT: D 306 ARG cc_start: 0.8720 (mmm160) cc_final: 0.8441 (mmm160) REVERT: D 313 LYS cc_start: 0.7237 (ptpp) cc_final: 0.6990 (ptpp) REVERT: D 325 GLN cc_start: 0.5104 (tm-30) cc_final: 0.4775 (tm-30) REVERT: D 360 MET cc_start: -0.1568 (ttm) cc_final: -0.1925 (ttm) REVERT: D 455 MET cc_start: 0.6109 (ppp) cc_final: 0.5723 (ppp) REVERT: D 457 GLU cc_start: 0.4128 (mm-30) cc_final: 0.3764 (mm-30) REVERT: D 474 MET cc_start: 0.4279 (ttp) cc_final: 0.3678 (mpp) REVERT: F 57 GLU cc_start: 0.6952 (mm-30) cc_final: 0.6722 (pt0) REVERT: F 68 LYS cc_start: 0.8694 (mtmm) cc_final: 0.8447 (mppt) REVERT: F 96 GLN cc_start: 0.6196 (mt0) cc_final: 0.5943 (mt0) REVERT: F 117 ASN cc_start: 0.7555 (m-40) cc_final: 0.7267 (m-40) REVERT: F 119 ILE cc_start: 0.3645 (tt) cc_final: 0.3226 (tt) REVERT: F 123 MET cc_start: 0.7392 (mtt) cc_final: 0.6898 (mtt) REVERT: F 313 LYS cc_start: 0.8160 (tmmt) cc_final: 0.7886 (tmmt) REVERT: F 323 MET cc_start: 0.7858 (mmt) cc_final: 0.7164 (mmt) REVERT: F 376 MET cc_start: 0.6388 (ttp) cc_final: 0.6145 (ttm) REVERT: F 514 ARG cc_start: 0.7826 (ptt90) cc_final: 0.7538 (ptt90) REVERT: F 557 MET cc_start: 0.6622 (tmm) cc_final: 0.6229 (tmm) REVERT: F 587 TYR cc_start: 0.6197 (t80) cc_final: 0.5668 (t80) outliers start: 140 outliers final: 85 residues processed: 901 average time/residue: 0.2318 time to fit residues: 345.2675 Evaluate side-chains 893 residues out of total 4269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 795 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 949 GLN Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 170 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 309 LYS Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 373 HIS Chi-restraints excluded: chain F residue 409 SER Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain E residue 86 GLN Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 411 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 116 optimal weight: 0.8980 chunk 473 optimal weight: 50.0000 chunk 119 optimal weight: 4.9990 chunk 217 optimal weight: 1.9990 chunk 239 optimal weight: 0.8980 chunk 274 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 121 optimal weight: 7.9990 chunk 174 optimal weight: 0.3980 chunk 77 optimal weight: 0.8980 chunk 344 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN A 762 GLN A 926 GLN A 965 GLN A1106 GLN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 ASN F 394 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.232054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.170172 restraints weight = 69502.720| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 3.71 r_work: 0.3647 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.4558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 40176 Z= 0.158 Angle : 0.611 13.013 54735 Z= 0.304 Chirality : 0.045 0.482 6117 Planarity : 0.004 0.061 7005 Dihedral : 5.063 75.227 6040 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.89 % Favored : 96.09 % Rotamer: Outliers : 3.70 % Allowed : 18.86 % Favored : 77.45 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.12), residues: 4809 helix: 1.10 (0.13), residues: 1749 sheet: -1.11 (0.20), residues: 604 loop : -1.61 (0.12), residues: 2456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 518 TYR 0.024 0.001 TYR C1110 PHE 0.037 0.002 PHE B 201 TRP 0.040 0.001 TRP D 461 HIS 0.008 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00349 (40104) covalent geometry : angle 0.59607 (54558) SS BOND : bond 0.00380 ( 30) SS BOND : angle 1.73687 ( 60) hydrogen bonds : bond 0.03682 ( 1623) hydrogen bonds : angle 4.64072 ( 4521) metal coordination : bond 0.00060 ( 3) link_NAG-ASN : bond 0.00416 ( 39) link_NAG-ASN : angle 2.67685 ( 117) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 991 residues out of total 4269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 834 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.7411 (mtp85) cc_final: 0.6918 (mmm-85) REVERT: A 53 ASP cc_start: 0.6928 (OUTLIER) cc_final: 0.6675 (t0) REVERT: A 58 PHE cc_start: 0.8377 (OUTLIER) cc_final: 0.8127 (m-80) REVERT: A 121 ASN cc_start: 0.7629 (m-40) cc_final: 0.6450 (t0) REVERT: A 271 GLN cc_start: 0.8256 (mm-40) cc_final: 0.7896 (mm-40) REVERT: A 277 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8475 (mt) REVERT: A 304 LYS cc_start: 0.8514 (mttt) cc_final: 0.8191 (ttmm) REVERT: A 317 ASN cc_start: 0.8438 (m-40) cc_final: 0.8219 (m-40) REVERT: A 324 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8081 (mp0) REVERT: A 339 ASP cc_start: 0.8672 (t70) cc_final: 0.8452 (t0) REVERT: A 498 ARG cc_start: 0.8176 (mtt-85) cc_final: 0.7896 (mmt-90) REVERT: A 534 VAL cc_start: 0.8664 (t) cc_final: 0.8408 (p) REVERT: A 542 ASN cc_start: 0.8123 (t0) cc_final: 0.7764 (t0) REVERT: A 543 PHE cc_start: 0.7770 (m-10) cc_final: 0.7420 (m-80) REVERT: A 554 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7607 (tm-30) REVERT: A 580 GLN cc_start: 0.7438 (mt0) cc_final: 0.6911 (mt0) REVERT: A 619 GLU cc_start: 0.6574 (pm20) cc_final: 0.6246 (mp0) REVERT: A 654 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7818 (mt-10) REVERT: A 658 ASN cc_start: 0.8822 (OUTLIER) cc_final: 0.7965 (p0) REVERT: A 690 GLN cc_start: 0.6970 (mm-40) cc_final: 0.6635 (tt0) REVERT: A 737 ASP cc_start: 0.7403 (t0) cc_final: 0.7081 (t0) REVERT: A 774 GLN cc_start: 0.8207 (mm-40) cc_final: 0.8005 (mp10) REVERT: A 787 GLN cc_start: 0.8746 (mt0) cc_final: 0.8532 (mt0) REVERT: A 824 ASN cc_start: 0.8592 (m-40) cc_final: 0.7998 (m-40) REVERT: A 864 LEU cc_start: 0.8371 (tp) cc_final: 0.8158 (tt) REVERT: A 963 VAL cc_start: 0.8751 (m) cc_final: 0.8465 (p) REVERT: A 969 LYS cc_start: 0.8656 (mttm) cc_final: 0.8058 (mtmt) REVERT: A 995 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7504 (ttm-80) REVERT: A 1045 LYS cc_start: 0.8482 (tmtt) cc_final: 0.8217 (tmtt) REVERT: A 1082 CYS cc_start: 0.7230 (t) cc_final: 0.6884 (t) REVERT: A 1088 HIS cc_start: 0.8340 (m-70) cc_final: 0.7838 (m170) REVERT: A 1107 ARG cc_start: 0.7557 (ptp90) cc_final: 0.7351 (mtt-85) REVERT: A 1130 ILE cc_start: 0.8802 (pt) cc_final: 0.8589 (mt) REVERT: B 54 LEU cc_start: 0.8261 (mt) cc_final: 0.8038 (mt) REVERT: B 58 PHE cc_start: 0.8486 (m-10) cc_final: 0.7981 (m-80) REVERT: B 119 ILE cc_start: 0.7776 (tt) cc_final: 0.7503 (pt) REVERT: B 190 ARG cc_start: 0.6402 (mtt180) cc_final: 0.5771 (ttm-80) REVERT: B 304 LYS cc_start: 0.8709 (mtpp) cc_final: 0.8462 (ttmm) REVERT: B 310 LYS cc_start: 0.8534 (ttpt) cc_final: 0.8227 (ttmt) REVERT: B 317 ASN cc_start: 0.8122 (m110) cc_final: 0.7534 (m-40) REVERT: B 329 PHE cc_start: 0.7913 (m-80) cc_final: 0.7670 (m-80) REVERT: B 555 SER cc_start: 0.8190 (OUTLIER) cc_final: 0.7704 (p) REVERT: B 556 ASN cc_start: 0.8168 (p0) cc_final: 0.7902 (t0) REVERT: B 558 LYS cc_start: 0.8247 (mmmt) cc_final: 0.7847 (mmmm) REVERT: B 606 ASN cc_start: 0.8366 (p0) cc_final: 0.8086 (p0) REVERT: B 646 ARG cc_start: 0.8296 (mmt180) cc_final: 0.8033 (mmt180) REVERT: B 654 GLU cc_start: 0.8237 (tt0) cc_final: 0.7989 (tt0) REVERT: B 656 VAL cc_start: 0.8523 (t) cc_final: 0.8217 (p) REVERT: B 671 CYS cc_start: 0.7323 (m) cc_final: 0.6993 (m) REVERT: B 698 SER cc_start: 0.8776 (t) cc_final: 0.8503 (p) REVERT: B 704 SER cc_start: 0.8802 (t) cc_final: 0.8544 (p) REVERT: B 776 LYS cc_start: 0.8795 (tttt) cc_final: 0.8443 (ttpp) REVERT: B 814 LYS cc_start: 0.8116 (mmtm) cc_final: 0.7772 (mmtm) REVERT: B 895 GLN cc_start: 0.8353 (pt0) cc_final: 0.8119 (pt0) REVERT: B 921 LYS cc_start: 0.8314 (mmmm) cc_final: 0.8042 (mmtm) REVERT: B 1019 ARG cc_start: 0.7586 (ttm110) cc_final: 0.7278 (ttp-170) REVERT: B 1029 MET cc_start: 0.8523 (tpp) cc_final: 0.8259 (ttm) REVERT: B 1118 ASP cc_start: 0.7981 (t70) cc_final: 0.7768 (t70) REVERT: C 45 SER cc_start: 0.8695 (t) cc_final: 0.8238 (p) REVERT: C 194 PHE cc_start: 0.7808 (m-80) cc_final: 0.6761 (m-80) REVERT: C 307 THR cc_start: 0.8536 (OUTLIER) cc_final: 0.7983 (p) REVERT: C 308 VAL cc_start: 0.8849 (p) cc_final: 0.8454 (m) REVERT: C 309 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7596 (mm-30) REVERT: C 369 TYR cc_start: 0.7234 (OUTLIER) cc_final: 0.6497 (p90) REVERT: C 542 ASN cc_start: 0.7877 (t0) cc_final: 0.7489 (t0) REVERT: C 572 THR cc_start: 0.8613 (t) cc_final: 0.8202 (p) REVERT: C 587 ILE cc_start: 0.8754 (mp) cc_final: 0.8493 (mt) REVERT: C 615 VAL cc_start: 0.7731 (OUTLIER) cc_final: 0.6723 (t) REVERT: C 644 GLN cc_start: 0.7959 (tp40) cc_final: 0.7488 (tp40) REVERT: C 656 VAL cc_start: 0.8613 (t) cc_final: 0.8268 (p) REVERT: C 674 TYR cc_start: 0.8145 (OUTLIER) cc_final: 0.7877 (t80) REVERT: C 693 ILE cc_start: 0.8401 (pt) cc_final: 0.8175 (mm) REVERT: C 737 ASP cc_start: 0.7989 (t0) cc_final: 0.7672 (t0) REVERT: C 770 ILE cc_start: 0.8708 (mm) cc_final: 0.8319 (tt) REVERT: C 788 ILE cc_start: 0.8764 (mt) cc_final: 0.8501 (mm) REVERT: C 791 THR cc_start: 0.7919 (OUTLIER) cc_final: 0.7670 (p) REVERT: C 824 ASN cc_start: 0.8300 (m-40) cc_final: 0.8049 (m-40) REVERT: C 904 TYR cc_start: 0.7769 (m-10) cc_final: 0.7542 (m-10) REVERT: C 916 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.8035 (tp) REVERT: C 949 GLN cc_start: 0.8488 (tt0) cc_final: 0.8170 (tt0) REVERT: C 1002 GLN cc_start: 0.8103 (tm-30) cc_final: 0.7766 (tm-30) REVERT: C 1005 GLN cc_start: 0.8432 (tp40) cc_final: 0.8080 (tp40) REVERT: C 1048 HIS cc_start: 0.8324 (t-90) cc_final: 0.8027 (t-170) REVERT: C 1075 PHE cc_start: 0.8053 (m-80) cc_final: 0.7728 (m-80) REVERT: C 1084 ASP cc_start: 0.8336 (OUTLIER) cc_final: 0.8124 (m-30) REVERT: C 1092 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7316 (mm-30) REVERT: C 1122 VAL cc_start: 0.8543 (t) cc_final: 0.8341 (m) REVERT: D 41 TYR cc_start: 0.6980 (t80) cc_final: 0.6458 (t80) REVERT: D 123 MET cc_start: 0.6045 (tmm) cc_final: 0.5399 (ptp) REVERT: D 208 GLU cc_start: 0.3848 (tt0) cc_final: 0.3607 (tt0) REVERT: D 306 ARG cc_start: 0.8641 (mmm160) cc_final: 0.8357 (mmm160) REVERT: D 325 GLN cc_start: 0.5023 (tm-30) cc_final: 0.4662 (tm-30) REVERT: D 457 GLU cc_start: 0.4227 (mm-30) cc_final: 0.3867 (mm-30) REVERT: D 474 MET cc_start: 0.4428 (ttp) cc_final: 0.3747 (mpp) REVERT: F 96 GLN cc_start: 0.6176 (mt0) cc_final: 0.5961 (mt0) REVERT: F 108 LEU cc_start: 0.6153 (mt) cc_final: 0.5441 (mt) REVERT: F 117 ASN cc_start: 0.7585 (m-40) cc_final: 0.7341 (m-40) REVERT: F 119 ILE cc_start: 0.3618 (tt) cc_final: 0.3215 (tt) REVERT: F 123 MET cc_start: 0.7430 (mtt) cc_final: 0.6973 (mtt) REVERT: F 309 LYS cc_start: 0.7351 (mttm) cc_final: 0.6962 (mttm) REVERT: F 313 LYS cc_start: 0.8233 (tmmt) cc_final: 0.7968 (tmmt) REVERT: F 323 MET cc_start: 0.7934 (mmt) cc_final: 0.7240 (mmt) REVERT: F 376 MET cc_start: 0.6886 (OUTLIER) cc_final: 0.6610 (ttp) REVERT: F 417 HIS cc_start: 0.7761 (t70) cc_final: 0.7459 (t-170) REVERT: F 470 LYS cc_start: 0.7029 (mmmt) cc_final: 0.6639 (mmmt) REVERT: F 514 ARG cc_start: 0.7934 (ptt90) cc_final: 0.7662 (ptt90) REVERT: F 557 MET cc_start: 0.6815 (tmm) cc_final: 0.6321 (tmm) outliers start: 157 outliers final: 97 residues processed: 929 average time/residue: 0.2387 time to fit residues: 366.5515 Evaluate side-chains 931 residues out of total 4269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 819 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 949 GLN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 537 LYS Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 949 GLN Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 170 TYR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 537 LYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 674 TYR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 309 LYS Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 38 ASP Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 271 TRP Chi-restraints excluded: chain F residue 315 PHE Chi-restraints excluded: chain F residue 376 MET Chi-restraints excluded: chain F residue 409 SER Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain E residue 86 GLN Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 193 optimal weight: 0.9990 chunk 427 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 467 optimal weight: 3.9990 chunk 272 optimal weight: 0.0010 chunk 115 optimal weight: 2.9990 chunk 271 optimal weight: 0.5980 chunk 42 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 162 optimal weight: 0.0170 overall best weight: 0.3824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN A 926 GLN A 965 GLN A1106 GLN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B 957 GLN B1058 HIS C 218 GLN C 505 HIS C 755 GLN C 935 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 373 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.232761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.170788 restraints weight = 69147.149| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 3.69 r_work: 0.3647 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.4744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 40176 Z= 0.119 Angle : 0.591 12.365 54735 Z= 0.295 Chirality : 0.044 0.563 6117 Planarity : 0.004 0.055 7005 Dihedral : 4.836 68.688 6040 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.49 % Favored : 96.49 % Rotamer: Outliers : 3.37 % Allowed : 19.70 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.12), residues: 4809 helix: 1.24 (0.13), residues: 1740 sheet: -0.99 (0.20), residues: 613 loop : -1.50 (0.12), residues: 2456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 518 TYR 0.022 0.001 TYR F 243 PHE 0.035 0.001 PHE E 369 TRP 0.039 0.001 TRP D 461 HIS 0.009 0.001 HIS E 373 Details of bonding type rmsd covalent geometry : bond 0.00263 (40104) covalent geometry : angle 0.57591 (54558) SS BOND : bond 0.00234 ( 30) SS BOND : angle 1.55311 ( 60) hydrogen bonds : bond 0.03452 ( 1623) hydrogen bonds : angle 4.57873 ( 4521) metal coordination : bond 0.00041 ( 3) link_NAG-ASN : bond 0.00665 ( 39) link_NAG-ASN : angle 2.70963 ( 117) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 973 residues out of total 4269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 830 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.7346 (mtp85) cc_final: 0.7047 (mmm-85) REVERT: A 58 PHE cc_start: 0.8453 (m-10) cc_final: 0.8205 (m-80) REVERT: A 121 ASN cc_start: 0.7584 (m-40) cc_final: 0.6448 (t0) REVERT: A 271 GLN cc_start: 0.8276 (mm-40) cc_final: 0.8051 (mp10) REVERT: A 277 LEU cc_start: 0.8661 (mt) cc_final: 0.8411 (mt) REVERT: A 304 LYS cc_start: 0.8499 (mttt) cc_final: 0.8192 (ttmm) REVERT: A 317 ASN cc_start: 0.8412 (m-40) cc_final: 0.8191 (m-40) REVERT: A 324 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8022 (mp0) REVERT: A 498 ARG cc_start: 0.8229 (mtt-85) cc_final: 0.7876 (mmm-85) REVERT: A 534 VAL cc_start: 0.8659 (t) cc_final: 0.8395 (p) REVERT: A 542 ASN cc_start: 0.8094 (t0) cc_final: 0.7745 (t0) REVERT: A 543 PHE cc_start: 0.7777 (m-10) cc_final: 0.7425 (m-80) REVERT: A 554 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7674 (tm-30) REVERT: A 580 GLN cc_start: 0.7486 (mt0) cc_final: 0.7145 (mt0) REVERT: A 619 GLU cc_start: 0.6352 (pm20) cc_final: 0.6066 (mp0) REVERT: A 654 GLU cc_start: 0.8295 (mt-10) cc_final: 0.8049 (mt-10) REVERT: A 658 ASN cc_start: 0.8785 (OUTLIER) cc_final: 0.8196 (p0) REVERT: A 690 GLN cc_start: 0.6992 (mm-40) cc_final: 0.6772 (tt0) REVERT: A 737 ASP cc_start: 0.7267 (t0) cc_final: 0.7018 (t0) REVERT: A 774 GLN cc_start: 0.8178 (mm-40) cc_final: 0.7942 (mp10) REVERT: A 790 LYS cc_start: 0.8557 (mtmt) cc_final: 0.8161 (mtmm) REVERT: A 796 TYR cc_start: 0.8239 (t80) cc_final: 0.8038 (t80) REVERT: A 819 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7715 (mt-10) REVERT: A 824 ASN cc_start: 0.8602 (m-40) cc_final: 0.8022 (m-40) REVERT: A 825 LYS cc_start: 0.8828 (tptm) cc_final: 0.8586 (tptm) REVERT: A 963 VAL cc_start: 0.8695 (m) cc_final: 0.8442 (p) REVERT: A 969 LYS cc_start: 0.8617 (mttm) cc_final: 0.8076 (mtmt) REVERT: A 983 ARG cc_start: 0.6801 (OUTLIER) cc_final: 0.6555 (mtm-85) REVERT: A 995 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7411 (ttm-80) REVERT: A 1045 LYS cc_start: 0.8448 (tmtt) cc_final: 0.8189 (tmtt) REVERT: A 1088 HIS cc_start: 0.8434 (m-70) cc_final: 0.7745 (m170) REVERT: A 1107 ARG cc_start: 0.7503 (ptp90) cc_final: 0.7283 (mtt90) REVERT: A 1130 ILE cc_start: 0.8816 (pt) cc_final: 0.8565 (mt) REVERT: B 34 ARG cc_start: 0.7315 (mtp85) cc_final: 0.6980 (mtp85) REVERT: B 42 VAL cc_start: 0.8705 (p) cc_final: 0.8455 (t) REVERT: B 54 LEU cc_start: 0.8195 (mt) cc_final: 0.7782 (mt) REVERT: B 58 PHE cc_start: 0.8546 (m-10) cc_final: 0.8058 (m-80) REVERT: B 119 ILE cc_start: 0.7835 (OUTLIER) cc_final: 0.7556 (pt) REVERT: B 221 SER cc_start: 0.7792 (m) cc_final: 0.7565 (p) REVERT: B 270 LEU cc_start: 0.8563 (mt) cc_final: 0.8307 (mt) REVERT: B 304 LYS cc_start: 0.8722 (mtpp) cc_final: 0.8488 (ttmm) REVERT: B 307 THR cc_start: 0.8742 (t) cc_final: 0.8405 (p) REVERT: B 310 LYS cc_start: 0.8540 (ttpt) cc_final: 0.8249 (ttmt) REVERT: B 317 ASN cc_start: 0.8096 (m110) cc_final: 0.7427 (m-40) REVERT: B 558 LYS cc_start: 0.8265 (mmmt) cc_final: 0.7875 (mmmm) REVERT: B 646 ARG cc_start: 0.8136 (mmt180) cc_final: 0.7883 (mmt180) REVERT: B 654 GLU cc_start: 0.8223 (tt0) cc_final: 0.7977 (tt0) REVERT: B 671 CYS cc_start: 0.7331 (m) cc_final: 0.6988 (m) REVERT: B 698 SER cc_start: 0.8747 (t) cc_final: 0.8462 (p) REVERT: B 776 LYS cc_start: 0.8840 (tttt) cc_final: 0.8480 (ttpp) REVERT: B 791 THR cc_start: 0.8124 (OUTLIER) cc_final: 0.7860 (p) REVERT: B 814 LYS cc_start: 0.8097 (mmtm) cc_final: 0.7838 (mmtm) REVERT: B 821 LEU cc_start: 0.8821 (tt) cc_final: 0.8604 (tt) REVERT: B 895 GLN cc_start: 0.8310 (pt0) cc_final: 0.8074 (pt0) REVERT: B 921 LYS cc_start: 0.8283 (mmmm) cc_final: 0.8044 (mmmm) REVERT: B 1019 ARG cc_start: 0.7564 (ttm110) cc_final: 0.7314 (ttp-170) REVERT: B 1029 MET cc_start: 0.8477 (tpp) cc_final: 0.8233 (ttm) REVERT: B 1054 GLN cc_start: 0.8423 (mm-40) cc_final: 0.8194 (mm-40) REVERT: B 1075 PHE cc_start: 0.8479 (m-80) cc_final: 0.8238 (m-80) REVERT: B 1105 THR cc_start: 0.8473 (t) cc_final: 0.8152 (p) REVERT: B 1118 ASP cc_start: 0.7994 (t70) cc_final: 0.7779 (t70) REVERT: C 45 SER cc_start: 0.8646 (t) cc_final: 0.8170 (p) REVERT: C 193 VAL cc_start: 0.7695 (t) cc_final: 0.7383 (t) REVERT: C 194 PHE cc_start: 0.7914 (m-80) cc_final: 0.6831 (m-80) REVERT: C 285 ILE cc_start: 0.8875 (mt) cc_final: 0.8622 (mm) REVERT: C 307 THR cc_start: 0.8544 (OUTLIER) cc_final: 0.7940 (p) REVERT: C 308 VAL cc_start: 0.8840 (p) cc_final: 0.8378 (m) REVERT: C 309 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7468 (mm-30) REVERT: C 316 SER cc_start: 0.8639 (t) cc_final: 0.8277 (p) REVERT: C 369 TYR cc_start: 0.7160 (OUTLIER) cc_final: 0.6529 (p90) REVERT: C 488 CYS cc_start: 0.5006 (OUTLIER) cc_final: 0.3873 (m) REVERT: C 501 TYR cc_start: 0.7142 (OUTLIER) cc_final: 0.6538 (t80) REVERT: C 542 ASN cc_start: 0.7794 (t0) cc_final: 0.7441 (t0) REVERT: C 572 THR cc_start: 0.8621 (t) cc_final: 0.8229 (p) REVERT: C 587 ILE cc_start: 0.8698 (mp) cc_final: 0.8469 (mt) REVERT: C 644 GLN cc_start: 0.8041 (tp40) cc_final: 0.7583 (tp40) REVERT: C 737 ASP cc_start: 0.7941 (t0) cc_final: 0.7589 (t0) REVERT: C 765 ARG cc_start: 0.7937 (mtp-110) cc_final: 0.7660 (mtp85) REVERT: C 770 ILE cc_start: 0.8713 (mm) cc_final: 0.8353 (tt) REVERT: C 788 ILE cc_start: 0.8799 (mt) cc_final: 0.8532 (mm) REVERT: C 791 THR cc_start: 0.7893 (OUTLIER) cc_final: 0.7645 (p) REVERT: C 824 ASN cc_start: 0.8281 (m-40) cc_final: 0.8033 (m-40) REVERT: C 916 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7965 (tp) REVERT: C 949 GLN cc_start: 0.8371 (tt0) cc_final: 0.8047 (tt0) REVERT: C 1002 GLN cc_start: 0.8069 (tm-30) cc_final: 0.7729 (tm-30) REVERT: C 1005 GLN cc_start: 0.8438 (tp40) cc_final: 0.7977 (tp40) REVERT: C 1048 HIS cc_start: 0.8314 (t-90) cc_final: 0.7992 (t-170) REVERT: C 1075 PHE cc_start: 0.8063 (m-80) cc_final: 0.7717 (m-80) REVERT: C 1084 ASP cc_start: 0.8368 (OUTLIER) cc_final: 0.8167 (m-30) REVERT: C 1092 GLU cc_start: 0.7554 (mm-30) cc_final: 0.7279 (mm-30) REVERT: C 1101 HIS cc_start: 0.8150 (OUTLIER) cc_final: 0.7811 (m170) REVERT: C 1105 THR cc_start: 0.8464 (t) cc_final: 0.8060 (p) REVERT: D 41 TYR cc_start: 0.6762 (t80) cc_final: 0.6264 (t80) REVERT: D 123 MET cc_start: 0.5993 (tmm) cc_final: 0.5324 (ptp) REVERT: D 208 GLU cc_start: 0.3986 (tt0) cc_final: 0.3706 (tt0) REVERT: D 306 ARG cc_start: 0.8670 (mmm160) cc_final: 0.8373 (mmm160) REVERT: D 325 GLN cc_start: 0.5115 (tm-30) cc_final: 0.4756 (tm-30) REVERT: D 360 MET cc_start: -0.1782 (ttm) cc_final: -0.1982 (ttm) REVERT: D 457 GLU cc_start: 0.4263 (mm-30) cc_final: 0.3869 (mm-30) REVERT: D 474 MET cc_start: 0.4385 (ttp) cc_final: 0.3720 (mpp) REVERT: D 483 GLU cc_start: 0.6458 (tt0) cc_final: 0.6153 (tp30) REVERT: F 23 GLU cc_start: 0.6561 (mp0) cc_final: 0.6356 (pm20) REVERT: F 96 GLN cc_start: 0.6201 (mt0) cc_final: 0.5983 (mt0) REVERT: F 108 LEU cc_start: 0.6055 (mt) cc_final: 0.5571 (mt) REVERT: F 117 ASN cc_start: 0.7594 (m-40) cc_final: 0.7351 (m-40) REVERT: F 119 ILE cc_start: 0.3623 (OUTLIER) cc_final: 0.3134 (tt) REVERT: F 123 MET cc_start: 0.7416 (mtt) cc_final: 0.6803 (mtt) REVERT: F 179 LEU cc_start: 0.6676 (mt) cc_final: 0.6423 (pp) REVERT: F 313 LYS cc_start: 0.8235 (tmmt) cc_final: 0.7953 (tmmt) REVERT: F 323 MET cc_start: 0.7828 (mmt) cc_final: 0.7256 (mmt) REVERT: F 332 MET cc_start: 0.3256 (pmm) cc_final: 0.0651 (tmm) REVERT: F 358 ILE cc_start: 0.6892 (mt) cc_final: 0.6057 (mt) REVERT: F 376 MET cc_start: 0.6902 (OUTLIER) cc_final: 0.6256 (ttm) REVERT: F 398 GLU cc_start: 0.5652 (tp30) cc_final: 0.5421 (tp30) REVERT: F 470 LYS cc_start: 0.7017 (mmmt) cc_final: 0.6661 (mmmt) REVERT: F 514 ARG cc_start: 0.7912 (ptt90) cc_final: 0.7518 (ptt90) REVERT: F 557 MET cc_start: 0.6825 (tmm) cc_final: 0.6328 (tmm) outliers start: 143 outliers final: 95 residues processed: 913 average time/residue: 0.2291 time to fit residues: 347.0152 Evaluate side-chains 909 residues out of total 4269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 798 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 926 GLN Chi-restraints excluded: chain A residue 949 GLN Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 537 LYS Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 505 HIS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 537 LYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1111 GLU Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 309 LYS Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 38 ASP Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 119 ILE Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 271 TRP Chi-restraints excluded: chain F residue 315 PHE Chi-restraints excluded: chain F residue 373 HIS Chi-restraints excluded: chain F residue 376 MET Chi-restraints excluded: chain F residue 409 SER Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 581 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 265 optimal weight: 0.2980 chunk 15 optimal weight: 4.9990 chunk 218 optimal weight: 0.7980 chunk 41 optimal weight: 10.0000 chunk 438 optimal weight: 30.0000 chunk 104 optimal weight: 1.9990 chunk 474 optimal weight: 30.0000 chunk 79 optimal weight: 0.5980 chunk 80 optimal weight: 0.8980 chunk 422 optimal weight: 6.9990 chunk 461 optimal weight: 8.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN A1106 GLN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 ASN C 321 GLN C 505 HIS ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 ASN F 305 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.230648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.169398 restraints weight = 69102.187| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 3.69 r_work: 0.3594 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.5105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 40176 Z= 0.173 Angle : 0.620 12.998 54735 Z= 0.312 Chirality : 0.045 0.537 6117 Planarity : 0.004 0.057 7005 Dihedral : 4.804 60.927 6038 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.93 % Favored : 96.05 % Rotamer: Outliers : 3.63 % Allowed : 19.96 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.12), residues: 4809 helix: 1.22 (0.13), residues: 1751 sheet: -0.96 (0.19), residues: 620 loop : -1.47 (0.12), residues: 2438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 518 TYR 0.024 0.001 TYR C 313 PHE 0.036 0.002 PHE B 201 TRP 0.045 0.001 TRP D 461 HIS 0.032 0.001 HIS C 505 Details of bonding type rmsd covalent geometry : bond 0.00381 (40104) covalent geometry : angle 0.60328 (54558) SS BOND : bond 0.00571 ( 30) SS BOND : angle 2.25322 ( 60) hydrogen bonds : bond 0.03684 ( 1623) hydrogen bonds : angle 4.63299 ( 4521) metal coordination : bond 0.00096 ( 3) link_NAG-ASN : bond 0.00624 ( 39) link_NAG-ASN : angle 2.68809 ( 117) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 959 residues out of total 4269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 805 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.7417 (mtp85) cc_final: 0.7146 (mmm-85) REVERT: A 121 ASN cc_start: 0.7665 (m-40) cc_final: 0.6572 (t0) REVERT: A 277 LEU cc_start: 0.8712 (mt) cc_final: 0.8482 (mt) REVERT: A 294 ASP cc_start: 0.7509 (OUTLIER) cc_final: 0.7259 (m-30) REVERT: A 304 LYS cc_start: 0.8594 (mttt) cc_final: 0.8341 (ttmm) REVERT: A 317 ASN cc_start: 0.8398 (m-40) cc_final: 0.8141 (m-40) REVERT: A 324 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7947 (mt-10) REVERT: A 498 ARG cc_start: 0.8258 (mtt-85) cc_final: 0.7861 (mmm-85) REVERT: A 542 ASN cc_start: 0.8254 (t0) cc_final: 0.7915 (t0) REVERT: A 543 PHE cc_start: 0.8033 (m-10) cc_final: 0.7298 (m-80) REVERT: A 544 ASN cc_start: 0.8198 (m110) cc_final: 0.7880 (m-40) REVERT: A 554 GLU cc_start: 0.8003 (tm-30) cc_final: 0.7706 (tm-30) REVERT: A 580 GLN cc_start: 0.7694 (mt0) cc_final: 0.7407 (mt0) REVERT: A 619 GLU cc_start: 0.6678 (pm20) cc_final: 0.6409 (mp0) REVERT: A 654 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7803 (mt-10) REVERT: A 658 ASN cc_start: 0.8854 (OUTLIER) cc_final: 0.8251 (p0) REVERT: A 660 TYR cc_start: 0.8602 (m-80) cc_final: 0.8394 (m-10) REVERT: A 690 GLN cc_start: 0.7150 (mm-40) cc_final: 0.6840 (tt0) REVERT: A 737 ASP cc_start: 0.7317 (t0) cc_final: 0.7036 (t0) REVERT: A 774 GLN cc_start: 0.8215 (mm-40) cc_final: 0.7998 (mp10) REVERT: A 790 LYS cc_start: 0.8606 (mtmt) cc_final: 0.8155 (mtmm) REVERT: A 824 ASN cc_start: 0.8592 (m-40) cc_final: 0.8020 (m-40) REVERT: A 864 LEU cc_start: 0.8453 (tp) cc_final: 0.8230 (tt) REVERT: A 963 VAL cc_start: 0.8764 (m) cc_final: 0.8523 (p) REVERT: A 969 LYS cc_start: 0.8657 (mttm) cc_final: 0.8133 (mtmt) REVERT: A 995 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7422 (ttm-80) REVERT: A 1045 LYS cc_start: 0.8499 (tmtt) cc_final: 0.8197 (tmtt) REVERT: A 1082 CYS cc_start: 0.7326 (t) cc_final: 0.7027 (t) REVERT: A 1088 HIS cc_start: 0.8468 (m-70) cc_final: 0.8254 (m170) REVERT: A 1125 ASN cc_start: 0.7821 (p0) cc_final: 0.7618 (p0) REVERT: A 1130 ILE cc_start: 0.8816 (pt) cc_final: 0.8603 (mt) REVERT: B 34 ARG cc_start: 0.7366 (mtp85) cc_final: 0.7060 (mtp85) REVERT: B 54 LEU cc_start: 0.8295 (mt) cc_final: 0.8075 (mt) REVERT: B 58 PHE cc_start: 0.8631 (m-10) cc_final: 0.8315 (m-80) REVERT: B 119 ILE cc_start: 0.7832 (OUTLIER) cc_final: 0.7592 (pt) REVERT: B 140 PHE cc_start: 0.6278 (t80) cc_final: 0.5956 (t80) REVERT: B 221 SER cc_start: 0.7892 (m) cc_final: 0.7661 (p) REVERT: B 239 GLN cc_start: 0.8200 (pm20) cc_final: 0.7608 (pm20) REVERT: B 304 LYS cc_start: 0.8740 (mtpp) cc_final: 0.8495 (ttmm) REVERT: B 307 THR cc_start: 0.8770 (t) cc_final: 0.8507 (p) REVERT: B 317 ASN cc_start: 0.8055 (m110) cc_final: 0.7400 (m-40) REVERT: B 558 LYS cc_start: 0.8169 (mmmt) cc_final: 0.7729 (mmmm) REVERT: B 646 ARG cc_start: 0.8348 (mmt180) cc_final: 0.8107 (mmt180) REVERT: B 654 GLU cc_start: 0.8167 (tt0) cc_final: 0.7933 (tt0) REVERT: B 656 VAL cc_start: 0.8611 (t) cc_final: 0.8307 (p) REVERT: B 698 SER cc_start: 0.8756 (t) cc_final: 0.8486 (p) REVERT: B 776 LYS cc_start: 0.8838 (tttt) cc_final: 0.8473 (ttpp) REVERT: B 791 THR cc_start: 0.8158 (OUTLIER) cc_final: 0.7929 (p) REVERT: B 814 LYS cc_start: 0.8135 (mmtm) cc_final: 0.7934 (mmtm) REVERT: B 895 GLN cc_start: 0.8327 (pt0) cc_final: 0.8073 (pt0) REVERT: B 921 LYS cc_start: 0.8297 (mmmm) cc_final: 0.8095 (mmmm) REVERT: B 929 SER cc_start: 0.8532 (t) cc_final: 0.8259 (p) REVERT: B 1019 ARG cc_start: 0.7598 (ttm110) cc_final: 0.7308 (ttp-170) REVERT: B 1029 MET cc_start: 0.8501 (tpp) cc_final: 0.8208 (ttm) REVERT: B 1105 THR cc_start: 0.8524 (t) cc_final: 0.8227 (p) REVERT: B 1118 ASP cc_start: 0.7986 (t70) cc_final: 0.7783 (t70) REVERT: C 45 SER cc_start: 0.8576 (t) cc_final: 0.8127 (p) REVERT: C 194 PHE cc_start: 0.8357 (m-80) cc_final: 0.7673 (m-80) REVERT: C 240 THR cc_start: 0.7950 (OUTLIER) cc_final: 0.7086 (p) REVERT: C 307 THR cc_start: 0.8540 (OUTLIER) cc_final: 0.7954 (p) REVERT: C 308 VAL cc_start: 0.8828 (p) cc_final: 0.8408 (m) REVERT: C 309 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7414 (mm-30) REVERT: C 316 SER cc_start: 0.8689 (t) cc_final: 0.8340 (p) REVERT: C 369 TYR cc_start: 0.7264 (OUTLIER) cc_final: 0.6535 (p90) REVERT: C 488 CYS cc_start: 0.5189 (OUTLIER) cc_final: 0.4196 (m) REVERT: C 501 TYR cc_start: 0.7261 (OUTLIER) cc_final: 0.6585 (t80) REVERT: C 542 ASN cc_start: 0.7933 (t0) cc_final: 0.7526 (t0) REVERT: C 572 THR cc_start: 0.8645 (t) cc_final: 0.8257 (p) REVERT: C 587 ILE cc_start: 0.8746 (mp) cc_final: 0.8365 (mt) REVERT: C 644 GLN cc_start: 0.8070 (tp40) cc_final: 0.7613 (tp40) REVERT: C 737 ASP cc_start: 0.8086 (t0) cc_final: 0.7612 (t0) REVERT: C 765 ARG cc_start: 0.8090 (mtp-110) cc_final: 0.7809 (mtp85) REVERT: C 788 ILE cc_start: 0.8796 (mt) cc_final: 0.8555 (mm) REVERT: C 791 THR cc_start: 0.7915 (OUTLIER) cc_final: 0.7662 (p) REVERT: C 822 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8339 (mp) REVERT: C 824 ASN cc_start: 0.8370 (m-40) cc_final: 0.8123 (m-40) REVERT: C 916 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8078 (tp) REVERT: C 949 GLN cc_start: 0.8383 (tt0) cc_final: 0.8054 (tt0) REVERT: C 1002 GLN cc_start: 0.8100 (tm-30) cc_final: 0.7761 (tm-30) REVERT: C 1005 GLN cc_start: 0.8493 (tp40) cc_final: 0.8024 (tp40) REVERT: C 1048 HIS cc_start: 0.8329 (t-90) cc_final: 0.8001 (t-170) REVERT: C 1084 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.8042 (m-30) REVERT: C 1101 HIS cc_start: 0.8182 (OUTLIER) cc_final: 0.7795 (m170) REVERT: D 41 TYR cc_start: 0.6903 (t80) cc_final: 0.6422 (t80) REVERT: D 123 MET cc_start: 0.5994 (tmm) cc_final: 0.5305 (ptp) REVERT: D 208 GLU cc_start: 0.4458 (tt0) cc_final: 0.4155 (tt0) REVERT: D 306 ARG cc_start: 0.8657 (mmm160) cc_final: 0.8355 (mmm160) REVERT: D 313 LYS cc_start: 0.7430 (ptpp) cc_final: 0.7203 (ptpp) REVERT: D 325 GLN cc_start: 0.5204 (tm-30) cc_final: 0.4835 (tm-30) REVERT: D 383 MET cc_start: 0.6852 (tmm) cc_final: 0.6480 (tmm) REVERT: D 408 MET cc_start: 0.4803 (mmt) cc_final: 0.4329 (mmt) REVERT: D 457 GLU cc_start: 0.4469 (mm-30) cc_final: 0.4064 (mm-30) REVERT: D 474 MET cc_start: 0.4372 (ttp) cc_final: 0.3672 (mpp) REVERT: D 483 GLU cc_start: 0.6374 (tt0) cc_final: 0.6064 (tp30) REVERT: F 23 GLU cc_start: 0.6649 (mp0) cc_final: 0.5613 (pm20) REVERT: F 68 LYS cc_start: 0.8608 (mtmm) cc_final: 0.8360 (mppt) REVERT: F 96 GLN cc_start: 0.6236 (mt0) cc_final: 0.5999 (mt0) REVERT: F 117 ASN cc_start: 0.7516 (m-40) cc_final: 0.7250 (m-40) REVERT: F 119 ILE cc_start: 0.3629 (OUTLIER) cc_final: 0.3125 (tt) REVERT: F 123 MET cc_start: 0.7500 (mtt) cc_final: 0.6907 (mtt) REVERT: F 179 LEU cc_start: 0.6728 (mt) cc_final: 0.6470 (pp) REVERT: F 189 GLU cc_start: 0.6500 (pt0) cc_final: 0.6154 (pt0) REVERT: F 313 LYS cc_start: 0.8238 (tmmt) cc_final: 0.7943 (tmmt) REVERT: F 323 MET cc_start: 0.7723 (mmt) cc_final: 0.7156 (mmt) REVERT: F 376 MET cc_start: 0.7125 (OUTLIER) cc_final: 0.6446 (ttm) REVERT: F 408 MET cc_start: 0.6910 (mmt) cc_final: 0.6678 (mmt) REVERT: F 470 LYS cc_start: 0.7128 (mmmt) cc_final: 0.6772 (mmmt) REVERT: F 514 ARG cc_start: 0.7940 (ptt90) cc_final: 0.7640 (ptt90) REVERT: F 557 MET cc_start: 0.6943 (tmm) cc_final: 0.6516 (tmm) REVERT: F 560 LEU cc_start: 0.5581 (mt) cc_final: 0.5247 (mt) REVERT: F 587 TYR cc_start: 0.6272 (t80) cc_final: 0.5723 (t80) outliers start: 154 outliers final: 106 residues processed: 893 average time/residue: 0.2359 time to fit residues: 349.4771 Evaluate side-chains 917 residues out of total 4269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 793 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 949 GLN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 718 PHE Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 949 GLN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 505 HIS Chi-restraints excluded: chain C residue 537 LYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 872 GLN Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1111 GLU Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 309 LYS Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 579 MET Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 38 ASP Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 119 ILE Chi-restraints excluded: chain F residue 271 TRP Chi-restraints excluded: chain F residue 315 PHE Chi-restraints excluded: chain F residue 373 HIS Chi-restraints excluded: chain F residue 376 MET Chi-restraints excluded: chain F residue 409 SER Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 581 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 475 optimal weight: 40.0000 chunk 157 optimal weight: 0.9990 chunk 274 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 349 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 173 optimal weight: 0.0370 chunk 331 optimal weight: 7.9990 chunk 221 optimal weight: 0.5980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN A 926 GLN A 965 GLN A1106 GLN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 305 GLN ** F 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.230736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.172157 restraints weight = 68471.744| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 3.65 r_work: 0.3611 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.5314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 40176 Z= 0.139 Angle : 0.604 12.729 54735 Z= 0.303 Chirality : 0.044 0.520 6117 Planarity : 0.004 0.057 7005 Dihedral : 4.665 54.773 6038 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.54 % Favored : 96.44 % Rotamer: Outliers : 3.23 % Allowed : 20.90 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.12), residues: 4809 helix: 1.32 (0.13), residues: 1745 sheet: -0.89 (0.19), residues: 612 loop : -1.41 (0.12), residues: 2452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 518 TYR 0.024 0.001 TYR C1110 PHE 0.034 0.001 PHE B 201 TRP 0.048 0.001 TRP D 461 HIS 0.028 0.001 HIS C 505 Details of bonding type rmsd covalent geometry : bond 0.00309 (40104) covalent geometry : angle 0.58997 (54558) SS BOND : bond 0.00529 ( 30) SS BOND : angle 1.60847 ( 60) hydrogen bonds : bond 0.03507 ( 1623) hydrogen bonds : angle 4.58258 ( 4521) metal coordination : bond 0.00086 ( 3) link_NAG-ASN : bond 0.00560 ( 39) link_NAG-ASN : angle 2.63582 ( 117) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 952 residues out of total 4269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 815 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.7363 (mtp85) cc_final: 0.7110 (mmm-85) REVERT: A 294 ASP cc_start: 0.7534 (OUTLIER) cc_final: 0.7302 (m-30) REVERT: A 296 LEU cc_start: 0.8617 (tp) cc_final: 0.8408 (tt) REVERT: A 304 LYS cc_start: 0.8605 (mttt) cc_final: 0.8316 (ttmm) REVERT: A 317 ASN cc_start: 0.8409 (m-40) cc_final: 0.8153 (m-40) REVERT: A 324 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.8060 (mp0) REVERT: A 498 ARG cc_start: 0.8285 (mtt-85) cc_final: 0.7937 (mmt-90) REVERT: A 542 ASN cc_start: 0.8279 (t0) cc_final: 0.7856 (t0) REVERT: A 543 PHE cc_start: 0.8066 (m-10) cc_final: 0.7335 (m-80) REVERT: A 544 ASN cc_start: 0.8173 (m110) cc_final: 0.7900 (m-40) REVERT: A 554 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7767 (tm-30) REVERT: A 580 GLN cc_start: 0.7731 (mt0) cc_final: 0.7484 (mt0) REVERT: A 619 GLU cc_start: 0.6528 (pm20) cc_final: 0.6300 (mp0) REVERT: A 654 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7776 (mt-10) REVERT: A 658 ASN cc_start: 0.8870 (OUTLIER) cc_final: 0.8310 (p0) REVERT: A 660 TYR cc_start: 0.8634 (m-80) cc_final: 0.8396 (m-10) REVERT: A 690 GLN cc_start: 0.7088 (mm-40) cc_final: 0.6803 (tt0) REVERT: A 737 ASP cc_start: 0.7390 (t0) cc_final: 0.7154 (t0) REVERT: A 774 GLN cc_start: 0.8192 (mm-40) cc_final: 0.7972 (mp10) REVERT: A 790 LYS cc_start: 0.8632 (mtmt) cc_final: 0.8178 (mtmm) REVERT: A 819 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7751 (mt-10) REVERT: A 824 ASN cc_start: 0.8565 (m-40) cc_final: 0.7999 (m-40) REVERT: A 864 LEU cc_start: 0.8405 (tp) cc_final: 0.8182 (tt) REVERT: A 878 LEU cc_start: 0.8207 (mt) cc_final: 0.7887 (mt) REVERT: A 963 VAL cc_start: 0.8712 (m) cc_final: 0.8479 (p) REVERT: A 969 LYS cc_start: 0.8649 (mttm) cc_final: 0.8129 (mtmt) REVERT: A 995 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7445 (ttm-80) REVERT: A 1045 LYS cc_start: 0.8354 (tmtt) cc_final: 0.8129 (tmtt) REVERT: A 1082 CYS cc_start: 0.7281 (t) cc_final: 0.6965 (t) REVERT: A 1125 ASN cc_start: 0.7764 (p0) cc_final: 0.7552 (p0) REVERT: A 1130 ILE cc_start: 0.8833 (pt) cc_final: 0.8592 (mt) REVERT: B 34 ARG cc_start: 0.7366 (mtp85) cc_final: 0.7067 (mtp85) REVERT: B 54 LEU cc_start: 0.8276 (mt) cc_final: 0.7969 (mt) REVERT: B 58 PHE cc_start: 0.8672 (m-10) cc_final: 0.8221 (m-80) REVERT: B 119 ILE cc_start: 0.7868 (OUTLIER) cc_final: 0.7662 (pt) REVERT: B 190 ARG cc_start: 0.8239 (mtm-85) cc_final: 0.6971 (mtm-85) REVERT: B 221 SER cc_start: 0.7920 (m) cc_final: 0.7695 (p) REVERT: B 239 GLN cc_start: 0.8105 (pm20) cc_final: 0.7588 (pm20) REVERT: B 304 LYS cc_start: 0.8719 (mtpp) cc_final: 0.8482 (ttmm) REVERT: B 307 THR cc_start: 0.8785 (t) cc_final: 0.8562 (p) REVERT: B 317 ASN cc_start: 0.8046 (m110) cc_final: 0.7326 (m-40) REVERT: B 558 LYS cc_start: 0.8042 (mmmt) cc_final: 0.7652 (mmmm) REVERT: B 646 ARG cc_start: 0.8200 (mmt180) cc_final: 0.7981 (mmt180) REVERT: B 654 GLU cc_start: 0.8171 (tt0) cc_final: 0.7933 (tt0) REVERT: B 656 VAL cc_start: 0.8595 (t) cc_final: 0.8261 (p) REVERT: B 704 SER cc_start: 0.8777 (t) cc_final: 0.8509 (p) REVERT: B 776 LYS cc_start: 0.8828 (tttt) cc_final: 0.8444 (ttpp) REVERT: B 791 THR cc_start: 0.8163 (OUTLIER) cc_final: 0.7935 (p) REVERT: B 821 LEU cc_start: 0.8750 (tt) cc_final: 0.8549 (tt) REVERT: B 895 GLN cc_start: 0.8301 (pt0) cc_final: 0.8053 (pt0) REVERT: B 921 LYS cc_start: 0.8218 (mmmm) cc_final: 0.7922 (mmtm) REVERT: B 929 SER cc_start: 0.8488 (t) cc_final: 0.8219 (p) REVERT: B 1019 ARG cc_start: 0.7565 (ttm110) cc_final: 0.7298 (ttp-170) REVERT: B 1029 MET cc_start: 0.8515 (tpp) cc_final: 0.8234 (ttm) REVERT: B 1054 GLN cc_start: 0.8489 (mm-40) cc_final: 0.8238 (mm-40) REVERT: B 1075 PHE cc_start: 0.8262 (m-80) cc_final: 0.7985 (m-80) REVERT: B 1105 THR cc_start: 0.8563 (t) cc_final: 0.8270 (p) REVERT: B 1118 ASP cc_start: 0.7961 (t70) cc_final: 0.7759 (t70) REVERT: C 45 SER cc_start: 0.8499 (t) cc_final: 0.8067 (p) REVERT: C 204 TYR cc_start: 0.7029 (m-80) cc_final: 0.6445 (m-80) REVERT: C 307 THR cc_start: 0.8536 (OUTLIER) cc_final: 0.7937 (p) REVERT: C 308 VAL cc_start: 0.8835 (p) cc_final: 0.8399 (m) REVERT: C 309 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7400 (mm-30) REVERT: C 316 SER cc_start: 0.8671 (t) cc_final: 0.8321 (p) REVERT: C 369 TYR cc_start: 0.7243 (OUTLIER) cc_final: 0.6602 (p90) REVERT: C 488 CYS cc_start: 0.5179 (OUTLIER) cc_final: 0.4218 (m) REVERT: C 501 TYR cc_start: 0.7149 (OUTLIER) cc_final: 0.6710 (t80) REVERT: C 542 ASN cc_start: 0.7847 (t0) cc_final: 0.7495 (t0) REVERT: C 572 THR cc_start: 0.8649 (t) cc_final: 0.8284 (p) REVERT: C 587 ILE cc_start: 0.8729 (mp) cc_final: 0.8331 (mt) REVERT: C 644 GLN cc_start: 0.8086 (tp40) cc_final: 0.7695 (tp40) REVERT: C 710 ASN cc_start: 0.8270 (m-40) cc_final: 0.7892 (t0) REVERT: C 737 ASP cc_start: 0.8077 (t0) cc_final: 0.7619 (t0) REVERT: C 765 ARG cc_start: 0.8020 (mtp-110) cc_final: 0.7729 (mtp85) REVERT: C 788 ILE cc_start: 0.8825 (mt) cc_final: 0.8549 (mm) REVERT: C 791 THR cc_start: 0.7925 (OUTLIER) cc_final: 0.7656 (p) REVERT: C 822 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8337 (mp) REVERT: C 824 ASN cc_start: 0.8360 (m-40) cc_final: 0.8108 (m-40) REVERT: C 916 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7955 (tp) REVERT: C 921 LYS cc_start: 0.8713 (mmmt) cc_final: 0.8475 (mmmm) REVERT: C 934 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8396 (tp) REVERT: C 949 GLN cc_start: 0.8333 (tt0) cc_final: 0.7991 (tt0) REVERT: C 1002 GLN cc_start: 0.8119 (tm-30) cc_final: 0.7797 (tm-30) REVERT: C 1005 GLN cc_start: 0.8442 (tp40) cc_final: 0.7992 (tp40) REVERT: C 1048 HIS cc_start: 0.8311 (t-90) cc_final: 0.7984 (t-170) REVERT: C 1084 ASP cc_start: 0.8311 (OUTLIER) cc_final: 0.8089 (m-30) REVERT: C 1101 HIS cc_start: 0.8169 (OUTLIER) cc_final: 0.7842 (m170) REVERT: D 41 TYR cc_start: 0.6811 (t80) cc_final: 0.6381 (t80) REVERT: D 123 MET cc_start: 0.5988 (tmm) cc_final: 0.5296 (ptp) REVERT: D 208 GLU cc_start: 0.4554 (tt0) cc_final: 0.4244 (tt0) REVERT: D 293 VAL cc_start: 0.0754 (p) cc_final: 0.0469 (m) REVERT: D 306 ARG cc_start: 0.8657 (mmm160) cc_final: 0.8375 (mmm160) REVERT: D 313 LYS cc_start: 0.7424 (ptpp) cc_final: 0.7214 (ptpp) REVERT: D 325 GLN cc_start: 0.5238 (tm-30) cc_final: 0.4869 (tm-30) REVERT: D 383 MET cc_start: 0.6876 (tmm) cc_final: 0.6553 (tmm) REVERT: D 457 GLU cc_start: 0.4443 (mm-30) cc_final: 0.4009 (mm-30) REVERT: D 474 MET cc_start: 0.4419 (ttp) cc_final: 0.3738 (mpp) REVERT: F 68 LYS cc_start: 0.8614 (mtmm) cc_final: 0.8395 (mppt) REVERT: F 96 GLN cc_start: 0.6203 (mt0) cc_final: 0.5960 (mt0) REVERT: F 117 ASN cc_start: 0.7566 (m-40) cc_final: 0.7311 (m-40) REVERT: F 119 ILE cc_start: 0.3645 (OUTLIER) cc_final: 0.3166 (tt) REVERT: F 123 MET cc_start: 0.7487 (mtt) cc_final: 0.6888 (mtt) REVERT: F 179 LEU cc_start: 0.6697 (mt) cc_final: 0.6480 (pp) REVERT: F 189 GLU cc_start: 0.6576 (pt0) cc_final: 0.6230 (pt0) REVERT: F 270 MET cc_start: 0.4735 (ttm) cc_final: 0.4365 (tpp) REVERT: F 313 LYS cc_start: 0.8202 (tmmt) cc_final: 0.7898 (tmmt) REVERT: F 323 MET cc_start: 0.7767 (mmt) cc_final: 0.7138 (mmt) REVERT: F 332 MET cc_start: 0.0522 (pmm) cc_final: -0.0594 (ttp) REVERT: F 358 ILE cc_start: 0.6832 (mt) cc_final: 0.6164 (mt) REVERT: F 376 MET cc_start: 0.7186 (OUTLIER) cc_final: 0.6521 (ttm) REVERT: F 408 MET cc_start: 0.6920 (mmt) cc_final: 0.6691 (mmt) REVERT: F 470 LYS cc_start: 0.7145 (mmmt) cc_final: 0.6800 (mmmt) REVERT: F 474 MET cc_start: 0.3961 (mmm) cc_final: 0.3059 (mmm) REVERT: F 557 MET cc_start: 0.6990 (tmm) cc_final: 0.6542 (tmm) REVERT: F 587 TYR cc_start: 0.6252 (t80) cc_final: 0.5666 (t80) outliers start: 137 outliers final: 97 residues processed: 894 average time/residue: 0.2361 time to fit residues: 350.1070 Evaluate side-chains 908 residues out of total 4269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 793 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 949 GLN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 949 GLN Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 537 LYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1111 GLU Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 309 LYS Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 579 MET Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 38 ASP Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 119 ILE Chi-restraints excluded: chain F residue 271 TRP Chi-restraints excluded: chain F residue 308 PHE Chi-restraints excluded: chain F residue 315 PHE Chi-restraints excluded: chain F residue 376 MET Chi-restraints excluded: chain F residue 409 SER Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain F residue 522 GLN Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 581 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 215 optimal weight: 0.0020 chunk 336 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 134 optimal weight: 5.9990 chunk 150 optimal weight: 2.9990 chunk 189 optimal weight: 0.6980 chunk 281 optimal weight: 0.9990 chunk 238 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 372 optimal weight: 0.5980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN A1106 GLN ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN C 321 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 305 GLN ** F 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.230357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.167748 restraints weight = 68412.139| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 3.44 r_work: 0.3608 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.5540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 40176 Z= 0.140 Angle : 0.606 12.535 54735 Z= 0.305 Chirality : 0.044 0.518 6117 Planarity : 0.004 0.054 7005 Dihedral : 4.579 53.626 6037 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.95 % Favored : 96.03 % Rotamer: Outliers : 2.94 % Allowed : 21.52 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.12), residues: 4809 helix: 1.34 (0.13), residues: 1755 sheet: -0.95 (0.20), residues: 611 loop : -1.32 (0.12), residues: 2443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 518 TYR 0.023 0.001 TYR C1110 PHE 0.033 0.001 PHE B 201 TRP 0.050 0.001 TRP D 461 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00312 (40104) covalent geometry : angle 0.59203 (54558) SS BOND : bond 0.00333 ( 30) SS BOND : angle 1.56328 ( 60) hydrogen bonds : bond 0.03534 ( 1623) hydrogen bonds : angle 4.61707 ( 4521) metal coordination : bond 0.00100 ( 3) link_NAG-ASN : bond 0.00574 ( 39) link_NAG-ASN : angle 2.61521 ( 117) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 942 residues out of total 4269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 817 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.8545 (OUTLIER) cc_final: 0.8344 (m-10) REVERT: A 289 VAL cc_start: 0.8804 (m) cc_final: 0.8544 (p) REVERT: A 294 ASP cc_start: 0.7618 (OUTLIER) cc_final: 0.7372 (m-30) REVERT: A 296 LEU cc_start: 0.8647 (tp) cc_final: 0.8433 (tt) REVERT: A 304 LYS cc_start: 0.8642 (mttt) cc_final: 0.8354 (ttmm) REVERT: A 306 PHE cc_start: 0.8779 (OUTLIER) cc_final: 0.8473 (m-80) REVERT: A 317 ASN cc_start: 0.8366 (m-40) cc_final: 0.8116 (m-40) REVERT: A 324 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7991 (mp0) REVERT: A 498 ARG cc_start: 0.8296 (mtt-85) cc_final: 0.7883 (mmt-90) REVERT: A 542 ASN cc_start: 0.8303 (t0) cc_final: 0.7895 (t0) REVERT: A 543 PHE cc_start: 0.8062 (m-10) cc_final: 0.7710 (m-10) REVERT: A 619 GLU cc_start: 0.6479 (pm20) cc_final: 0.5682 (mp0) REVERT: A 654 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7935 (mt-10) REVERT: A 658 ASN cc_start: 0.8878 (OUTLIER) cc_final: 0.8297 (p0) REVERT: A 690 GLN cc_start: 0.7157 (mm-40) cc_final: 0.6908 (tt0) REVERT: A 737 ASP cc_start: 0.7343 (t0) cc_final: 0.7045 (t0) REVERT: A 774 GLN cc_start: 0.8132 (mm-40) cc_final: 0.7918 (mp10) REVERT: A 790 LYS cc_start: 0.8621 (mtmt) cc_final: 0.8185 (mtmm) REVERT: A 808 ASP cc_start: 0.8173 (t0) cc_final: 0.7950 (t0) REVERT: A 819 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7687 (mt-10) REVERT: A 824 ASN cc_start: 0.8587 (m-40) cc_final: 0.8048 (m-40) REVERT: A 864 LEU cc_start: 0.8409 (tp) cc_final: 0.8189 (tt) REVERT: A 878 LEU cc_start: 0.8190 (mt) cc_final: 0.7877 (mt) REVERT: A 922 LEU cc_start: 0.8926 (tp) cc_final: 0.8712 (tt) REVERT: A 963 VAL cc_start: 0.8711 (m) cc_final: 0.8493 (p) REVERT: A 969 LYS cc_start: 0.8661 (mttm) cc_final: 0.8141 (mtmt) REVERT: A 995 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7401 (ttm-80) REVERT: A 1045 LYS cc_start: 0.8393 (tmtt) cc_final: 0.8151 (tmtt) REVERT: A 1082 CYS cc_start: 0.7133 (t) cc_final: 0.6830 (t) REVERT: A 1130 ILE cc_start: 0.8844 (pt) cc_final: 0.8604 (mt) REVERT: B 34 ARG cc_start: 0.7288 (mtp85) cc_final: 0.6988 (mtp85) REVERT: B 54 LEU cc_start: 0.8253 (mt) cc_final: 0.8047 (mt) REVERT: B 58 PHE cc_start: 0.8701 (m-10) cc_final: 0.8290 (m-80) REVERT: B 190 ARG cc_start: 0.8199 (mtm-85) cc_final: 0.6939 (mtm-85) REVERT: B 239 GLN cc_start: 0.8110 (pm20) cc_final: 0.7594 (pm20) REVERT: B 278 LYS cc_start: 0.8868 (ptmt) cc_final: 0.8641 (tttt) REVERT: B 304 LYS cc_start: 0.8687 (mtpp) cc_final: 0.8447 (ttmm) REVERT: B 307 THR cc_start: 0.8787 (t) cc_final: 0.8584 (p) REVERT: B 310 LYS cc_start: 0.8462 (ttmt) cc_final: 0.8205 (ttmt) REVERT: B 317 ASN cc_start: 0.8025 (m110) cc_final: 0.7290 (m-40) REVERT: B 558 LYS cc_start: 0.8053 (mmmt) cc_final: 0.7670 (mmmm) REVERT: B 654 GLU cc_start: 0.8184 (tt0) cc_final: 0.7963 (tt0) REVERT: B 656 VAL cc_start: 0.8563 (t) cc_final: 0.8248 (p) REVERT: B 776 LYS cc_start: 0.8826 (tttt) cc_final: 0.8447 (ttpp) REVERT: B 791 THR cc_start: 0.8142 (OUTLIER) cc_final: 0.7914 (p) REVERT: B 821 LEU cc_start: 0.8751 (tt) cc_final: 0.8548 (tt) REVERT: B 895 GLN cc_start: 0.8288 (pt0) cc_final: 0.8041 (pt0) REVERT: B 921 LYS cc_start: 0.8180 (mmmm) cc_final: 0.7882 (mmtm) REVERT: B 929 SER cc_start: 0.8475 (t) cc_final: 0.8233 (p) REVERT: B 995 ARG cc_start: 0.7893 (ttp-170) cc_final: 0.7692 (mtp180) REVERT: B 1019 ARG cc_start: 0.7553 (ttm110) cc_final: 0.7253 (ttp-170) REVERT: B 1029 MET cc_start: 0.8508 (tpp) cc_final: 0.8218 (ttm) REVERT: B 1054 GLN cc_start: 0.8450 (mm-40) cc_final: 0.8210 (mm-40) REVERT: B 1105 THR cc_start: 0.8579 (t) cc_final: 0.8312 (p) REVERT: C 45 SER cc_start: 0.8494 (t) cc_final: 0.8058 (p) REVERT: C 204 TYR cc_start: 0.7128 (m-80) cc_final: 0.6524 (m-80) REVERT: C 231 ILE cc_start: 0.2937 (OUTLIER) cc_final: 0.2702 (pt) REVERT: C 273 ARG cc_start: 0.7776 (ptm160) cc_final: 0.7233 (mtp85) REVERT: C 307 THR cc_start: 0.8556 (OUTLIER) cc_final: 0.7949 (p) REVERT: C 308 VAL cc_start: 0.8858 (p) cc_final: 0.8409 (m) REVERT: C 309 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7373 (mm-30) REVERT: C 316 SER cc_start: 0.8617 (t) cc_final: 0.8265 (p) REVERT: C 365 TYR cc_start: 0.7322 (m-80) cc_final: 0.6973 (m-80) REVERT: C 369 TYR cc_start: 0.7271 (OUTLIER) cc_final: 0.6618 (p90) REVERT: C 488 CYS cc_start: 0.5261 (OUTLIER) cc_final: 0.4448 (m) REVERT: C 542 ASN cc_start: 0.7876 (t0) cc_final: 0.7550 (t0) REVERT: C 572 THR cc_start: 0.8664 (t) cc_final: 0.8325 (p) REVERT: C 587 ILE cc_start: 0.8750 (mp) cc_final: 0.8354 (mt) REVERT: C 644 GLN cc_start: 0.8094 (tp40) cc_final: 0.7761 (tp40) REVERT: C 737 ASP cc_start: 0.8081 (t0) cc_final: 0.7642 (t0) REVERT: C 748 GLU cc_start: 0.8699 (pm20) cc_final: 0.8161 (pm20) REVERT: C 765 ARG cc_start: 0.8010 (mtp-110) cc_final: 0.7727 (mtp85) REVERT: C 788 ILE cc_start: 0.8815 (mt) cc_final: 0.8568 (mm) REVERT: C 791 THR cc_start: 0.7900 (OUTLIER) cc_final: 0.7644 (p) REVERT: C 824 ASN cc_start: 0.8359 (m-40) cc_final: 0.8095 (m-40) REVERT: C 934 ILE cc_start: 0.8685 (OUTLIER) cc_final: 0.8445 (tp) REVERT: C 949 GLN cc_start: 0.8303 (tt0) cc_final: 0.7984 (tt0) REVERT: C 1002 GLN cc_start: 0.8133 (tm-30) cc_final: 0.7742 (tm-30) REVERT: C 1005 GLN cc_start: 0.8446 (tp40) cc_final: 0.7985 (tp40) REVERT: C 1017 GLU cc_start: 0.8340 (tp30) cc_final: 0.7913 (tp30) REVERT: C 1048 HIS cc_start: 0.8300 (t-90) cc_final: 0.7975 (t-170) REVERT: C 1084 ASP cc_start: 0.8331 (OUTLIER) cc_final: 0.8125 (m-30) REVERT: C 1101 HIS cc_start: 0.8254 (OUTLIER) cc_final: 0.7940 (m170) REVERT: D 41 TYR cc_start: 0.6775 (t80) cc_final: 0.6211 (t80) REVERT: D 123 MET cc_start: 0.6018 (tmm) cc_final: 0.5364 (ptp) REVERT: D 208 GLU cc_start: 0.4705 (tt0) cc_final: 0.4388 (tt0) REVERT: D 306 ARG cc_start: 0.8663 (mmm160) cc_final: 0.8403 (mmm160) REVERT: D 313 LYS cc_start: 0.7466 (ptpp) cc_final: 0.7247 (ptpp) REVERT: D 325 GLN cc_start: 0.5299 (tm-30) cc_final: 0.4955 (tm-30) REVERT: D 447 VAL cc_start: 0.2578 (t) cc_final: 0.2245 (m) REVERT: D 455 MET cc_start: 0.6065 (ppp) cc_final: 0.5716 (ppp) REVERT: D 457 GLU cc_start: 0.4502 (mm-30) cc_final: 0.4067 (mm-30) REVERT: D 474 MET cc_start: 0.4446 (ttp) cc_final: 0.3781 (mpp) REVERT: F 22 GLU cc_start: 0.6584 (pp20) cc_final: 0.6141 (pp20) REVERT: F 23 GLU cc_start: 0.6586 (pm20) cc_final: 0.6174 (pm20) REVERT: F 68 LYS cc_start: 0.8644 (mtmm) cc_final: 0.8416 (mppt) REVERT: F 72 PHE cc_start: 0.6561 (t80) cc_final: 0.6284 (t80) REVERT: F 96 GLN cc_start: 0.6223 (mt0) cc_final: 0.5972 (mt0) REVERT: F 117 ASN cc_start: 0.7630 (m-40) cc_final: 0.7386 (m-40) REVERT: F 119 ILE cc_start: 0.3627 (OUTLIER) cc_final: 0.3142 (tt) REVERT: F 123 MET cc_start: 0.7471 (mtt) cc_final: 0.6868 (mtt) REVERT: F 179 LEU cc_start: 0.6676 (mt) cc_final: 0.6465 (pp) REVERT: F 190 MET cc_start: 0.4011 (mmm) cc_final: 0.3634 (mmm) REVERT: F 215 TYR cc_start: 0.5201 (m-80) cc_final: 0.4547 (m-80) REVERT: F 313 LYS cc_start: 0.8242 (tmmt) cc_final: 0.7936 (tmmt) REVERT: F 323 MET cc_start: 0.7816 (mmt) cc_final: 0.7248 (mmt) REVERT: F 332 MET cc_start: 0.0548 (pmm) cc_final: -0.0284 (ttp) REVERT: F 358 ILE cc_start: 0.6877 (mt) cc_final: 0.6146 (mt) REVERT: F 376 MET cc_start: 0.7315 (OUTLIER) cc_final: 0.6697 (ttm) REVERT: F 378 HIS cc_start: 0.5440 (m170) cc_final: 0.4490 (m170) REVERT: F 408 MET cc_start: 0.6947 (mmt) cc_final: 0.6712 (mmt) REVERT: F 417 HIS cc_start: 0.7776 (t-170) cc_final: 0.7425 (t-170) REVERT: F 470 LYS cc_start: 0.7107 (mmmt) cc_final: 0.6776 (mmmt) REVERT: F 474 MET cc_start: 0.3974 (mmm) cc_final: 0.2978 (mmm) REVERT: F 557 MET cc_start: 0.7120 (tmm) cc_final: 0.6660 (tmm) REVERT: F 587 TYR cc_start: 0.6245 (t80) cc_final: 0.5661 (t80) outliers start: 125 outliers final: 89 residues processed: 886 average time/residue: 0.2296 time to fit residues: 336.4166 Evaluate side-chains 906 residues out of total 4269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 800 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 949 GLN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 949 GLN Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 537 LYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 872 GLN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1111 GLU Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 309 LYS Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 38 ASP Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 119 ILE Chi-restraints excluded: chain F residue 271 TRP Chi-restraints excluded: chain F residue 308 PHE Chi-restraints excluded: chain F residue 315 PHE Chi-restraints excluded: chain F residue 376 MET Chi-restraints excluded: chain F residue 409 SER Chi-restraints excluded: chain F residue 522 GLN Chi-restraints excluded: chain E residue 581 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 9 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 263 optimal weight: 3.9990 chunk 264 optimal weight: 0.8980 chunk 327 optimal weight: 4.9990 chunk 391 optimal weight: 0.4980 chunk 55 optimal weight: 0.4980 chunk 177 optimal weight: 0.8980 chunk 359 optimal weight: 8.9990 chunk 170 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN B1106 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1071 GLN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 305 GLN ** F 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 493 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.229871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.170098 restraints weight = 67959.788| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 3.89 r_work: 0.3610 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.5746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 40176 Z= 0.142 Angle : 0.625 13.503 54735 Z= 0.313 Chirality : 0.045 0.569 6117 Planarity : 0.004 0.053 7005 Dihedral : 4.567 52.951 6037 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.76 % Favored : 96.22 % Rotamer: Outliers : 2.57 % Allowed : 22.03 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.12), residues: 4809 helix: 1.34 (0.13), residues: 1762 sheet: -0.91 (0.20), residues: 586 loop : -1.28 (0.12), residues: 2461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 567 TYR 0.026 0.001 TYR C1110 PHE 0.036 0.002 PHE A 194 TRP 0.053 0.001 TRP D 461 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00313 (40104) covalent geometry : angle 0.61005 (54558) SS BOND : bond 0.00337 ( 30) SS BOND : angle 1.59832 ( 60) hydrogen bonds : bond 0.03491 ( 1623) hydrogen bonds : angle 4.61006 ( 4521) metal coordination : bond 0.00037 ( 3) link_NAG-ASN : bond 0.00718 ( 39) link_NAG-ASN : angle 2.75869 ( 117) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 937 residues out of total 4269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 828 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.7302 (mmm-85) cc_final: 0.7016 (mmm-85) REVERT: A 58 PHE cc_start: 0.8624 (m-10) cc_final: 0.8350 (m-80) REVERT: A 121 ASN cc_start: 0.7581 (m-40) cc_final: 0.6771 (t0) REVERT: A 294 ASP cc_start: 0.7650 (OUTLIER) cc_final: 0.7396 (m-30) REVERT: A 296 LEU cc_start: 0.8670 (tp) cc_final: 0.8454 (tt) REVERT: A 304 LYS cc_start: 0.8682 (mttt) cc_final: 0.8370 (ttmm) REVERT: A 306 PHE cc_start: 0.8740 (OUTLIER) cc_final: 0.8471 (m-80) REVERT: A 317 ASN cc_start: 0.8373 (m-40) cc_final: 0.8120 (m-40) REVERT: A 324 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7978 (mp0) REVERT: A 498 ARG cc_start: 0.8350 (mtt-85) cc_final: 0.8004 (mmt-90) REVERT: A 542 ASN cc_start: 0.8345 (t0) cc_final: 0.7962 (t0) REVERT: A 543 PHE cc_start: 0.8063 (m-10) cc_final: 0.7855 (m-10) REVERT: A 554 GLU cc_start: 0.8052 (tp30) cc_final: 0.7787 (tp30) REVERT: A 654 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7852 (mt-10) REVERT: A 658 ASN cc_start: 0.8912 (OUTLIER) cc_final: 0.8460 (p0) REVERT: A 737 ASP cc_start: 0.7430 (t0) cc_final: 0.7162 (t0) REVERT: A 774 GLN cc_start: 0.8246 (mm-40) cc_final: 0.8039 (mp10) REVERT: A 790 LYS cc_start: 0.8647 (mtmt) cc_final: 0.8213 (mtmm) REVERT: A 808 ASP cc_start: 0.8160 (t0) cc_final: 0.7909 (t0) REVERT: A 824 ASN cc_start: 0.8591 (m-40) cc_final: 0.8066 (m-40) REVERT: A 864 LEU cc_start: 0.8397 (tp) cc_final: 0.8174 (tt) REVERT: A 878 LEU cc_start: 0.8220 (mt) cc_final: 0.7927 (mt) REVERT: A 922 LEU cc_start: 0.8916 (tp) cc_final: 0.8705 (tt) REVERT: A 963 VAL cc_start: 0.8696 (m) cc_final: 0.8482 (p) REVERT: A 969 LYS cc_start: 0.8645 (mttm) cc_final: 0.8148 (mtmt) REVERT: A 995 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7413 (ttm-80) REVERT: A 1045 LYS cc_start: 0.8378 (tmtt) cc_final: 0.8137 (tmtt) REVERT: A 1082 CYS cc_start: 0.7320 (t) cc_final: 0.7007 (t) REVERT: A 1130 ILE cc_start: 0.8848 (pt) cc_final: 0.8582 (mt) REVERT: B 54 LEU cc_start: 0.8284 (mt) cc_final: 0.8083 (mt) REVERT: B 58 PHE cc_start: 0.8721 (m-10) cc_final: 0.8335 (m-80) REVERT: B 190 ARG cc_start: 0.8205 (mtm-85) cc_final: 0.6975 (mtm-85) REVERT: B 239 GLN cc_start: 0.8158 (pm20) cc_final: 0.7597 (pm20) REVERT: B 278 LYS cc_start: 0.8877 (ptmt) cc_final: 0.8642 (tttt) REVERT: B 304 LYS cc_start: 0.8710 (mtpp) cc_final: 0.8486 (ttmm) REVERT: B 307 THR cc_start: 0.8821 (t) cc_final: 0.8589 (p) REVERT: B 310 LYS cc_start: 0.8488 (ttmt) cc_final: 0.8231 (ttmt) REVERT: B 317 ASN cc_start: 0.8047 (m110) cc_final: 0.7340 (m-40) REVERT: B 558 LYS cc_start: 0.8069 (mmmt) cc_final: 0.7669 (mmmm) REVERT: B 606 ASN cc_start: 0.8360 (p0) cc_final: 0.8127 (p0) REVERT: B 654 GLU cc_start: 0.8235 (tt0) cc_final: 0.8026 (tt0) REVERT: B 656 VAL cc_start: 0.8602 (t) cc_final: 0.8252 (p) REVERT: B 776 LYS cc_start: 0.8811 (tttt) cc_final: 0.8433 (ttpp) REVERT: B 791 THR cc_start: 0.8160 (OUTLIER) cc_final: 0.7938 (p) REVERT: B 804 GLN cc_start: 0.7865 (mt0) cc_final: 0.7542 (mt0) REVERT: B 895 GLN cc_start: 0.8265 (pt0) cc_final: 0.8006 (pt0) REVERT: B 921 LYS cc_start: 0.8212 (mmmm) cc_final: 0.7921 (mmtm) REVERT: B 929 SER cc_start: 0.8491 (t) cc_final: 0.8213 (p) REVERT: B 995 ARG cc_start: 0.7968 (ttp-170) cc_final: 0.7750 (mtp180) REVERT: B 1019 ARG cc_start: 0.7564 (ttm110) cc_final: 0.7243 (ttp-170) REVERT: B 1054 GLN cc_start: 0.8520 (mm-40) cc_final: 0.8269 (mm-40) REVERT: B 1105 THR cc_start: 0.8622 (t) cc_final: 0.8348 (p) REVERT: C 45 SER cc_start: 0.8421 (t) cc_final: 0.8007 (p) REVERT: C 204 TYR cc_start: 0.7223 (m-80) cc_final: 0.6581 (m-80) REVERT: C 273 ARG cc_start: 0.7804 (ptm160) cc_final: 0.7390 (mtp85) REVERT: C 307 THR cc_start: 0.8563 (OUTLIER) cc_final: 0.7961 (p) REVERT: C 308 VAL cc_start: 0.8860 (p) cc_final: 0.8404 (m) REVERT: C 309 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7436 (mm-30) REVERT: C 316 SER cc_start: 0.8619 (t) cc_final: 0.8277 (p) REVERT: C 369 TYR cc_start: 0.7264 (OUTLIER) cc_final: 0.6599 (p90) REVERT: C 429 PHE cc_start: 0.6647 (t80) cc_final: 0.6423 (t80) REVERT: C 488 CYS cc_start: 0.5352 (OUTLIER) cc_final: 0.4410 (m) REVERT: C 501 TYR cc_start: 0.7089 (OUTLIER) cc_final: 0.6460 (t80) REVERT: C 505 HIS cc_start: 0.7674 (m-70) cc_final: 0.6956 (t-90) REVERT: C 542 ASN cc_start: 0.7832 (t0) cc_final: 0.7505 (t0) REVERT: C 572 THR cc_start: 0.8718 (t) cc_final: 0.8393 (p) REVERT: C 587 ILE cc_start: 0.8734 (mp) cc_final: 0.8366 (mt) REVERT: C 646 ARG cc_start: 0.7829 (mtp180) cc_final: 0.7627 (mtp180) REVERT: C 710 ASN cc_start: 0.8398 (m-40) cc_final: 0.8044 (t0) REVERT: C 737 ASP cc_start: 0.8194 (t0) cc_final: 0.7801 (t0) REVERT: C 748 GLU cc_start: 0.8673 (pm20) cc_final: 0.8096 (pm20) REVERT: C 765 ARG cc_start: 0.8009 (mtp-110) cc_final: 0.7707 (mtp85) REVERT: C 770 ILE cc_start: 0.8622 (mm) cc_final: 0.8372 (tt) REVERT: C 788 ILE cc_start: 0.8860 (mt) cc_final: 0.8591 (mm) REVERT: C 791 THR cc_start: 0.7894 (OUTLIER) cc_final: 0.7635 (p) REVERT: C 804 GLN cc_start: 0.8285 (mt0) cc_final: 0.7868 (mt0) REVERT: C 824 ASN cc_start: 0.8420 (m-40) cc_final: 0.8161 (m-40) REVERT: C 904 TYR cc_start: 0.7976 (m-10) cc_final: 0.7717 (m-80) REVERT: C 934 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8463 (tp) REVERT: C 949 GLN cc_start: 0.8241 (tt0) cc_final: 0.7932 (tt0) REVERT: C 1002 GLN cc_start: 0.8113 (tm-30) cc_final: 0.7854 (tm-30) REVERT: C 1005 GLN cc_start: 0.8451 (tp40) cc_final: 0.7994 (tp40) REVERT: C 1017 GLU cc_start: 0.8321 (tp30) cc_final: 0.7912 (tp30) REVERT: C 1048 HIS cc_start: 0.8252 (t-90) cc_final: 0.7931 (t-170) REVERT: C 1101 HIS cc_start: 0.8214 (OUTLIER) cc_final: 0.7981 (m170) REVERT: D 41 TYR cc_start: 0.6857 (t80) cc_final: 0.6516 (t80) REVERT: D 123 MET cc_start: 0.6015 (tmm) cc_final: 0.5365 (ptp) REVERT: D 208 GLU cc_start: 0.4924 (tt0) cc_final: 0.4614 (tt0) REVERT: D 306 ARG cc_start: 0.8691 (mmm160) cc_final: 0.8412 (mmm160) REVERT: D 313 LYS cc_start: 0.7541 (ptpp) cc_final: 0.7323 (ptpp) REVERT: D 325 GLN cc_start: 0.5364 (tm-30) cc_final: 0.5004 (tm-30) REVERT: D 357 ARG cc_start: 0.5888 (mtt180) cc_final: 0.5491 (mtt180) REVERT: D 447 VAL cc_start: 0.2558 (t) cc_final: 0.2271 (m) REVERT: D 455 MET cc_start: 0.6053 (ppp) cc_final: 0.5691 (ppp) REVERT: D 457 GLU cc_start: 0.4613 (mm-30) cc_final: 0.4178 (mm-30) REVERT: D 474 MET cc_start: 0.4482 (ttp) cc_final: 0.3796 (mpp) REVERT: F 22 GLU cc_start: 0.6616 (pp20) cc_final: 0.6145 (pp20) REVERT: F 72 PHE cc_start: 0.6595 (t80) cc_final: 0.6272 (t80) REVERT: F 117 ASN cc_start: 0.7648 (m-40) cc_final: 0.7390 (m-40) REVERT: F 119 ILE cc_start: 0.3690 (OUTLIER) cc_final: 0.3252 (tt) REVERT: F 123 MET cc_start: 0.7474 (mtt) cc_final: 0.6863 (mtt) REVERT: F 179 LEU cc_start: 0.6698 (mt) cc_final: 0.6481 (pp) REVERT: F 189 GLU cc_start: 0.6747 (pt0) cc_final: 0.6350 (pp20) REVERT: F 190 MET cc_start: 0.3793 (mmm) cc_final: 0.3096 (mmm) REVERT: F 215 TYR cc_start: 0.5218 (m-80) cc_final: 0.4580 (m-80) REVERT: F 313 LYS cc_start: 0.8247 (tmmt) cc_final: 0.7939 (tmmt) REVERT: F 323 MET cc_start: 0.7820 (mmt) cc_final: 0.7293 (mmt) REVERT: F 332 MET cc_start: 0.0323 (pmm) cc_final: -0.0562 (ttp) REVERT: F 358 ILE cc_start: 0.6920 (mt) cc_final: 0.6205 (mt) REVERT: F 376 MET cc_start: 0.7425 (OUTLIER) cc_final: 0.6799 (ttm) REVERT: F 378 HIS cc_start: 0.5381 (m170) cc_final: 0.4240 (m170) REVERT: F 398 GLU cc_start: 0.5850 (tp30) cc_final: 0.5529 (tp30) REVERT: F 417 HIS cc_start: 0.7726 (t-170) cc_final: 0.7373 (t-170) REVERT: F 587 TYR cc_start: 0.6289 (t80) cc_final: 0.5646 (t80) outliers start: 109 outliers final: 82 residues processed: 890 average time/residue: 0.2253 time to fit residues: 332.7713 Evaluate side-chains 898 residues out of total 4269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 801 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 949 GLN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 949 GLN Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 537 LYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 309 LYS Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 119 ILE Chi-restraints excluded: chain F residue 271 TRP Chi-restraints excluded: chain F residue 308 PHE Chi-restraints excluded: chain F residue 315 PHE Chi-restraints excluded: chain F residue 376 MET Chi-restraints excluded: chain F residue 409 SER Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain F residue 522 GLN Chi-restraints excluded: chain E residue 360 MET Chi-restraints excluded: chain E residue 581 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 214 optimal weight: 0.0980 chunk 275 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 143 optimal weight: 40.0000 chunk 126 optimal weight: 0.9980 chunk 58 optimal weight: 0.1980 chunk 35 optimal weight: 0.9990 chunk 163 optimal weight: 1.9990 chunk 310 optimal weight: 3.9990 chunk 468 optimal weight: 6.9990 chunk 314 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.228360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.167825 restraints weight = 67950.927| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 3.73 r_work: 0.3603 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.5982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 40176 Z= 0.166 Angle : 0.640 13.215 54735 Z= 0.322 Chirality : 0.046 0.695 6117 Planarity : 0.004 0.054 7005 Dihedral : 4.650 52.147 6037 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.10 % Favored : 95.88 % Rotamer: Outliers : 2.68 % Allowed : 22.46 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.12), residues: 4809 helix: 1.38 (0.13), residues: 1749 sheet: -0.80 (0.20), residues: 578 loop : -1.25 (0.12), residues: 2482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C1000 TYR 0.030 0.001 TYR C1110 PHE 0.031 0.002 PHE B 201 TRP 0.054 0.001 TRP D 461 HIS 0.008 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00372 (40104) covalent geometry : angle 0.62534 (54558) SS BOND : bond 0.00308 ( 30) SS BOND : angle 1.67370 ( 60) hydrogen bonds : bond 0.03666 ( 1623) hydrogen bonds : angle 4.61975 ( 4521) metal coordination : bond 0.00013 ( 3) link_NAG-ASN : bond 0.00638 ( 39) link_NAG-ASN : angle 2.78964 ( 117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13205.70 seconds wall clock time: 225 minutes 56.02 seconds (13556.02 seconds total)