Starting phenix.real_space_refine on Fri Mar 6 06:27:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k90_22737/03_2026/7k90_22737_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k90_22737/03_2026/7k90_22737.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7k90_22737/03_2026/7k90_22737_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k90_22737/03_2026/7k90_22737_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7k90_22737/03_2026/7k90_22737.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k90_22737/03_2026/7k90_22737.map" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 126 5.16 5 C 18327 2.51 5 N 4758 2.21 5 O 5652 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 199 residue(s): 0.03s 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: 28863 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1000, 7664 Classifications: {'peptide': 1000} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 54, 'TRANS': 945} Chain breaks: 9 Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASN:plan1': 3, 'ARG:plan': 4, 'GLN:plan1': 3, 'PHE:plan': 2, 'GLU:plan': 5, 'TYR:plan': 3, 'ASP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 105 Chain: "B" Number of atoms: 7664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1000, 7664 Classifications: {'peptide': 1000} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 54, 'TRANS': 945} Chain breaks: 9 Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASN:plan1': 3, 'ARG:plan': 4, 'GLN:plan1': 3, 'PHE:plan': 2, 'GLU:plan': 5, 'TYR:plan': 3, 'ASP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 105 Chain: "C" Number of atoms: 7664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1000, 7664 Classifications: {'peptide': 1000} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 54, 'TRANS': 945} Chain breaks: 9 Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASN:plan1': 3, 'ARG:plan': 4, 'GLN:plan1': 3, 'PHE:plan': 2, 'GLU:plan': 5, 'TYR:plan': 3, 'ASP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 105 Chain: "H" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1013 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 126} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1013 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 126} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "O" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1013 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 126} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 790 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "N" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 790 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "P" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 790 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} 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 Time building chain proxies: 7.02, per 1000 atoms: 0.24 Number of scatterers: 28863 At special positions: 0 Unit cell: (130.35, 130.35, 196.394, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 126 16.00 O 5652 8.00 N 4758 7.00 C 18327 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 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=1.86 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=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " 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=1.86 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=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.87 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 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 93 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 93 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 93 " 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 A 122 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 603 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A 717 " " NAG A1310 " - " ASN A1098 " " NAG A1311 " - " ASN A1134 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B 717 " " NAG B1310 " - " ASN B1098 " " NAG B1311 " - " ASN B1134 " " NAG C1301 " - " ASN C 122 " " NAG C1302 " - " ASN C 165 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 603 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 657 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C 717 " " NAG C1310 " - " ASN C1098 " " NAG C1311 " - " ASN C1134 " Time building additional restraints: 2.80 Conformation dependent library (CDL) restraints added in 1.5 seconds 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6882 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 64 sheets defined 20.0% alpha, 27.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.713A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 386 through 389 removed outlier: 3.731A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 386 through 389' Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.580A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 759 through 764 Processing helix chain 'A' and resid 765 through 770 Processing helix chain 'A' and resid 772 through 783 Processing helix chain 'A' and resid 811 through 815 removed outlier: 3.668A pdb=" N LYS A 814 " --> pdb=" O LYS A 811 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG A 815 " --> pdb=" O PRO A 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 811 through 815' Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 874 Processing helix chain 'A' and resid 875 through 884 removed outlier: 3.541A pdb=" N THR A 881 " --> pdb=" O LEU A 877 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.895A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 906 removed outlier: 3.973A pdb=" N ALA A 903 " --> pdb=" O PRO A 899 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 910 removed outlier: 3.884A pdb=" N GLY A 910 " --> pdb=" O ASN A 907 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 907 through 910' Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.664A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.699A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 938 " --> pdb=" O ILE A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.560A pdb=" N VAL A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 968 removed outlier: 3.713A pdb=" N SER A 968 " --> pdb=" O GLN A 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 965 through 968' Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.412A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER A1021 " --> pdb=" O GLU A1017 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU A1024 " --> pdb=" O ALA A1020 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR A1027 " --> pdb=" O ASN A1023 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER A1030 " --> pdb=" O ALA A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.712A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 386 through 389 removed outlier: 3.731A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 386 through 389' Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.580A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 759 through 764 Processing helix chain 'B' and resid 765 through 770 Processing helix chain 'B' and resid 772 through 783 Processing helix chain 'B' and resid 811 through 815 removed outlier: 3.668A pdb=" N LYS B 814 " --> pdb=" O LYS B 811 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG B 815 " --> pdb=" O PRO B 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 811 through 815' Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 874 Processing helix chain 'B' and resid 875 through 884 removed outlier: 3.541A pdb=" N THR B 881 " --> pdb=" O LEU B 877 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.895A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 906 removed outlier: 3.973A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 907 through 910 removed outlier: 3.884A pdb=" N GLY B 910 " --> pdb=" O ASN B 907 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 907 through 910' Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.664A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.699A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU B 938 " --> pdb=" O ILE B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 964 removed outlier: 3.560A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 968 removed outlier: 3.713A pdb=" N SER B 968 " --> pdb=" O GLN B 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 965 through 968' Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.412A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU B1024 " --> pdb=" O ALA B1020 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR B1027 " --> pdb=" O ASN B1023 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER B1030 " --> pdb=" O ALA B1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.712A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 386 through 389 removed outlier: 3.731A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 386 through 389' Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.581A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 759 through 764 Processing helix chain 'C' and resid 765 through 770 Processing helix chain 'C' and resid 772 through 783 Processing helix chain 'C' and resid 811 through 815 removed outlier: 3.668A pdb=" N LYS C 814 " --> pdb=" O LYS C 811 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG C 815 " --> pdb=" O PRO C 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 811 through 815' Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 874 Processing helix chain 'C' and resid 875 through 884 removed outlier: 3.541A pdb=" N THR C 881 " --> pdb=" O LEU C 877 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE C 882 " --> pdb=" O LEU C 878 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.895A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 906 removed outlier: 3.973A pdb=" N ALA C 903 " --> pdb=" O PRO C 899 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 907 through 910 removed outlier: 3.885A pdb=" N GLY C 910 " --> pdb=" O ASN C 907 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 907 through 910' Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.665A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.699A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU C 938 " --> pdb=" O ILE C 934 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 964 removed outlier: 3.560A pdb=" N VAL C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 965 through 968 removed outlier: 3.713A pdb=" N SER C 968 " --> pdb=" O GLN C 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 965 through 968' Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.412A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER C1021 " --> pdb=" O GLU C1017 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU C1024 " --> pdb=" O ALA C1020 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR C1027 " --> pdb=" O ASN C1023 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER C1030 " --> pdb=" O ALA C1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 100 through 100D removed outlier: 3.941A pdb=" N ASP H 100D" --> pdb=" O GLY H 100A" (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'M' and resid 100 through 100D removed outlier: 3.536A pdb=" N ASN M 100C" --> pdb=" O GLU M 100 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ASP M 100D" --> pdb=" O GLY M 100A" (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 100 through 100D' Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'O' and resid 100 through 100D removed outlier: 3.535A pdb=" N ASN O 100C" --> pdb=" O GLU O 100 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASP O 100D" --> pdb=" O GLY O 100A" (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 100 through 100D' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.524A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 51 removed outlier: 6.306A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.030A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.905A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR A 645 " --> pdb=" O GLY A 648 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 355 Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.862A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'A' and resid 538 through 543 removed outlier: 3.533A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.124A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 727 removed outlier: 6.985A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 727 removed outlier: 6.985A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.326A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AB6, first strand: chain 'A' and resid 1089 through 1090 Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.524A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 51 removed outlier: 6.306A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.030A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.906A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR B 612 " --> pdb=" O CYS B 649 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR B 645 " --> pdb=" O GLY B 648 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 327 through 328 Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 355 Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.863A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 538 through 539 removed outlier: 5.397A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.124A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 727 removed outlier: 6.985A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 727 removed outlier: 6.985A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.326A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AD5, first strand: chain 'B' and resid 1089 through 1090 Processing sheet with id=AD6, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD7, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.523A pdb=" N GLU C 96 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 48 through 51 removed outlier: 6.305A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.029A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.905A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR C 645 " --> pdb=" O GLY C 648 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 355 Processing sheet with id=AE4, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.864A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE6, first strand: chain 'C' and resid 538 through 543 removed outlier: 3.532A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.125A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 727 removed outlier: 6.985A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 727 removed outlier: 6.985A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.326A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AF3, first strand: chain 'C' and resid 1089 through 1090 Processing sheet with id=AF4, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF5, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AF6, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.078A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.818A pdb=" N CYS H 93 " --> pdb=" O TRP H 104 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N TRP H 104 " --> pdb=" O CYS H 93 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ARG H 95 " --> pdb=" O ASP H 102 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AF9, first strand: chain 'M' and resid 11 through 12 removed outlier: 6.079A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'M' and resid 11 through 12 removed outlier: 6.818A pdb=" N CYS M 93 " --> pdb=" O TRP M 104 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N TRP M 104 " --> pdb=" O CYS M 93 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ARG M 95 " --> pdb=" O ASP M 102 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AG3, first strand: chain 'O' and resid 11 through 12 removed outlier: 6.078A pdb=" N ARG O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N TRP O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'O' and resid 11 through 12 removed outlier: 6.818A pdb=" N CYS O 93 " --> pdb=" O TRP O 104 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N TRP O 104 " --> pdb=" O CYS O 93 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ARG O 95 " --> pdb=" O ASP O 102 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.139A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 18 through 24 Processing sheet with id=AG7, first strand: chain 'N' and resid 9 through 13 removed outlier: 6.137A pdb=" N GLN N 37 " --> pdb=" O LEU N 46 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N LEU N 46 " --> pdb=" O GLN N 37 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'N' and resid 18 through 24 Processing sheet with id=AG9, first strand: chain 'P' and resid 9 through 13 removed outlier: 6.138A pdb=" N GLN P 37 " --> pdb=" O LEU P 46 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N LEU P 46 " --> pdb=" O GLN P 37 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'P' and resid 18 through 24 964 hydrogen bonds defined for protein. 2535 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: 8.34 Time building geometry restraints manager: 3.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4868 1.32 - 1.45: 8681 1.45 - 1.58: 15791 1.58 - 1.71: 0 1.71 - 1.84: 159 Bond restraints: 29499 Sorted by residual: bond pdb=" C ARG C 457 " pdb=" O ARG C 457 " ideal model delta sigma weight residual 1.242 1.198 0.044 1.00e-02 1.00e+04 1.90e+01 bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.487 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.487 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.58e+01 bond pdb=" CA SER C 443 " pdb=" CB SER C 443 " ideal model delta sigma weight residual 1.530 1.486 0.044 1.24e-02 6.50e+03 1.23e+01 ... (remaining 29494 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 39281 2.26 - 4.53: 758 4.53 - 6.79: 104 6.79 - 9.06: 11 9.06 - 11.32: 7 Bond angle restraints: 40161 Sorted by residual: angle pdb=" CA TYR A 453 " pdb=" C TYR A 453 " pdb=" O TYR A 453 " ideal model delta sigma weight residual 120.32 112.18 8.14 1.02e+00 9.61e-01 6.37e+01 angle pdb=" CA PHE C 456 " pdb=" CB PHE C 456 " pdb=" CG PHE C 456 " ideal model delta sigma weight residual 113.80 121.41 -7.61 1.00e+00 1.00e+00 5.79e+01 angle pdb=" O SER A 443 " pdb=" C SER A 443 " pdb=" N LYS A 444 " ideal model delta sigma weight residual 121.79 128.27 -6.48 9.80e-01 1.04e+00 4.38e+01 angle pdb=" N PRO C 491 " pdb=" CA PRO C 491 " pdb=" C PRO C 491 " ideal model delta sigma weight residual 113.53 122.71 -9.18 1.39e+00 5.18e-01 4.36e+01 angle pdb=" N PRO B 491 " pdb=" CA PRO B 491 " pdb=" C PRO B 491 " ideal model delta sigma weight residual 113.53 122.47 -8.94 1.39e+00 5.18e-01 4.14e+01 ... (remaining 40156 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.97: 16829 23.97 - 47.94: 912 47.94 - 71.91: 133 71.91 - 95.88: 36 95.88 - 119.85: 9 Dihedral angle restraints: 17919 sinusoidal: 7185 harmonic: 10734 Sorted by residual: dihedral pdb=" C PHE C 456 " pdb=" N PHE C 456 " pdb=" CA PHE C 456 " pdb=" CB PHE C 456 " ideal model delta harmonic sigma weight residual -122.60 -145.82 23.22 0 2.50e+00 1.60e-01 8.63e+01 dihedral pdb=" N PHE C 456 " pdb=" C PHE C 456 " pdb=" CA PHE C 456 " pdb=" CB PHE C 456 " ideal model delta harmonic sigma weight residual 122.80 145.81 -23.01 0 2.50e+00 1.60e-01 8.47e+01 dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual -86.00 -5.09 -80.91 1 1.00e+01 1.00e-02 8.08e+01 ... (remaining 17916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.183: 4620 0.183 - 0.366: 34 0.366 - 0.550: 3 0.550 - 0.733: 1 0.733 - 0.916: 1 Chirality restraints: 4659 Sorted by residual: chirality pdb=" CA PHE C 456 " pdb=" N PHE C 456 " pdb=" C PHE C 456 " pdb=" CB PHE C 456 " both_signs ideal model delta sigma weight residual False 2.51 1.59 0.92 2.00e-01 2.50e+01 2.10e+01 chirality pdb=" CA TYR A 453 " pdb=" N TYR A 453 " pdb=" C TYR A 453 " pdb=" CB TYR A 453 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.11e+00 chirality pdb=" CA TYR C 453 " pdb=" N TYR C 453 " pdb=" C TYR C 453 " pdb=" CB TYR C 453 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.02e+00 ... (remaining 4656 not shown) Planarity restraints: 5190 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 489 " 0.019 2.00e-02 2.50e+03 3.82e-02 1.46e+01 pdb=" C TYR B 489 " -0.066 2.00e-02 2.50e+03 pdb=" O TYR B 489 " 0.025 2.00e-02 2.50e+03 pdb=" N PHE B 490 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 489 " 0.019 2.00e-02 2.50e+03 3.76e-02 1.41e+01 pdb=" C TYR C 489 " -0.065 2.00e-02 2.50e+03 pdb=" O TYR C 489 " 0.025 2.00e-02 2.50e+03 pdb=" N PHE C 490 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 451 " -0.018 2.00e-02 2.50e+03 3.72e-02 1.39e+01 pdb=" C TYR C 451 " 0.064 2.00e-02 2.50e+03 pdb=" O TYR C 451 " -0.025 2.00e-02 2.50e+03 pdb=" N LEU C 452 " -0.022 2.00e-02 2.50e+03 ... (remaining 5187 not shown) Histogram of nonbonded interaction distances: 1.17 - 1.92: 3 1.92 - 2.66: 638 2.66 - 3.41: 38194 3.41 - 4.15: 68316 4.15 - 4.90: 125359 Nonbonded interactions: 232510 Sorted by model distance: nonbonded pdb=" OE2 GLU H 100 " pdb=" N TYR H 100I" model vdw 1.169 3.120 nonbonded pdb=" OE2 GLU H 100 " pdb=" CA TYR H 100I" model vdw 1.368 3.470 nonbonded pdb=" NH1 ARG B 457 " pdb=" O SER B 459 " model vdw 1.855 3.120 nonbonded pdb=" O ASN C 540 " pdb=" OD1 ASN C 540 " model vdw 1.949 3.040 nonbonded pdb=" NE2 GLN B 493 " pdb=" OD1 ASN H 31 " model vdw 1.966 3.120 ... (remaining 232505 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 'H' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 31.450 Find NCS groups from input model: 0.580 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: 0.000 Load rotamer database and sin/cos tables:1.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 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 : 0.007 0.842 29574 Z= 0.361 Angle : 0.891 67.634 40344 Z= 0.498 Chirality : 0.056 0.916 4659 Planarity : 0.004 0.038 5157 Dihedral : 14.743 119.851 10911 Min Nonbonded Distance : 1.169 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.03 % Favored : 94.64 % Rotamer: Outliers : 1.22 % Allowed : 11.73 % Favored : 87.05 % Cbeta Deviations : 0.32 % 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: -4.00 (0.12), residues: 3639 helix: -4.08 (0.12), residues: 690 sheet: -2.08 (0.15), residues: 870 loop : -2.43 (0.12), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 100M TYR 0.050 0.001 TYR B 453 PHE 0.038 0.001 PHE A 86 TRP 0.010 0.001 TRP M 104 HIS 0.008 0.001 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00451 (29499) covalent geometry : angle 0.72781 (40161) SS BOND : bond 0.13512 ( 42) SS BOND : angle 11.01108 ( 84) hydrogen bonds : bond 0.27247 ( 934) hydrogen bonds : angle 11.47549 ( 2535) link_NAG-ASN : bond 0.00531 ( 33) link_NAG-ASN : angle 2.41427 ( 99) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 521 time to evaluate : 1.040 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: A 198 ASP cc_start: 0.6562 (m-30) cc_final: 0.6330 (m-30) REVERT: A 821 LEU cc_start: 0.7281 (tp) cc_final: 0.7080 (tp) REVERT: B 237 ARG cc_start: 0.7646 (mtm180) cc_final: 0.7402 (mtm-85) REVERT: B 239 GLN cc_start: 0.6570 (tt0) cc_final: 0.5998 (tm-30) REVERT: B 319 ARG cc_start: 0.7099 (ttm170) cc_final: 0.6617 (ttp80) REVERT: B 456 PHE cc_start: 0.7864 (OUTLIER) cc_final: 0.7627 (p90) REVERT: B 474 GLN cc_start: 0.6277 (pp30) cc_final: 0.5942 (pt0) REVERT: B 709 ASN cc_start: 0.7204 (p0) cc_final: 0.6959 (p0) REVERT: C 34 ARG cc_start: 0.6961 (mtp85) cc_final: 0.6332 (mtm180) REVERT: C 168 PHE cc_start: 0.8685 (t80) cc_final: 0.8330 (t80) REVERT: C 450 ASN cc_start: 0.7708 (m-40) cc_final: 0.7431 (m-40) REVERT: C 508 TYR cc_start: 0.7899 (m-80) cc_final: 0.7618 (m-80) REVERT: C 697 MET cc_start: 0.8504 (ptm) cc_final: 0.8281 (ptp) REVERT: C 902 MET cc_start: 0.8265 (mmt) cc_final: 0.8034 (tpt) REVERT: C 904 TYR cc_start: 0.5877 (t80) cc_final: 0.5610 (t80) REVERT: C 1038 LYS cc_start: 0.8028 (mmmt) cc_final: 0.7680 (mmtm) REVERT: C 1118 ASP cc_start: 0.7043 (p0) cc_final: 0.6619 (m-30) REVERT: O 2 VAL cc_start: 0.7672 (t) cc_final: 0.6957 (m) REVERT: O 56 SER cc_start: 0.7152 (m) cc_final: 0.6754 (m) REVERT: O 96 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6733 (tp30) REVERT: P 35 TRP cc_start: 0.6574 (m100) cc_final: 0.6285 (m100) REVERT: P 87 TYR cc_start: 0.5634 (m-80) cc_final: 0.5274 (m-80) outliers start: 38 outliers final: 15 residues processed: 554 average time/residue: 0.2001 time to fit residues: 176.6578 Evaluate side-chains 358 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 341 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain H residue 100 TRP Chi-restraints excluded: chain O residue 96 GLU Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain P residue 48 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 197 optimal weight: 0.4980 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 1.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 280 ASN A 334 ASN A 493 GLN A 607 GLN A 755 GLN A 762 GLN A 853 GLN A 901 GLN A 913 GLN A 965 GLN A1106 GLN A1135 ASN B 52 GLN B 196 ASN B 207 HIS B 409 GLN B 450 ASN B 493 GLN B 580 GLN B 607 GLN B 613 GLN B 755 GLN B 762 GLN B 774 GLN B 901 GLN B 913 GLN B 965 GLN B1101 HIS B1106 GLN C 52 GLN C 196 ASN C 580 GLN C 607 GLN C 613 GLN C 655 HIS C 755 GLN C 762 GLN C 779 GLN C 787 GLN C 853 GLN C 901 GLN C 913 GLN C 919 ASN C 965 GLN C1101 HIS C1106 GLN H 39 GLN M 31 ASN M 39 GLN O 39 GLN ** O 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN L 39 HIS N 17 GLN N 38 GLN N 39 HIS P 17 GLN P 38 GLN P 39 HIS Total number of N/Q/H flips: 59 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.186497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.142331 restraints weight = 35162.612| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 3.08 r_work: 0.3353 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 29574 Z= 0.235 Angle : 0.709 10.379 40344 Z= 0.364 Chirality : 0.051 0.380 4659 Planarity : 0.005 0.059 5157 Dihedral : 8.203 98.054 4695 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.96 % Favored : 93.98 % Rotamer: Outliers : 3.76 % Allowed : 16.39 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.04 (0.12), residues: 3639 helix: -2.92 (0.16), residues: 654 sheet: -1.41 (0.17), residues: 819 loop : -2.00 (0.12), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 273 TYR 0.020 0.002 TYR B 904 PHE 0.028 0.002 PHE B 541 TRP 0.015 0.002 TRP A 886 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00547 (29499) covalent geometry : angle 0.69445 (40161) SS BOND : bond 0.01191 ( 42) SS BOND : angle 1.57801 ( 84) hydrogen bonds : bond 0.04032 ( 934) hydrogen bonds : angle 6.89368 ( 2535) link_NAG-ASN : bond 0.00633 ( 33) link_NAG-ASN : angle 2.70544 ( 99) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 378 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 ASP cc_start: 0.7931 (m-30) cc_final: 0.7543 (m-30) REVERT: A 452 LEU cc_start: 0.8264 (mt) cc_final: 0.8007 (mt) REVERT: A 456 PHE cc_start: 0.7946 (OUTLIER) cc_final: 0.7345 (p90) REVERT: A 492 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7887 (pp) REVERT: A 666 ILE cc_start: 0.8737 (mt) cc_final: 0.8514 (mt) REVERT: A 726 ILE cc_start: 0.9010 (OUTLIER) cc_final: 0.8792 (mt) REVERT: A 779 GLN cc_start: 0.7965 (tt0) cc_final: 0.7319 (mt0) REVERT: A 859 THR cc_start: 0.8821 (m) cc_final: 0.8477 (p) REVERT: A 895 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7607 (pt0) REVERT: A 904 TYR cc_start: 0.7040 (t80) cc_final: 0.6759 (t80) REVERT: A 1010 GLN cc_start: 0.8148 (mt0) cc_final: 0.7896 (mm-40) REVERT: A 1038 LYS cc_start: 0.8758 (mmmt) cc_final: 0.8361 (mptt) REVERT: B 34 ARG cc_start: 0.7667 (mtp85) cc_final: 0.5869 (mtm180) REVERT: B 120 VAL cc_start: 0.7862 (t) cc_final: 0.7516 (m) REVERT: B 316 SER cc_start: 0.8794 (t) cc_final: 0.8400 (p) REVERT: B 319 ARG cc_start: 0.8237 (ttm170) cc_final: 0.7492 (mtp85) REVERT: B 357 ARG cc_start: 0.7729 (mtp-110) cc_final: 0.7401 (mtp85) REVERT: B 474 GLN cc_start: 0.6541 (pp30) cc_final: 0.6185 (pt0) REVERT: B 764 ASN cc_start: 0.8780 (m-40) cc_final: 0.8532 (m-40) REVERT: B 779 GLN cc_start: 0.8045 (tt0) cc_final: 0.7261 (mt0) REVERT: B 895 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.7906 (pt0) REVERT: B 904 TYR cc_start: 0.7106 (t80) cc_final: 0.6856 (t80) REVERT: B 1010 GLN cc_start: 0.8078 (mt0) cc_final: 0.7796 (mm-40) REVERT: C 34 ARG cc_start: 0.7435 (mtp85) cc_final: 0.6278 (mtm180) REVERT: C 105 ILE cc_start: 0.7224 (OUTLIER) cc_final: 0.6887 (mt) REVERT: C 280 ASN cc_start: 0.7849 (t0) cc_final: 0.7441 (t0) REVERT: C 421 TYR cc_start: 0.8634 (m-10) cc_final: 0.8360 (m-10) REVERT: C 450 ASN cc_start: 0.7709 (m-40) cc_final: 0.7504 (m-40) REVERT: C 452 LEU cc_start: 0.8230 (mt) cc_final: 0.8018 (mt) REVERT: C 456 PHE cc_start: 0.7087 (OUTLIER) cc_final: 0.6682 (p90) REVERT: C 764 ASN cc_start: 0.8722 (m-40) cc_final: 0.8503 (m-40) REVERT: C 776 LYS cc_start: 0.8797 (tttp) cc_final: 0.8548 (ttmt) REVERT: C 780 GLU cc_start: 0.8352 (mt-10) cc_final: 0.7720 (mm-30) REVERT: C 807 PRO cc_start: 0.8576 (Cg_exo) cc_final: 0.8357 (Cg_endo) REVERT: C 990 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7466 (mt-10) REVERT: C 1010 GLN cc_start: 0.8068 (mt0) cc_final: 0.7864 (mm-40) REVERT: C 1038 LYS cc_start: 0.8764 (mmmt) cc_final: 0.8229 (mmtm) REVERT: H 22 CYS cc_start: 0.7849 (t) cc_final: 0.7359 (t) REVERT: H 92 TYR cc_start: 0.5891 (m-80) cc_final: 0.5650 (m-80) REVERT: H 111 THR cc_start: 0.6413 (OUTLIER) cc_final: 0.6168 (p) REVERT: M 52 TYR cc_start: 0.7448 (m-10) cc_final: 0.7065 (m-80) REVERT: M 92 TYR cc_start: 0.6538 (m-80) cc_final: 0.6297 (m-10) REVERT: M 103 TYR cc_start: 0.7270 (m-80) cc_final: 0.5041 (m-10) REVERT: O 102 ASP cc_start: 0.6912 (m-30) cc_final: 0.6620 (m-30) REVERT: L 87 TYR cc_start: 0.5278 (m-80) cc_final: 0.4957 (m-80) REVERT: N 27 ASP cc_start: 0.4438 (OUTLIER) cc_final: 0.4073 (p0) REVERT: N 35 TRP cc_start: 0.5690 (m100) cc_final: 0.5205 (m100) REVERT: N 87 TYR cc_start: 0.5692 (m-80) cc_final: 0.5459 (m-80) REVERT: P 27 ASP cc_start: 0.4577 (OUTLIER) cc_final: 0.4296 (p0) outliers start: 117 outliers final: 56 residues processed: 460 average time/residue: 0.1923 time to fit residues: 143.2805 Evaluate side-chains 371 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 305 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 100 TRP Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 99 VAL Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 27 ASP Chi-restraints excluded: chain P residue 27 ASP Chi-restraints excluded: chain P residue 52 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 41 optimal weight: 0.0030 chunk 302 optimal weight: 0.8980 chunk 48 optimal weight: 9.9990 chunk 333 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 325 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 135 optimal weight: 7.9990 overall best weight: 1.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 280 ASN A 613 GLN A 764 ASN A 856 ASN B 121 ASN B 196 ASN B 207 HIS B 334 ASN B 856 ASN C 207 HIS C 334 ASN C 779 GLN C 949 GLN M 31 ASN M 39 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.184712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.127970 restraints weight = 34829.250| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.49 r_work: 0.3325 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 29574 Z= 0.228 Angle : 0.676 10.356 40344 Z= 0.344 Chirality : 0.050 0.361 4659 Planarity : 0.005 0.050 5157 Dihedral : 7.438 94.265 4668 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.63 % Favored : 94.28 % Rotamer: Outliers : 4.34 % Allowed : 17.45 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.66 (0.13), residues: 3639 helix: -2.27 (0.18), residues: 660 sheet: -1.22 (0.16), residues: 852 loop : -1.85 (0.12), residues: 2127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 96 TYR 0.020 0.002 TYR B 453 PHE 0.026 0.002 PHE B1121 TRP 0.014 0.001 TRP C 886 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00543 (29499) covalent geometry : angle 0.66172 (40161) SS BOND : bond 0.00445 ( 42) SS BOND : angle 1.39081 ( 84) hydrogen bonds : bond 0.03918 ( 934) hydrogen bonds : angle 6.44397 ( 2535) link_NAG-ASN : bond 0.00560 ( 33) link_NAG-ASN : angle 2.63670 ( 99) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 328 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ILE cc_start: 0.7408 (OUTLIER) cc_final: 0.7022 (mt) REVERT: A 287 ASP cc_start: 0.7996 (m-30) cc_final: 0.7605 (m-30) REVERT: A 456 PHE cc_start: 0.8050 (OUTLIER) cc_final: 0.7341 (p90) REVERT: A 574 ASP cc_start: 0.7583 (t0) cc_final: 0.7226 (t0) REVERT: A 584 ILE cc_start: 0.7616 (pt) cc_final: 0.7340 (pt) REVERT: A 895 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.7716 (pt0) REVERT: A 904 TYR cc_start: 0.7091 (t80) cc_final: 0.6854 (t80) REVERT: B 278 LYS cc_start: 0.8073 (tttt) cc_final: 0.7761 (tttm) REVERT: B 316 SER cc_start: 0.8857 (t) cc_final: 0.8542 (p) REVERT: B 319 ARG cc_start: 0.8192 (ttm170) cc_final: 0.7363 (mtp85) REVERT: B 474 GLN cc_start: 0.6743 (pp30) cc_final: 0.6531 (pt0) REVERT: B 816 SER cc_start: 0.8775 (m) cc_final: 0.8533 (m) REVERT: B 895 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.7876 (pt0) REVERT: B 904 TYR cc_start: 0.7376 (t80) cc_final: 0.7033 (t80) REVERT: B 1113 GLN cc_start: 0.8216 (mt0) cc_final: 0.7943 (mt0) REVERT: B 1135 ASN cc_start: 0.7995 (t0) cc_final: 0.7729 (t0) REVERT: C 202 LYS cc_start: 0.8169 (mttt) cc_final: 0.7013 (mtpt) REVERT: C 280 ASN cc_start: 0.8051 (t0) cc_final: 0.7644 (t0) REVERT: C 423 TYR cc_start: 0.8811 (t80) cc_final: 0.8472 (t80) REVERT: C 450 ASN cc_start: 0.7923 (m-40) cc_final: 0.7670 (m-40) REVERT: C 456 PHE cc_start: 0.7282 (OUTLIER) cc_final: 0.6766 (p90) REVERT: C 574 ASP cc_start: 0.7660 (t0) cc_final: 0.7455 (t0) REVERT: C 764 ASN cc_start: 0.8768 (m-40) cc_final: 0.8431 (m-40) REVERT: C 776 LYS cc_start: 0.8872 (tttp) cc_final: 0.8611 (ttmt) REVERT: C 780 GLU cc_start: 0.8385 (mt-10) cc_final: 0.7793 (mm-30) REVERT: C 796 ASP cc_start: 0.7385 (p0) cc_final: 0.7134 (p0) REVERT: C 1038 LYS cc_start: 0.8718 (mmmt) cc_final: 0.8362 (mptt) REVERT: H 22 CYS cc_start: 0.8131 (t) cc_final: 0.7559 (t) REVERT: H 56 SER cc_start: 0.6799 (OUTLIER) cc_final: 0.6481 (m) REVERT: H 111 THR cc_start: 0.6710 (OUTLIER) cc_final: 0.6509 (p) REVERT: M 13 GLN cc_start: 0.7275 (OUTLIER) cc_final: 0.6944 (mp10) REVERT: M 52 TYR cc_start: 0.7444 (m-10) cc_final: 0.7212 (m-80) REVERT: M 92 TYR cc_start: 0.6576 (m-80) cc_final: 0.6372 (m-10) REVERT: O 56 SER cc_start: 0.7001 (OUTLIER) cc_final: 0.6658 (m) REVERT: L 87 TYR cc_start: 0.5147 (m-80) cc_final: 0.4944 (m-80) REVERT: N 27 ASP cc_start: 0.4889 (OUTLIER) cc_final: 0.4420 (p0) REVERT: N 35 TRP cc_start: 0.5959 (m100) cc_final: 0.5592 (m100) REVERT: N 87 TYR cc_start: 0.5722 (m-80) cc_final: 0.5347 (m-80) REVERT: P 88 CYS cc_start: 0.6015 (t) cc_final: 0.5783 (p) outliers start: 135 outliers final: 79 residues processed: 434 average time/residue: 0.1824 time to fit residues: 129.5219 Evaluate side-chains 369 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 280 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 983 ARG Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 100 TRP Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 13 GLN Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 11 LEU Chi-restraints excluded: chain O residue 56 SER Chi-restraints excluded: chain O residue 61 ASP Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain O residue 99 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 27 ASP Chi-restraints excluded: chain N residue 70 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 73 optimal weight: 0.8980 chunk 314 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 143 optimal weight: 0.7980 chunk 353 optimal weight: 20.0000 chunk 116 optimal weight: 9.9990 chunk 145 optimal weight: 0.9990 chunk 294 optimal weight: 1.9990 chunk 239 optimal weight: 6.9990 chunk 128 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 280 ASN A 655 HIS B 121 ASN B 196 ASN B 207 HIS B 764 ASN B 955 ASN C 207 HIS C 437 ASN H 39 GLN ** O 82AASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.187603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.143594 restraints weight = 34717.375| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.86 r_work: 0.3353 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29574 Z= 0.135 Angle : 0.606 10.769 40344 Z= 0.305 Chirality : 0.047 0.338 4659 Planarity : 0.004 0.050 5157 Dihedral : 6.774 88.468 4664 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.56 % Favored : 95.36 % Rotamer: Outliers : 3.66 % Allowed : 18.55 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.24 (0.13), residues: 3639 helix: -1.65 (0.19), residues: 672 sheet: -1.04 (0.16), residues: 927 loop : -1.63 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 273 TYR 0.019 0.001 TYR O 59 PHE 0.020 0.001 PHE C 456 TRP 0.010 0.001 TRP B 886 HIS 0.003 0.001 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00309 (29499) covalent geometry : angle 0.59120 (40161) SS BOND : bond 0.00282 ( 42) SS BOND : angle 1.43616 ( 84) hydrogen bonds : bond 0.03309 ( 934) hydrogen bonds : angle 5.84039 ( 2535) link_NAG-ASN : bond 0.00484 ( 33) link_NAG-ASN : angle 2.48941 ( 99) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 324 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 ASN cc_start: 0.7867 (t0) cc_final: 0.7599 (t0) REVERT: A 287 ASP cc_start: 0.7826 (m-30) cc_final: 0.7490 (m-30) REVERT: A 452 LEU cc_start: 0.8325 (mt) cc_final: 0.8120 (mm) REVERT: A 584 ILE cc_start: 0.7539 (pt) cc_final: 0.7251 (pt) REVERT: A 904 TYR cc_start: 0.7149 (t80) cc_final: 0.6895 (t80) REVERT: B 104 TRP cc_start: 0.7949 (m-90) cc_final: 0.7556 (m-90) REVERT: B 226 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7632 (mp) REVERT: B 278 LYS cc_start: 0.8148 (tttt) cc_final: 0.7923 (tttm) REVERT: B 316 SER cc_start: 0.8809 (t) cc_final: 0.8507 (p) REVERT: B 319 ARG cc_start: 0.8167 (ttm170) cc_final: 0.7343 (mtp85) REVERT: B 357 ARG cc_start: 0.7769 (mtp85) cc_final: 0.7540 (mtp85) REVERT: B 474 GLN cc_start: 0.6586 (pp30) cc_final: 0.6373 (pt0) REVERT: B 780 GLU cc_start: 0.8446 (mt-10) cc_final: 0.7790 (mm-30) REVERT: B 816 SER cc_start: 0.8678 (m) cc_final: 0.8470 (m) REVERT: B 904 TYR cc_start: 0.7373 (t80) cc_final: 0.6996 (t80) REVERT: B 1113 GLN cc_start: 0.8194 (mt0) cc_final: 0.7921 (mt0) REVERT: B 1135 ASN cc_start: 0.8009 (t0) cc_final: 0.7704 (t0) REVERT: C 202 LYS cc_start: 0.8180 (mttt) cc_final: 0.7027 (mtpt) REVERT: C 280 ASN cc_start: 0.7988 (t0) cc_final: 0.7608 (t0) REVERT: C 456 PHE cc_start: 0.7396 (OUTLIER) cc_final: 0.6787 (p90) REVERT: C 574 ASP cc_start: 0.7706 (t0) cc_final: 0.7504 (t0) REVERT: C 764 ASN cc_start: 0.8779 (m-40) cc_final: 0.8491 (m-40) REVERT: C 776 LYS cc_start: 0.8850 (tttp) cc_final: 0.8549 (ttmt) REVERT: C 780 GLU cc_start: 0.8322 (mt-10) cc_final: 0.7725 (mm-30) REVERT: C 796 ASP cc_start: 0.7342 (p0) cc_final: 0.7111 (p0) REVERT: C 878 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8101 (mt) REVERT: C 1038 LYS cc_start: 0.8669 (mmmt) cc_final: 0.8220 (mmtm) REVERT: C 1135 ASN cc_start: 0.7508 (t0) cc_final: 0.7227 (t0) REVERT: H 22 CYS cc_start: 0.8082 (t) cc_final: 0.7541 (t) REVERT: H 56 SER cc_start: 0.7013 (OUTLIER) cc_final: 0.6072 (p) REVERT: H 111 THR cc_start: 0.6751 (OUTLIER) cc_final: 0.6546 (p) REVERT: M 13 GLN cc_start: 0.7255 (OUTLIER) cc_final: 0.6941 (mp10) REVERT: M 28 THR cc_start: 0.8215 (OUTLIER) cc_final: 0.7879 (m) REVERT: M 52 TYR cc_start: 0.7420 (m-10) cc_final: 0.7133 (m-80) REVERT: M 92 TYR cc_start: 0.6511 (m-80) cc_final: 0.6285 (m-10) REVERT: O 56 SER cc_start: 0.7131 (OUTLIER) cc_final: 0.6697 (m) REVERT: N 27 ASP cc_start: 0.5016 (OUTLIER) cc_final: 0.4597 (p0) REVERT: N 35 TRP cc_start: 0.6071 (m100) cc_final: 0.5780 (m100) REVERT: N 87 TYR cc_start: 0.5735 (m-80) cc_final: 0.5385 (m-80) outliers start: 114 outliers final: 63 residues processed: 417 average time/residue: 0.1877 time to fit residues: 127.3531 Evaluate side-chains 359 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 287 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 100 TRP Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain M residue 13 GLN Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain M residue 93 CYS Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 11 LEU Chi-restraints excluded: chain O residue 56 SER Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain N residue 27 ASP Chi-restraints excluded: chain P residue 106 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 341 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 326 optimal weight: 5.9990 chunk 121 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 246 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 chunk 139 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 chunk 309 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 ASN A 856 ASN B 196 ASN B 207 HIS B 544 ASN B 655 HIS B1142 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN C 779 GLN C1142 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.183033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.125697 restraints weight = 35066.222| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.52 r_work: 0.3280 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 29574 Z= 0.320 Angle : 0.758 11.012 40344 Z= 0.385 Chirality : 0.053 0.376 4659 Planarity : 0.005 0.055 5157 Dihedral : 7.315 83.466 4664 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.84 % Favored : 93.05 % Rotamer: Outliers : 4.98 % Allowed : 18.58 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.36 (0.13), residues: 3639 helix: -1.92 (0.18), residues: 660 sheet: -0.98 (0.17), residues: 867 loop : -1.72 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 100M TYR 0.024 0.002 TYR B 453 PHE 0.030 0.002 PHE B1121 TRP 0.018 0.002 TRP C 886 HIS 0.005 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00772 (29499) covalent geometry : angle 0.74017 (40161) SS BOND : bond 0.00511 ( 42) SS BOND : angle 1.84182 ( 84) hydrogen bonds : bond 0.03911 ( 934) hydrogen bonds : angle 6.30294 ( 2535) link_NAG-ASN : bond 0.00621 ( 33) link_NAG-ASN : angle 2.96569 ( 99) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 281 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 PHE cc_start: 0.8637 (t80) cc_final: 0.8411 (t80) REVERT: A 280 ASN cc_start: 0.7982 (t0) cc_final: 0.7739 (t0) REVERT: A 287 ASP cc_start: 0.7979 (m-30) cc_final: 0.7632 (m-30) REVERT: A 584 ILE cc_start: 0.7675 (pt) cc_final: 0.7430 (pt) REVERT: A 585 LEU cc_start: 0.7186 (OUTLIER) cc_final: 0.6915 (mt) REVERT: A 895 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.7710 (pt0) REVERT: A 904 TYR cc_start: 0.7294 (t80) cc_final: 0.7050 (t80) REVERT: B 105 ILE cc_start: 0.7487 (OUTLIER) cc_final: 0.7110 (mt) REVERT: B 287 ASP cc_start: 0.7821 (m-30) cc_final: 0.7522 (m-30) REVERT: B 316 SER cc_start: 0.8887 (t) cc_final: 0.8607 (p) REVERT: B 319 ARG cc_start: 0.8405 (ttm170) cc_final: 0.7565 (mtp85) REVERT: B 357 ARG cc_start: 0.8067 (mtp85) cc_final: 0.7236 (mtp85) REVERT: B 456 PHE cc_start: 0.8170 (OUTLIER) cc_final: 0.7815 (p90) REVERT: B 779 GLN cc_start: 0.8146 (tt0) cc_final: 0.7839 (tt0) REVERT: B 816 SER cc_start: 0.8896 (m) cc_final: 0.8670 (m) REVERT: B 895 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7800 (pt0) REVERT: B 1113 GLN cc_start: 0.8230 (mt0) cc_final: 0.8004 (mt0) REVERT: C 202 LYS cc_start: 0.8168 (mttt) cc_final: 0.6994 (mtpt) REVERT: C 280 ASN cc_start: 0.8144 (t0) cc_final: 0.7774 (t0) REVERT: C 440 ASN cc_start: 0.8134 (t0) cc_final: 0.7765 (m-40) REVERT: C 456 PHE cc_start: 0.7498 (OUTLIER) cc_final: 0.6664 (p90) REVERT: C 493 GLN cc_start: 0.8894 (tp40) cc_final: 0.8623 (tp40) REVERT: C 574 ASP cc_start: 0.7649 (t0) cc_final: 0.7428 (t0) REVERT: C 584 ILE cc_start: 0.7729 (pt) cc_final: 0.7409 (pt) REVERT: C 776 LYS cc_start: 0.8876 (tttp) cc_final: 0.8621 (ttmt) REVERT: C 780 GLU cc_start: 0.8446 (mt-10) cc_final: 0.7786 (mm-30) REVERT: C 796 ASP cc_start: 0.7464 (p0) cc_final: 0.7178 (p0) REVERT: C 878 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8216 (mt) REVERT: C 895 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.8201 (pt0) REVERT: C 1038 LYS cc_start: 0.8712 (mmmt) cc_final: 0.8391 (mptt) REVERT: C 1127 ASP cc_start: 0.7586 (t0) cc_final: 0.7380 (t0) REVERT: H 22 CYS cc_start: 0.8209 (t) cc_final: 0.7642 (t) REVERT: H 52 TYR cc_start: 0.7395 (m-10) cc_final: 0.7135 (m-80) REVERT: H 56 SER cc_start: 0.7439 (OUTLIER) cc_final: 0.7162 (m) REVERT: M 13 GLN cc_start: 0.7336 (OUTLIER) cc_final: 0.6864 (mp10) REVERT: M 28 THR cc_start: 0.8319 (OUTLIER) cc_final: 0.7987 (m) REVERT: M 100 TYR cc_start: 0.7960 (m-80) cc_final: 0.7197 (m-80) REVERT: O 52 TYR cc_start: 0.7492 (m-10) cc_final: 0.7024 (m-80) REVERT: O 56 SER cc_start: 0.7269 (OUTLIER) cc_final: 0.7022 (m) REVERT: N 27 ASP cc_start: 0.5141 (OUTLIER) cc_final: 0.4813 (p0) REVERT: N 35 TRP cc_start: 0.6177 (m100) cc_final: 0.5945 (m100) REVERT: N 87 TYR cc_start: 0.5861 (m-80) cc_final: 0.5315 (m-80) outliers start: 155 outliers final: 101 residues processed: 410 average time/residue: 0.1840 time to fit residues: 124.1452 Evaluate side-chains 381 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 267 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 100 TRP Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 13 GLN Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 11 LEU Chi-restraints excluded: chain O residue 56 SER Chi-restraints excluded: chain O residue 61 ASP Chi-restraints excluded: chain O residue 82 LEU Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 27 ASP Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain P residue 26 THR Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 88 CYS Chi-restraints excluded: chain P residue 106 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 331 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 300 optimal weight: 9.9990 chunk 110 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 274 optimal weight: 0.7980 chunk 113 optimal weight: 0.8980 chunk 118 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 chunk 346 optimal weight: 8.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN B 207 HIS ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 334 ASN O 39 GLN ** P 17 GLN ** 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 = 0.4116 r_free = 0.4116 target = 0.183967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.131241 restraints weight = 34790.577| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.48 r_work: 0.3305 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.4710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 29574 Z= 0.206 Angle : 0.663 11.226 40344 Z= 0.335 Chirality : 0.049 0.361 4659 Planarity : 0.004 0.054 5157 Dihedral : 6.687 75.712 4664 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.55 % Favored : 94.34 % Rotamer: Outliers : 4.40 % Allowed : 19.61 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.22 (0.13), residues: 3639 helix: -1.77 (0.19), residues: 669 sheet: -0.90 (0.16), residues: 879 loop : -1.62 (0.13), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 273 TYR 0.019 0.002 TYR B 453 PHE 0.025 0.002 PHE B1121 TRP 0.014 0.001 TRP B 886 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00490 (29499) covalent geometry : angle 0.64590 (40161) SS BOND : bond 0.00364 ( 42) SS BOND : angle 1.48204 ( 84) hydrogen bonds : bond 0.03457 ( 934) hydrogen bonds : angle 5.96029 ( 2535) link_NAG-ASN : bond 0.00504 ( 33) link_NAG-ASN : angle 2.85375 ( 99) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 282 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 ASN cc_start: 0.7956 (t0) cc_final: 0.7713 (t0) REVERT: A 287 ASP cc_start: 0.7940 (m-30) cc_final: 0.7620 (m-30) REVERT: A 321 GLN cc_start: 0.8438 (mm110) cc_final: 0.8131 (mm-40) REVERT: A 452 LEU cc_start: 0.8512 (mt) cc_final: 0.8303 (mt) REVERT: A 584 ILE cc_start: 0.7587 (OUTLIER) cc_final: 0.7345 (pt) REVERT: A 895 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7760 (pt0) REVERT: A 904 TYR cc_start: 0.7252 (t80) cc_final: 0.6989 (t80) REVERT: B 287 ASP cc_start: 0.7772 (m-30) cc_final: 0.7467 (m-30) REVERT: B 316 SER cc_start: 0.8894 (OUTLIER) cc_final: 0.8621 (p) REVERT: B 319 ARG cc_start: 0.8395 (ttm170) cc_final: 0.7583 (mtp85) REVERT: B 357 ARG cc_start: 0.7935 (mtp85) cc_final: 0.7699 (mtp85) REVERT: B 474 GLN cc_start: 0.6733 (pp30) cc_final: 0.6474 (pt0) REVERT: B 779 GLN cc_start: 0.8148 (tt0) cc_final: 0.7832 (tt0) REVERT: B 895 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.7846 (pt0) REVERT: B 1113 GLN cc_start: 0.8218 (mt0) cc_final: 0.7999 (mt0) REVERT: C 202 LYS cc_start: 0.8222 (mttt) cc_final: 0.7080 (mtpt) REVERT: C 280 ASN cc_start: 0.8094 (t0) cc_final: 0.7752 (t0) REVERT: C 321 GLN cc_start: 0.8395 (mm110) cc_final: 0.8170 (mm-40) REVERT: C 456 PHE cc_start: 0.7420 (OUTLIER) cc_final: 0.6489 (p90) REVERT: C 584 ILE cc_start: 0.7649 (pt) cc_final: 0.7347 (pt) REVERT: C 776 LYS cc_start: 0.8898 (tttp) cc_final: 0.8653 (ttmt) REVERT: C 780 GLU cc_start: 0.8436 (mt-10) cc_final: 0.7865 (mm-30) REVERT: C 796 ASP cc_start: 0.7406 (p0) cc_final: 0.7117 (p0) REVERT: C 878 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8175 (mt) REVERT: C 1038 LYS cc_start: 0.8641 (mmmt) cc_final: 0.8335 (mptt) REVERT: C 1127 ASP cc_start: 0.7591 (t0) cc_final: 0.7338 (t0) REVERT: H 22 CYS cc_start: 0.8121 (t) cc_final: 0.7489 (t) REVERT: H 52 TYR cc_start: 0.7386 (m-10) cc_final: 0.7101 (m-80) REVERT: H 56 SER cc_start: 0.7381 (OUTLIER) cc_final: 0.7109 (m) REVERT: H 100 TYR cc_start: 0.7918 (m-80) cc_final: 0.7488 (m-80) REVERT: M 13 GLN cc_start: 0.7374 (OUTLIER) cc_final: 0.6908 (mp10) REVERT: M 52 TYR cc_start: 0.7431 (m-80) cc_final: 0.7087 (m-80) REVERT: O 52 TYR cc_start: 0.7423 (m-10) cc_final: 0.7043 (m-80) REVERT: O 56 SER cc_start: 0.7315 (OUTLIER) cc_final: 0.7020 (m) REVERT: O 96 GLU cc_start: 0.7863 (tp30) cc_final: 0.7648 (mm-30) REVERT: L 87 TYR cc_start: 0.4859 (OUTLIER) cc_final: 0.3436 (t80) REVERT: N 27 ASP cc_start: 0.5400 (OUTLIER) cc_final: 0.5019 (p0) REVERT: N 35 TRP cc_start: 0.6320 (m100) cc_final: 0.5985 (m100) REVERT: N 87 TYR cc_start: 0.5696 (m-80) cc_final: 0.5201 (m-80) outliers start: 137 outliers final: 98 residues processed: 396 average time/residue: 0.1771 time to fit residues: 116.2869 Evaluate side-chains 372 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 263 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 100 TRP Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 13 GLN Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 11 LEU Chi-restraints excluded: chain O residue 56 SER Chi-restraints excluded: chain O residue 61 ASP Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 82 LEU Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain O residue 103 TYR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 87 TYR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 27 ASP Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 88 CYS Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 88 CYS Chi-restraints excluded: chain P residue 106 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 270 optimal weight: 0.0010 chunk 268 optimal weight: 0.9980 chunk 142 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 160 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 348 optimal weight: 0.5980 chunk 256 optimal weight: 0.7980 chunk 342 optimal weight: 20.0000 chunk 81 optimal weight: 0.9990 chunk 178 optimal weight: 0.9980 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 ASN B 207 HIS C 121 ASN C 207 HIS C 334 ASN C 388 ASN C 544 ASN ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.189716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.145474 restraints weight = 34824.276| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.78 r_work: 0.3356 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.4816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29574 Z= 0.117 Angle : 0.594 9.691 40344 Z= 0.297 Chirality : 0.046 0.331 4659 Planarity : 0.004 0.051 5157 Dihedral : 5.852 57.587 4664 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.08 % Favored : 94.81 % Rotamer: Outliers : 3.83 % Allowed : 20.70 % Favored : 75.47 % 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: -1.88 (0.13), residues: 3639 helix: -1.21 (0.20), residues: 651 sheet: -0.76 (0.16), residues: 909 loop : -1.48 (0.13), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 273 TYR 0.021 0.001 TYR M 100N PHE 0.020 0.001 PHE C 456 TRP 0.013 0.001 TRP A 104 HIS 0.003 0.001 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00261 (29499) covalent geometry : angle 0.57574 (40161) SS BOND : bond 0.00300 ( 42) SS BOND : angle 1.19117 ( 84) hydrogen bonds : bond 0.03124 ( 934) hydrogen bonds : angle 5.45791 ( 2535) link_NAG-ASN : bond 0.00448 ( 33) link_NAG-ASN : angle 2.81468 ( 99) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 296 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 ASN cc_start: 0.7834 (t0) cc_final: 0.7539 (t0) REVERT: A 287 ASP cc_start: 0.7620 (m-30) cc_final: 0.7301 (m-30) REVERT: A 321 GLN cc_start: 0.8373 (mm110) cc_final: 0.8095 (mm-40) REVERT: A 584 ILE cc_start: 0.7480 (OUTLIER) cc_final: 0.7211 (pt) REVERT: A 780 GLU cc_start: 0.8225 (mm-30) cc_final: 0.8015 (mm-30) REVERT: A 904 TYR cc_start: 0.7079 (t80) cc_final: 0.6802 (t80) REVERT: B 316 SER cc_start: 0.8746 (t) cc_final: 0.8435 (p) REVERT: B 319 ARG cc_start: 0.8228 (ttm170) cc_final: 0.7407 (mtp85) REVERT: B 357 ARG cc_start: 0.7656 (mtp85) cc_final: 0.7427 (mtp85) REVERT: B 474 GLN cc_start: 0.6588 (pp30) cc_final: 0.6278 (pt0) REVERT: B 546 LEU cc_start: 0.7107 (tt) cc_final: 0.6717 (pp) REVERT: B 779 GLN cc_start: 0.8054 (tt0) cc_final: 0.7572 (tp40) REVERT: B 780 GLU cc_start: 0.8371 (mt-10) cc_final: 0.7720 (mm-30) REVERT: B 895 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.7827 (pt0) REVERT: B 1113 GLN cc_start: 0.8185 (mt0) cc_final: 0.7959 (mt0) REVERT: B 1135 ASN cc_start: 0.7984 (t0) cc_final: 0.7755 (t0) REVERT: C 65 PHE cc_start: 0.7326 (m-80) cc_final: 0.7044 (m-80) REVERT: C 280 ASN cc_start: 0.7905 (t0) cc_final: 0.7617 (t0) REVERT: C 456 PHE cc_start: 0.7265 (OUTLIER) cc_final: 0.6288 (p90) REVERT: C 493 GLN cc_start: 0.8828 (tp40) cc_final: 0.8536 (tp40) REVERT: C 546 LEU cc_start: 0.7063 (tt) cc_final: 0.6546 (pp) REVERT: C 584 ILE cc_start: 0.7618 (pt) cc_final: 0.7318 (pt) REVERT: C 764 ASN cc_start: 0.8777 (m-40) cc_final: 0.8454 (m-40) REVERT: C 776 LYS cc_start: 0.8834 (tttp) cc_final: 0.8503 (ttmt) REVERT: C 780 GLU cc_start: 0.8332 (mt-10) cc_final: 0.7784 (mm-30) REVERT: C 878 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.7857 (mt) REVERT: C 882 ILE cc_start: 0.9146 (mt) cc_final: 0.8908 (mt) REVERT: C 1038 LYS cc_start: 0.8650 (mmmt) cc_final: 0.8165 (mmtm) REVERT: C 1127 ASP cc_start: 0.7495 (t0) cc_final: 0.7231 (t0) REVERT: H 22 CYS cc_start: 0.8036 (t) cc_final: 0.7472 (t) REVERT: H 56 SER cc_start: 0.7256 (OUTLIER) cc_final: 0.7009 (m) REVERT: M 13 GLN cc_start: 0.7414 (OUTLIER) cc_final: 0.6932 (mp10) REVERT: M 28 THR cc_start: 0.8074 (OUTLIER) cc_final: 0.7725 (m) REVERT: M 52 TYR cc_start: 0.7366 (m-80) cc_final: 0.7062 (m-80) REVERT: M 100 TYR cc_start: 0.7850 (m-80) cc_final: 0.7056 (m-80) REVERT: O 52 TYR cc_start: 0.7377 (m-10) cc_final: 0.7023 (m-80) REVERT: O 56 SER cc_start: 0.7129 (OUTLIER) cc_final: 0.6838 (m) REVERT: L 69 ASN cc_start: 0.6408 (m-40) cc_final: 0.6205 (m110) REVERT: L 87 TYR cc_start: 0.4673 (OUTLIER) cc_final: 0.3261 (t80) REVERT: N 27 ASP cc_start: 0.5452 (OUTLIER) cc_final: 0.5081 (p0) REVERT: N 35 TRP cc_start: 0.6390 (m100) cc_final: 0.6075 (m100) outliers start: 119 outliers final: 83 residues processed: 399 average time/residue: 0.1714 time to fit residues: 113.4386 Evaluate side-chains 367 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 274 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 100 TRP Chi-restraints excluded: chain H residue 103 TYR Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 13 GLN Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 11 LEU Chi-restraints excluded: chain O residue 56 SER Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 82 LEU Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain O residue 103 TYR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 87 TYR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain N residue 27 ASP Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 88 CYS Chi-restraints excluded: chain P residue 47 MET Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 88 CYS Chi-restraints excluded: chain P residue 106 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 4 optimal weight: 3.9990 chunk 321 optimal weight: 10.0000 chunk 330 optimal weight: 0.2980 chunk 126 optimal weight: 1.9990 chunk 193 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 116 optimal weight: 0.8980 chunk 297 optimal weight: 3.9990 chunk 290 optimal weight: 0.8980 chunk 268 optimal weight: 2.9990 chunk 172 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1010 GLN B 207 HIS B 856 ASN C 207 HIS C 564 GLN ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 17 GLN ** 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 = 0.4155 r_free = 0.4155 target = 0.188936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.135611 restraints weight = 34883.833| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.45 r_work: 0.3342 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.4916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 29574 Z= 0.145 Angle : 0.609 11.047 40344 Z= 0.305 Chirality : 0.047 0.336 4659 Planarity : 0.004 0.053 5157 Dihedral : 5.732 53.030 4664 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.52 % Favored : 94.37 % Rotamer: Outliers : 4.05 % Allowed : 20.67 % Favored : 75.28 % 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: -1.76 (0.13), residues: 3639 helix: -1.15 (0.20), residues: 654 sheet: -0.64 (0.17), residues: 891 loop : -1.41 (0.13), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 273 TYR 0.026 0.001 TYR N 87 PHE 0.029 0.001 PHE B 541 TRP 0.016 0.001 TRP A 104 HIS 0.002 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00339 (29499) covalent geometry : angle 0.59022 (40161) SS BOND : bond 0.00302 ( 42) SS BOND : angle 1.42635 ( 84) hydrogen bonds : bond 0.03190 ( 934) hydrogen bonds : angle 5.43518 ( 2535) link_NAG-ASN : bond 0.00456 ( 33) link_NAG-ASN : angle 2.85564 ( 99) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 277 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8627 (mt-10) REVERT: A 228 ASP cc_start: 0.7702 (OUTLIER) cc_final: 0.7402 (t0) REVERT: A 280 ASN cc_start: 0.7875 (t0) cc_final: 0.7602 (t0) REVERT: A 287 ASP cc_start: 0.7700 (m-30) cc_final: 0.7375 (m-30) REVERT: A 321 GLN cc_start: 0.8379 (mm110) cc_final: 0.8111 (mm-40) REVERT: A 546 LEU cc_start: 0.7458 (tt) cc_final: 0.7082 (pp) REVERT: A 584 ILE cc_start: 0.7490 (OUTLIER) cc_final: 0.7265 (pt) REVERT: A 780 GLU cc_start: 0.8275 (mm-30) cc_final: 0.8042 (mm-30) REVERT: A 895 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7736 (pt0) REVERT: A 904 TYR cc_start: 0.7167 (t80) cc_final: 0.6915 (t80) REVERT: B 316 SER cc_start: 0.8780 (OUTLIER) cc_final: 0.8510 (p) REVERT: B 319 ARG cc_start: 0.8295 (ttm170) cc_final: 0.7490 (mtp85) REVERT: B 357 ARG cc_start: 0.7674 (mtp85) cc_final: 0.7472 (mtp85) REVERT: B 474 GLN cc_start: 0.6670 (pp30) cc_final: 0.6392 (pt0) REVERT: B 546 LEU cc_start: 0.7157 (tt) cc_final: 0.6797 (pp) REVERT: B 780 GLU cc_start: 0.8432 (mt-10) cc_final: 0.7786 (mm-30) REVERT: B 895 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7901 (pt0) REVERT: B 1113 GLN cc_start: 0.8236 (mt0) cc_final: 0.8026 (mt0) REVERT: C 280 ASN cc_start: 0.7922 (t0) cc_final: 0.7641 (t0) REVERT: C 456 PHE cc_start: 0.7307 (OUTLIER) cc_final: 0.6429 (p90) REVERT: C 493 GLN cc_start: 0.8832 (tp40) cc_final: 0.8527 (tp40) REVERT: C 546 LEU cc_start: 0.7292 (tt) cc_final: 0.6860 (pp) REVERT: C 584 ILE cc_start: 0.7659 (pt) cc_final: 0.7359 (pt) REVERT: C 764 ASN cc_start: 0.8774 (m-40) cc_final: 0.8482 (m-40) REVERT: C 776 LYS cc_start: 0.8915 (tttp) cc_final: 0.8625 (ttmt) REVERT: C 780 GLU cc_start: 0.8403 (mt-10) cc_final: 0.7866 (mm-30) REVERT: C 878 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8055 (mt) REVERT: C 1038 LYS cc_start: 0.8642 (mmmt) cc_final: 0.8220 (mmtm) REVERT: C 1127 ASP cc_start: 0.7545 (t0) cc_final: 0.7254 (t0) REVERT: H 22 CYS cc_start: 0.8023 (t) cc_final: 0.7514 (t) REVERT: H 56 SER cc_start: 0.7288 (OUTLIER) cc_final: 0.7040 (m) REVERT: H 66 ARG cc_start: 0.7655 (ttp80) cc_final: 0.7420 (ttp80) REVERT: M 13 GLN cc_start: 0.7393 (OUTLIER) cc_final: 0.6602 (mp10) REVERT: M 28 THR cc_start: 0.8074 (OUTLIER) cc_final: 0.7714 (m) REVERT: M 52 TYR cc_start: 0.7397 (m-80) cc_final: 0.7119 (m-80) REVERT: O 52 TYR cc_start: 0.7500 (m-10) cc_final: 0.6999 (m-80) REVERT: O 56 SER cc_start: 0.7161 (OUTLIER) cc_final: 0.6865 (m) REVERT: L 87 TYR cc_start: 0.4646 (OUTLIER) cc_final: 0.3253 (t80) REVERT: N 27 ASP cc_start: 0.5493 (OUTLIER) cc_final: 0.5120 (p0) REVERT: N 35 TRP cc_start: 0.6462 (m100) cc_final: 0.6137 (m100) outliers start: 126 outliers final: 95 residues processed: 384 average time/residue: 0.1746 time to fit residues: 111.5589 Evaluate side-chains 363 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 254 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 100 TRP Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 13 GLN Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 11 LEU Chi-restraints excluded: chain O residue 56 SER Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 82 LEU Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain O residue 103 TYR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 87 TYR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain N residue 27 ASP Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 88 CYS Chi-restraints excluded: chain P residue 47 MET Chi-restraints excluded: chain P residue 88 CYS Chi-restraints excluded: chain P residue 106 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 319 optimal weight: 8.9990 chunk 9 optimal weight: 0.5980 chunk 335 optimal weight: 9.9990 chunk 217 optimal weight: 5.9990 chunk 119 optimal weight: 0.8980 chunk 152 optimal weight: 0.7980 chunk 328 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 53 optimal weight: 0.0670 chunk 20 optimal weight: 0.9980 chunk 113 optimal weight: 4.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN A1010 GLN B 207 HIS B 856 ASN C 207 HIS ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 17 GLN ** 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 = 0.4168 r_free = 0.4168 target = 0.190172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.133342 restraints weight = 34803.097| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.34 r_work: 0.3373 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.4991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29574 Z= 0.120 Angle : 0.585 10.905 40344 Z= 0.293 Chirality : 0.046 0.332 4659 Planarity : 0.004 0.051 5157 Dihedral : 5.487 52.697 4664 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.97 % Favored : 94.92 % Rotamer: Outliers : 3.66 % Allowed : 21.15 % Favored : 75.18 % 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: -1.57 (0.13), residues: 3639 helix: -0.95 (0.20), residues: 654 sheet: -0.49 (0.17), residues: 900 loop : -1.32 (0.13), residues: 2085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 273 TYR 0.022 0.001 TYR P 87 PHE 0.023 0.001 PHE B 541 TRP 0.017 0.001 TRP A 104 HIS 0.003 0.001 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00274 (29499) covalent geometry : angle 0.56721 (40161) SS BOND : bond 0.00265 ( 42) SS BOND : angle 1.30297 ( 84) hydrogen bonds : bond 0.03081 ( 934) hydrogen bonds : angle 5.27434 ( 2535) link_NAG-ASN : bond 0.00451 ( 33) link_NAG-ASN : angle 2.74386 ( 99) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 282 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8633 (mt-10) REVERT: A 228 ASP cc_start: 0.7512 (OUTLIER) cc_final: 0.7155 (t0) REVERT: A 280 ASN cc_start: 0.7792 (t0) cc_final: 0.7561 (t0) REVERT: A 287 ASP cc_start: 0.7598 (m-30) cc_final: 0.7284 (m-30) REVERT: A 321 GLN cc_start: 0.8385 (mm110) cc_final: 0.8171 (mm-40) REVERT: A 546 LEU cc_start: 0.7253 (tt) cc_final: 0.6931 (pp) REVERT: A 584 ILE cc_start: 0.7448 (OUTLIER) cc_final: 0.7222 (pt) REVERT: A 895 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7680 (pt0) REVERT: A 1002 GLN cc_start: 0.8445 (tt0) cc_final: 0.8182 (tt0) REVERT: B 316 SER cc_start: 0.8695 (OUTLIER) cc_final: 0.8415 (p) REVERT: B 319 ARG cc_start: 0.8232 (ttm170) cc_final: 0.7437 (mtp85) REVERT: B 474 GLN cc_start: 0.6615 (pp30) cc_final: 0.6317 (pt0) REVERT: B 546 LEU cc_start: 0.7153 (tt) cc_final: 0.6817 (pp) REVERT: B 780 GLU cc_start: 0.8409 (mt-10) cc_final: 0.7759 (mm-30) REVERT: B 895 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7917 (pt0) REVERT: B 1113 GLN cc_start: 0.8216 (mt0) cc_final: 0.8005 (mt0) REVERT: C 65 PHE cc_start: 0.7206 (m-80) cc_final: 0.6840 (m-80) REVERT: C 280 ASN cc_start: 0.7809 (t0) cc_final: 0.7583 (t0) REVERT: C 456 PHE cc_start: 0.7219 (OUTLIER) cc_final: 0.6423 (p90) REVERT: C 493 GLN cc_start: 0.8790 (tp40) cc_final: 0.8485 (tp40) REVERT: C 546 LEU cc_start: 0.7075 (tt) cc_final: 0.6700 (pp) REVERT: C 584 ILE cc_start: 0.7636 (pt) cc_final: 0.7330 (pt) REVERT: C 764 ASN cc_start: 0.8732 (m-40) cc_final: 0.8431 (m-40) REVERT: C 776 LYS cc_start: 0.8875 (tttp) cc_final: 0.8573 (ttmt) REVERT: C 780 GLU cc_start: 0.8337 (mt-10) cc_final: 0.7831 (mm-30) REVERT: C 1038 LYS cc_start: 0.8654 (mmmt) cc_final: 0.8200 (mmtm) REVERT: C 1127 ASP cc_start: 0.7545 (t0) cc_final: 0.7250 (t0) REVERT: H 22 CYS cc_start: 0.7920 (t) cc_final: 0.7428 (t) REVERT: H 56 SER cc_start: 0.7182 (OUTLIER) cc_final: 0.6821 (m) REVERT: H 66 ARG cc_start: 0.7485 (ttp80) cc_final: 0.7141 (ttp80) REVERT: M 13 GLN cc_start: 0.7393 (OUTLIER) cc_final: 0.6607 (mp10) REVERT: M 52 TYR cc_start: 0.7362 (m-80) cc_final: 0.7055 (m-80) REVERT: O 50 VAL cc_start: 0.7669 (p) cc_final: 0.7464 (t) REVERT: O 52 TYR cc_start: 0.7433 (m-10) cc_final: 0.6951 (m-80) REVERT: O 56 SER cc_start: 0.7151 (OUTLIER) cc_final: 0.6876 (m) REVERT: L 87 TYR cc_start: 0.4198 (OUTLIER) cc_final: 0.2572 (t80) REVERT: N 27 ASP cc_start: 0.5469 (OUTLIER) cc_final: 0.5083 (p0) REVERT: N 35 TRP cc_start: 0.6476 (m100) cc_final: 0.6170 (m100) outliers start: 114 outliers final: 93 residues processed: 376 average time/residue: 0.1749 time to fit residues: 109.6003 Evaluate side-chains 372 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 267 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 100 TRP Chi-restraints excluded: chain H residue 103 TYR Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 13 GLN Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain M residue 103 TYR Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 11 LEU Chi-restraints excluded: chain O residue 56 SER Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain O residue 103 TYR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 87 TYR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain N residue 27 ASP Chi-restraints excluded: chain N residue 88 CYS Chi-restraints excluded: chain P residue 47 MET Chi-restraints excluded: chain P residue 88 CYS Chi-restraints excluded: chain P residue 106 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 306 optimal weight: 4.9990 chunk 321 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 chunk 259 optimal weight: 0.6980 chunk 353 optimal weight: 20.0000 chunk 20 optimal weight: 3.9990 chunk 195 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 256 optimal weight: 0.9980 chunk 264 optimal weight: 4.9990 chunk 337 optimal weight: 5.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN B 207 HIS B 856 ASN C 207 HIS C 544 ASN L 69 ASN ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 69 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.187674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.129548 restraints weight = 34634.658| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.28 r_work: 0.3352 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.5027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 29574 Z= 0.180 Angle : 0.623 11.406 40344 Z= 0.312 Chirality : 0.048 0.341 4659 Planarity : 0.004 0.054 5157 Dihedral : 5.628 53.743 4664 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.66 % Favored : 94.23 % Rotamer: Outliers : 3.73 % Allowed : 21.38 % Favored : 74.90 % 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: -1.66 (0.13), residues: 3639 helix: -1.22 (0.19), residues: 675 sheet: -0.46 (0.17), residues: 876 loop : -1.33 (0.13), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 273 TYR 0.020 0.001 TYR C 423 PHE 0.024 0.002 PHE B1121 TRP 0.014 0.001 TRP A 104 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00427 (29499) covalent geometry : angle 0.60466 (40161) SS BOND : bond 0.00312 ( 42) SS BOND : angle 1.43294 ( 84) hydrogen bonds : bond 0.03277 ( 934) hydrogen bonds : angle 5.44157 ( 2535) link_NAG-ASN : bond 0.00467 ( 33) link_NAG-ASN : angle 2.86710 ( 99) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 261 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8629 (mt-10) REVERT: A 228 ASP cc_start: 0.7480 (OUTLIER) cc_final: 0.7113 (t0) REVERT: A 280 ASN cc_start: 0.7879 (t0) cc_final: 0.7629 (t0) REVERT: A 287 ASP cc_start: 0.7637 (m-30) cc_final: 0.7298 (m-30) REVERT: A 321 GLN cc_start: 0.8393 (mm110) cc_final: 0.8174 (mm-40) REVERT: A 546 LEU cc_start: 0.7215 (tt) cc_final: 0.6910 (pp) REVERT: A 584 ILE cc_start: 0.7541 (OUTLIER) cc_final: 0.7329 (pt) REVERT: A 895 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7721 (pt0) REVERT: A 904 TYR cc_start: 0.7124 (t80) cc_final: 0.6876 (t80) REVERT: B 316 SER cc_start: 0.8807 (OUTLIER) cc_final: 0.8517 (p) REVERT: B 319 ARG cc_start: 0.8275 (ttm170) cc_final: 0.7463 (mtp85) REVERT: B 357 ARG cc_start: 0.7510 (mtp85) cc_final: 0.6991 (ttp80) REVERT: B 474 GLN cc_start: 0.6703 (pp30) cc_final: 0.6415 (pt0) REVERT: B 546 LEU cc_start: 0.7104 (tt) cc_final: 0.6726 (pp) REVERT: B 780 GLU cc_start: 0.8421 (mt-10) cc_final: 0.7757 (mm-30) REVERT: B 895 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.7850 (pt0) REVERT: B 1113 GLN cc_start: 0.8216 (mt0) cc_final: 0.7997 (mt0) REVERT: C 202 LYS cc_start: 0.8185 (mttt) cc_final: 0.6965 (mtpt) REVERT: C 280 ASN cc_start: 0.7885 (t0) cc_final: 0.7641 (t0) REVERT: C 456 PHE cc_start: 0.7172 (OUTLIER) cc_final: 0.6335 (p90) REVERT: C 546 LEU cc_start: 0.7070 (tt) cc_final: 0.6619 (pp) REVERT: C 584 ILE cc_start: 0.7672 (pt) cc_final: 0.7342 (pt) REVERT: C 776 LYS cc_start: 0.8910 (tttp) cc_final: 0.8611 (ttmt) REVERT: C 780 GLU cc_start: 0.8399 (mt-10) cc_final: 0.7856 (mm-30) REVERT: C 1038 LYS cc_start: 0.8618 (mmmt) cc_final: 0.8295 (mptt) REVERT: C 1127 ASP cc_start: 0.7531 (t70) cc_final: 0.7242 (t0) REVERT: H 28 THR cc_start: 0.7606 (OUTLIER) cc_final: 0.7334 (m) REVERT: H 50 VAL cc_start: 0.7636 (p) cc_final: 0.7397 (t) REVERT: H 56 SER cc_start: 0.7323 (OUTLIER) cc_final: 0.7053 (m) REVERT: H 66 ARG cc_start: 0.7492 (ttp80) cc_final: 0.7157 (ttp80) REVERT: M 13 GLN cc_start: 0.7369 (OUTLIER) cc_final: 0.6605 (mp10) REVERT: M 28 THR cc_start: 0.8080 (OUTLIER) cc_final: 0.7712 (m) REVERT: M 52 TYR cc_start: 0.7384 (m-80) cc_final: 0.7065 (m-80) REVERT: O 19 ARG cc_start: 0.6888 (mtm180) cc_final: 0.6612 (ttp80) REVERT: O 52 TYR cc_start: 0.7502 (m-10) cc_final: 0.7038 (m-80) REVERT: O 56 SER cc_start: 0.7024 (OUTLIER) cc_final: 0.6723 (m) REVERT: L 69 ASN cc_start: 0.6177 (OUTLIER) cc_final: 0.5783 (m-40) REVERT: L 87 TYR cc_start: 0.4336 (OUTLIER) cc_final: 0.2677 (t80) REVERT: N 27 ASP cc_start: 0.5542 (OUTLIER) cc_final: 0.5073 (p0) REVERT: P 87 TYR cc_start: 0.5110 (OUTLIER) cc_final: 0.4346 (t80) outliers start: 116 outliers final: 99 residues processed: 361 average time/residue: 0.1840 time to fit residues: 110.6208 Evaluate side-chains 368 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 253 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 983 ARG Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 100 TRP Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 13 GLN Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 11 LEU Chi-restraints excluded: chain O residue 56 SER Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 82 LEU Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 69 ASN Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 87 TYR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 27 ASP Chi-restraints excluded: chain N residue 88 CYS Chi-restraints excluded: chain P residue 47 MET Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 87 TYR Chi-restraints excluded: chain P residue 88 CYS Chi-restraints excluded: chain P residue 106 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 234 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 224 optimal weight: 0.0980 chunk 126 optimal weight: 1.9990 chunk 198 optimal weight: 0.6980 chunk 135 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 121 optimal weight: 1.9990 chunk 301 optimal weight: 6.9990 chunk 175 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN A 935 GLN A1010 GLN B 207 HIS B 856 ASN C 207 HIS L 69 ASN ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.187918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.133228 restraints weight = 34907.730| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.48 r_work: 0.3325 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.5037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.292 29574 Z= 0.251 Angle : 0.828 59.195 40344 Z= 0.476 Chirality : 0.049 0.790 4659 Planarity : 0.005 0.174 5157 Dihedral : 5.633 53.743 4664 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.66 % Favored : 94.23 % Rotamer: Outliers : 4.08 % Allowed : 21.15 % Favored : 74.77 % Cbeta Deviations : 0.09 % 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: -1.66 (0.13), residues: 3639 helix: -1.22 (0.19), residues: 675 sheet: -0.48 (0.17), residues: 879 loop : -1.33 (0.13), residues: 2085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 273 TYR 0.016 0.001 TYR C 423 PHE 0.024 0.002 PHE B1121 TRP 0.013 0.001 TRP A 104 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00529 (29499) covalent geometry : angle 0.81377 (40161) SS BOND : bond 0.00344 ( 42) SS BOND : angle 1.80587 ( 84) hydrogen bonds : bond 0.03285 ( 934) hydrogen bonds : angle 5.44071 ( 2535) link_NAG-ASN : bond 0.00468 ( 33) link_NAG-ASN : angle 2.86743 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9234.26 seconds wall clock time: 158 minutes 30.04 seconds (9510.04 seconds total)