Starting phenix.real_space_refine on Tue Jun 24 10:13:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7whi_32500/06_2025/7whi_32500.cif Found real_map, /net/cci-nas-00/data/ceres_data/7whi_32500/06_2025/7whi_32500.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7whi_32500/06_2025/7whi_32500.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7whi_32500/06_2025/7whi_32500.map" model { file = "/net/cci-nas-00/data/ceres_data/7whi_32500/06_2025/7whi_32500.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7whi_32500/06_2025/7whi_32500.cif" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 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 138 5.16 5 C 18093 2.51 5 N 4666 2.21 5 O 5453 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.79s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 28350 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 8122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1042, 8122 Classifications: {'peptide': 1042} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 58, 'TRANS': 983} Chain breaks: 7 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "B" Number of atoms: 7984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 7984 Classifications: {'peptide': 1025} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 56, 'TRANS': 968} Chain breaks: 7 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "C" Number of atoms: 8133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1043, 8133 Classifications: {'peptide': 1043} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 58, 'TRANS': 984} Chain breaks: 7 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "D" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 899 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "E" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 893 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "F" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 893 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "G" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 922 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 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: 17.93, per 1000 atoms: 0.63 Number of scatterers: 28350 At special positions: 0 Unit cell: (147.896, 153.216, 197.904, 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 138 16.00 O 5453 8.00 N 4666 7.00 C 18093 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.06 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=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 95 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " 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 234 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 717 " " NAG A1304 " - " ASN A 801 " " NAG A1305 " - " ASN A1074 " " NAG A1306 " - " ASN A1098 " " NAG A1307 " - " ASN A1134 " " NAG A1308 " - " ASN A 616 " " NAG A1309 " - " ASN A 122 " " NAG A1310 " - " ASN A 61 " " NAG A1311 " - " ASN A 282 " " NAG A1312 " - " ASN A 343 " " NAG A1313 " - " ASN A 709 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 709 " " NAG B1303 " - " ASN B 717 " " NAG B1304 " - " ASN B 801 " " NAG B1305 " - " ASN B1074 " " NAG B1306 " - " ASN B1098 " " NAG B1307 " - " ASN B1134 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 122 " " NAG B1310 " - " ASN B 657 " " NAG B1311 " - " ASN B 61 " " NAG B1312 " - " ASN B 282 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 709 " " NAG C1304 " - " ASN C 717 " " NAG C1305 " - " ASN C1098 " " NAG C1306 " - " ASN C1134 " " NAG C1307 " - " ASN C 122 " " NAG C1308 " - " ASN C 801 " " NAG C1309 " - " ASN C 282 " " NAG C1310 " - " ASN C 165 " " NAG C1311 " - " ASN C 616 " Time building additional restraints: 6.60 Conformation dependent library (CDL) restraints added in 3.7 seconds 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6690 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 63 sheets defined 20.4% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.62 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.614A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.733A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 386 through 390' Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 417 through 422 removed outlier: 3.504A pdb=" N ASN A 422 " --> pdb=" O ILE A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 753 Processing helix chain 'A' and resid 754 through 757 removed outlier: 4.154A pdb=" N GLY A 757 " --> pdb=" O LEU A 754 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 754 through 757' Processing helix chain 'A' and resid 758 through 782 removed outlier: 3.630A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 849 through 853 removed outlier: 3.964A pdb=" N GLN A 853 " --> pdb=" O LEU A 849 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 849 through 853' Processing helix chain 'A' and resid 854 through 857 removed outlier: 3.532A pdb=" N GLY A 857 " --> pdb=" O LYS A 854 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 854 through 857' Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.861A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.569A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.024A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.808A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.856A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.611A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG A 983 " --> pdb=" O ASP A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.718A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 404 through 408 removed outlier: 3.522A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 408' Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 753 removed outlier: 3.724A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 757 removed outlier: 3.553A pdb=" N GLY B 757 " --> pdb=" O LEU B 754 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 754 through 757' Processing helix chain 'B' and resid 758 through 782 removed outlier: 3.797A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 removed outlier: 3.632A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 854 Processing helix chain 'B' and resid 855 through 857 No H-bonds generated for 'chain 'B' and resid 855 through 857' Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.839A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.532A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.090A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.666A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER B 939 " --> pdb=" O GLN B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.509A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.917A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'C' and resid 294 through 302 Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 747 through 754 Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.738A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 818 through 826 removed outlier: 3.547A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 852 removed outlier: 3.502A pdb=" N ALA C 852 " --> pdb=" O LEU C 849 " (cutoff:3.500A) Processing helix chain 'C' and resid 853 through 856 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.625A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 941 removed outlier: 4.149A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.753A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.878A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.723A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 90 removed outlier: 3.784A pdb=" N ASP D 89 " --> pdb=" O ARG D 86 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N THR D 90 " --> pdb=" O ALA D 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 86 through 90' Processing helix chain 'E' and resid 86 through 90 removed outlier: 3.778A pdb=" N THR E 90 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 65 removed outlier: 4.080A pdb=" N LYS G 65 " --> pdb=" O ASP G 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 62 through 65' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 51 removed outlier: 6.351A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 66 through 67 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.059A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 224 through 227 removed outlier: 6.779A pdb=" N ILE A 201 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.884A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 394 through 403 removed outlier: 3.561A pdb=" N VAL A 512 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A 510 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR A 508 " --> pdb=" O ILE A 402 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AA9, first strand: chain 'A' and resid 538 through 542 Processing sheet with id=AB1, first strand: chain 'A' and resid 584 through 586 removed outlier: 3.609A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.804A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.595A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.770A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 735 Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 789 removed outlier: 6.238A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.765A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 Processing sheet with id=AC1, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.981A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 54 through 55 removed outlier: 3.637A pdb=" N PHE B 55 " --> pdb=" O GLN B 271 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 66 through 67 Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.945A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 224 through 230 removed outlier: 6.036A pdb=" N SER B 203 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ASN B 186 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU B 96 " --> pdb=" O ASN B 186 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 316 removed outlier: 7.010A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.131A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N THR B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N ASN B 437 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N PHE B 374 " --> pdb=" O ASN B 437 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.568A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 538 through 542 Processing sheet with id=AD3, first strand: chain 'B' and resid 565 through 566 removed outlier: 3.816A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.848A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 722 removed outlier: 6.740A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 722 removed outlier: 6.740A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 735 removed outlier: 4.392A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 787 through 789 Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.503A pdb=" N SER B1123 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N CYS B1082 " --> pdb=" O VAL B1133 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 1094 through 1097 removed outlier: 4.808A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 28 through 30 Processing sheet with id=AE3, first strand: chain 'C' and resid 48 through 51 removed outlier: 3.657A pdb=" N LYS C 278 " --> pdb=" O ASP C 287 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 54 through 55 removed outlier: 3.689A pdb=" N PHE C 55 " --> pdb=" O GLN C 271 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN C 271 " --> pdb=" O PHE C 55 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'C' and resid 65 through 67 Processing sheet with id=AE6, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.031A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 224 through 229 removed outlier: 6.097A pdb=" N SER C 203 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU C 229 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N PHE C 199 " --> pdb=" O LEU C 229 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.643A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.552A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE C 402 " --> pdb=" O TYR C 508 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AF2, first strand: chain 'C' and resid 539 through 542 Processing sheet with id=AF3, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.964A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.694A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1122 removed outlier: 3.813A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF8, first strand: chain 'D' and resid 5 through 6 Processing sheet with id=AF9, first strand: chain 'D' and resid 11 through 12 Processing sheet with id=AG1, first strand: chain 'D' and resid 17 through 20 Processing sheet with id=AG2, first strand: chain 'D' and resid 46 through 50 removed outlier: 5.720A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR D 93 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR D 112 " --> pdb=" O TYR D 93 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 5 through 7 Processing sheet with id=AG4, first strand: chain 'E' and resid 47 through 51 removed outlier: 7.150A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLY E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 5 through 7 Processing sheet with id=AG6, first strand: chain 'F' and resid 57 through 58 removed outlier: 3.617A pdb=" N TYR F 58 " --> pdb=" O SER F 50 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER F 50 " --> pdb=" O TYR F 58 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 5 through 7 removed outlier: 3.599A pdb=" N VAL G 5 " --> pdb=" O ALA G 23 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU G 18 " --> pdb=" O MET G 83 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER G 71 " --> pdb=" O TYR G 80 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR G 69 " --> pdb=" O GLN G 82 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.524A pdb=" N VAL G 12 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR G 114 " --> pdb=" O TYR G 94 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR G 94 " --> pdb=" O THR G 114 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL G 116 " --> pdb=" O ALA G 92 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA G 92 " --> pdb=" O VAL G 116 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.524A pdb=" N VAL G 12 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR G 114 " --> pdb=" O TYR G 94 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR G 94 " --> pdb=" O THR G 114 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL G 116 " --> pdb=" O ALA G 92 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA G 92 " --> pdb=" O VAL G 116 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR G 98 " --> pdb=" O TYR G 109 " (cutoff:3.500A) 885 hydrogen bonds defined for protein. 2409 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: 13.84 Time building geometry restraints manager: 8.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5619 1.33 - 1.45: 7401 1.45 - 1.57: 15808 1.57 - 1.70: 0 1.70 - 1.82: 182 Bond restraints: 29010 Sorted by residual: bond pdb=" CA ASN A 801 " pdb=" C ASN A 801 " ideal model delta sigma weight residual 1.523 1.466 0.057 1.23e-02 6.61e+03 2.12e+01 bond pdb=" CA ASN B1134 " pdb=" C ASN B1134 " ideal model delta sigma weight residual 1.523 1.469 0.054 1.28e-02 6.10e+03 1.76e+01 bond pdb=" CA ASN A 717 " pdb=" C ASN A 717 " ideal model delta sigma weight residual 1.525 1.474 0.051 1.25e-02 6.40e+03 1.65e+01 bond pdb=" CA ALA B 123 " pdb=" C ALA B 123 " ideal model delta sigma weight residual 1.523 1.469 0.054 1.34e-02 5.57e+03 1.61e+01 bond pdb=" CA ASN B 717 " pdb=" C ASN B 717 " ideal model delta sigma weight residual 1.525 1.477 0.048 1.25e-02 6.40e+03 1.49e+01 ... (remaining 29005 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 38832 2.29 - 4.58: 606 4.58 - 6.86: 36 6.86 - 9.15: 11 9.15 - 11.44: 4 Bond angle restraints: 39489 Sorted by residual: angle pdb=" N ALA A 163 " pdb=" CA ALA A 163 " pdb=" C ALA A 163 " ideal model delta sigma weight residual 109.96 121.40 -11.44 1.58e+00 4.01e-01 5.24e+01 angle pdb=" N TYR A 160 " pdb=" CA TYR A 160 " pdb=" C TYR A 160 " ideal model delta sigma weight residual 109.81 118.79 -8.98 1.53e+00 4.27e-01 3.44e+01 angle pdb=" C ALA B 123 " pdb=" N THR B 124 " pdb=" CA THR B 124 " ideal model delta sigma weight residual 122.65 113.37 9.28 1.60e+00 3.91e-01 3.36e+01 angle pdb=" N ALA B 852 " pdb=" CA ALA B 852 " pdb=" C ALA B 852 " ideal model delta sigma weight residual 114.75 107.56 7.19 1.26e+00 6.30e-01 3.25e+01 angle pdb=" N SER A 161 " pdb=" CA SER A 161 " pdb=" C SER A 161 " ideal model delta sigma weight residual 112.57 106.70 5.87 1.13e+00 7.83e-01 2.70e+01 ... (remaining 39484 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 16736 17.38 - 34.76: 766 34.76 - 52.14: 184 52.14 - 69.53: 36 69.53 - 86.91: 20 Dihedral angle restraints: 17742 sinusoidal: 7330 harmonic: 10412 Sorted by residual: dihedral pdb=" CA TYR A 160 " pdb=" C TYR A 160 " pdb=" N SER A 161 " pdb=" CA SER A 161 " ideal model delta harmonic sigma weight residual 180.00 152.91 27.09 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA PRO C 213 " pdb=" C PRO C 213 " pdb=" N GLU C 214 " pdb=" CA GLU C 214 " ideal model delta harmonic sigma weight residual -180.00 -157.94 -22.06 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" C TYR A 160 " pdb=" N TYR A 160 " pdb=" CA TYR A 160 " pdb=" CB TYR A 160 " ideal model delta harmonic sigma weight residual -122.60 -132.12 9.52 0 2.50e+00 1.60e-01 1.45e+01 ... (remaining 17739 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 4360 0.102 - 0.204: 175 0.204 - 0.306: 18 0.306 - 0.408: 5 0.408 - 0.509: 4 Chirality restraints: 4562 Sorted by residual: chirality pdb=" C1 NAG C1310 " pdb=" ND2 ASN C 165 " pdb=" C2 NAG C1310 " pdb=" O5 NAG C1310 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.49e+00 chirality pdb=" C1 NAG C1302 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 5.88e+00 chirality pdb=" C1 NAG C1309 " pdb=" ND2 ASN C 282 " pdb=" C2 NAG C1309 " pdb=" O5 NAG C1309 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.69e+00 ... (remaining 4559 not shown) Planarity restraints: 5091 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1309 " -0.354 2.00e-02 2.50e+03 3.05e-01 1.16e+03 pdb=" C7 NAG C1309 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG C1309 " -0.127 2.00e-02 2.50e+03 pdb=" N2 NAG C1309 " 0.542 2.00e-02 2.50e+03 pdb=" O7 NAG C1309 " -0.146 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1311 " -0.352 2.00e-02 2.50e+03 3.03e-01 1.15e+03 pdb=" C7 NAG A1311 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG A1311 " -0.120 2.00e-02 2.50e+03 pdb=" N2 NAG A1311 " 0.540 2.00e-02 2.50e+03 pdb=" O7 NAG A1311 " -0.153 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1305 " 0.349 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" C7 NAG B1305 " -0.089 2.00e-02 2.50e+03 pdb=" C8 NAG B1305 " 0.168 2.00e-02 2.50e+03 pdb=" N2 NAG B1305 " -0.526 2.00e-02 2.50e+03 pdb=" O7 NAG B1305 " 0.098 2.00e-02 2.50e+03 ... (remaining 5088 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2809 2.75 - 3.29: 27495 3.29 - 3.83: 46371 3.83 - 4.36: 53603 4.36 - 4.90: 93195 Nonbonded interactions: 223473 Sorted by model distance: nonbonded pdb=" O GLY A 880 " pdb=" OG SER A 884 " model vdw 2.213 3.040 nonbonded pdb=" O THR B 393 " pdb=" OG1 THR B 523 " model vdw 2.217 3.040 nonbonded pdb=" O GLY B 880 " pdb=" OG SER B 884 " model vdw 2.244 3.040 nonbonded pdb=" OG1 THR A 961 " pdb=" OE1 GLN C 762 " model vdw 2.268 3.040 nonbonded pdb=" O GLU B 661 " pdb=" OH TYR B 695 " model vdw 2.271 3.040 ... (remaining 223468 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 26 through 177 or resid 182 through 244 or resid 262 throu \ gh 827 or resid 849 through 1147 or resid 1301 through 1311)) selection = (chain 'B' and (resid 26 through 1147 or resid 1301 through 1311)) selection = (chain 'C' and (resid 26 through 177 or resid 182 through 244 or resid 262 throu \ gh 827 or resid 849 through 1147 or resid 1301 through 1311)) } ncs_group { reference = (chain 'D' and resid 1 through 116) selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.300 Check model and map are aligned: 0.250 Set scattering table: 0.290 Process input model: 69.540 Find NCS groups from input model: 1.640 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:17.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 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 : 0.004 0.057 29091 Z= 0.222 Angle : 0.665 11.440 39687 Z= 0.381 Chirality : 0.050 0.509 4562 Planarity : 0.016 0.305 5055 Dihedral : 10.721 86.907 10917 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.51 % Favored : 94.32 % Rotamer: Outliers : 5.48 % Allowed : 9.18 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.55 (0.12), residues: 3522 helix: -0.48 (0.19), residues: 629 sheet: -2.05 (0.17), residues: 736 loop : -3.25 (0.11), residues: 2157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 36 HIS 0.002 0.000 HIS C 205 PHE 0.012 0.001 PHE B 175 TYR 0.015 0.001 TYR C 265 ARG 0.002 0.000 ARG A 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00666 ( 36) link_NAG-ASN : angle 3.28351 ( 108) hydrogen bonds : bond 0.15862 ( 879) hydrogen bonds : angle 7.43770 ( 2409) SS BOND : bond 0.00439 ( 45) SS BOND : angle 0.88884 ( 90) covalent geometry : bond 0.00357 (29010) covalent geometry : angle 0.64234 (39489) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 851 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 682 time to evaluate : 3.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.7027 (OUTLIER) cc_final: 0.6459 (m) REVERT: A 126 VAL cc_start: 0.8044 (t) cc_final: 0.7823 (m) REVERT: A 127 VAL cc_start: 0.8248 (t) cc_final: 0.7890 (m) REVERT: A 129 LYS cc_start: 0.7875 (mmtt) cc_final: 0.7314 (tppp) REVERT: A 173 GLN cc_start: 0.5061 (OUTLIER) cc_final: 0.4383 (tm130) REVERT: A 189 GLU cc_start: 0.7317 (mt-10) cc_final: 0.6915 (mt-10) REVERT: A 235 ILE cc_start: 0.3149 (OUTLIER) cc_final: 0.2924 (mp) REVERT: A 281 GLU cc_start: 0.6762 (pm20) cc_final: 0.6520 (pm20) REVERT: A 434 ILE cc_start: 0.8032 (OUTLIER) cc_final: 0.7524 (tp) REVERT: A 516 GLU cc_start: 0.6354 (OUTLIER) cc_final: 0.5783 (tm-30) REVERT: A 517 LEU cc_start: 0.7487 (tm) cc_final: 0.7198 (pp) REVERT: A 539 VAL cc_start: 0.8337 (t) cc_final: 0.8065 (m) REVERT: A 776 LYS cc_start: 0.8477 (ttpt) cc_final: 0.8186 (ttpp) REVERT: A 821 LEU cc_start: 0.7505 (mt) cc_final: 0.7053 (mp) REVERT: A 943 SER cc_start: 0.7884 (OUTLIER) cc_final: 0.7683 (t) REVERT: A 1118 ASP cc_start: 0.6901 (t0) cc_final: 0.6659 (t0) REVERT: B 52 GLN cc_start: 0.7316 (tm-30) cc_final: 0.6610 (tm-30) REVERT: B 340 GLU cc_start: 0.6937 (tm-30) cc_final: 0.6612 (tm-30) REVERT: B 449 TYR cc_start: 0.6601 (m-80) cc_final: 0.6167 (m-80) REVERT: B 586 ASP cc_start: 0.6809 (t0) cc_final: 0.6539 (t0) REVERT: B 773 GLU cc_start: 0.7101 (tt0) cc_final: 0.6405 (tt0) REVERT: B 933 LYS cc_start: 0.8200 (mtmm) cc_final: 0.7795 (mtmm) REVERT: C 81 ASN cc_start: 0.7547 (t0) cc_final: 0.7189 (t0) REVERT: C 96 GLU cc_start: 0.5650 (mt-10) cc_final: 0.5232 (mt-10) REVERT: C 297 SER cc_start: 0.8080 (p) cc_final: 0.7846 (m) REVERT: C 317 ASN cc_start: 0.7947 (m110) cc_final: 0.7711 (m-40) REVERT: C 407 VAL cc_start: 0.6467 (OUTLIER) cc_final: 0.6228 (t) REVERT: C 425 LEU cc_start: 0.5964 (OUTLIER) cc_final: 0.5707 (pp) REVERT: C 551 VAL cc_start: 0.7959 (OUTLIER) cc_final: 0.7654 (p) REVERT: C 654 GLU cc_start: 0.6864 (mp0) cc_final: 0.6661 (pm20) REVERT: C 675 GLN cc_start: 0.7101 (mm-40) cc_final: 0.6881 (mp10) REVERT: C 772 VAL cc_start: 0.8669 (t) cc_final: 0.8440 (m) REVERT: C 814 LYS cc_start: 0.7983 (mmtm) cc_final: 0.7605 (mppt) REVERT: C 869 MET cc_start: 0.8291 (mtt) cc_final: 0.8047 (mtm) REVERT: D 18 LEU cc_start: 0.7832 (mm) cc_final: 0.7004 (mm) REVERT: D 34 MET cc_start: 0.6870 (ttm) cc_final: 0.6539 (ttp) REVERT: D 35 SER cc_start: 0.7290 (m) cc_final: 0.6935 (t) REVERT: D 54 SER cc_start: 0.8296 (t) cc_final: 0.8066 (t) REVERT: D 82 MET cc_start: 0.6351 (ppp) cc_final: 0.5915 (ppp) REVERT: E 3 GLN cc_start: 0.3907 (OUTLIER) cc_final: 0.3614 (tm-30) REVERT: E 4 LEU cc_start: -0.5314 (OUTLIER) cc_final: -0.5517 (tt) REVERT: E 31 ASP cc_start: 0.5855 (OUTLIER) cc_final: 0.5431 (p0) REVERT: E 99 TRP cc_start: 0.4310 (OUTLIER) cc_final: 0.2987 (t60) REVERT: F 110 GLN cc_start: 0.3230 (OUTLIER) cc_final: 0.2948 (pm20) REVERT: G 28 TYR cc_start: 0.6568 (OUTLIER) cc_final: 0.5885 (p90) REVERT: G 34 MET cc_start: 0.7087 (OUTLIER) cc_final: 0.6603 (tpt) outliers start: 169 outliers final: 56 residues processed: 824 average time/residue: 1.2267 time to fit residues: 1202.1055 Evaluate side-chains 563 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 491 time to evaluate : 2.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain D residue 1 GLU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 71 ARG Chi-restraints excluded: chain E residue 99 TRP Chi-restraints excluded: chain F residue 95 CYS Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain G residue 28 TYR Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 116 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 298 optimal weight: 0.9990 chunk 268 optimal weight: 0.7980 chunk 148 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 180 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 277 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 168 optimal weight: 1.9990 chunk 206 optimal weight: 20.0000 chunk 321 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN A 134 GLN A 173 GLN A 218 GLN A 334 ASN A 409 GLN A 422 ASN A 448 ASN A 460 ASN A 506 GLN A 540 ASN A 658 ASN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 GLN A 901 GLN A 907 ASN A 957 GLN A 978 ASN A1002 GLN A1005 GLN A1048 HIS A1083 HIS A1106 GLN B 49 HIS B 121 ASN B 354 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN B 448 ASN B 450 ASN B 474 GLN B 540 ASN B 784 GLN B 901 GLN B 907 ASN B 957 GLN B 965 GLN B1010 GLN B1048 HIS B1058 HIS B1106 GLN C 30 ASN C 49 HIS C 66 HIS C 81 ASN C 99 ASN C 271 GLN C 334 ASN C 354 ASN C 409 GLN C 450 ASN C 519 HIS C 540 ASN C 542 ASN C 564 GLN C 751 ASN C 957 GLN C 960 ASN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN C1010 GLN C1048 HIS C1074 ASN C1106 GLN C1119 ASN D 13 GLN D 73 ASN E 60 ASN F 3 GLN F 73 ASN G 3 GLN G 39 GLN Total number of N/Q/H flips: 69 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.168614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.128975 restraints weight = 47003.189| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.66 r_work: 0.3445 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 29091 Z= 0.216 Angle : 0.693 10.811 39687 Z= 0.345 Chirality : 0.049 0.431 4562 Planarity : 0.005 0.040 5055 Dihedral : 7.393 81.748 4743 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.81 % Favored : 93.10 % Rotamer: Outliers : 5.67 % Allowed : 16.57 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.13), residues: 3522 helix: 0.35 (0.21), residues: 646 sheet: -1.65 (0.17), residues: 784 loop : -2.70 (0.12), residues: 2092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 436 HIS 0.005 0.001 HIS A1064 PHE 0.030 0.002 PHE C 541 TYR 0.026 0.002 TYR B1067 ARG 0.009 0.001 ARG B1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00610 ( 36) link_NAG-ASN : angle 2.40652 ( 108) hydrogen bonds : bond 0.03980 ( 879) hydrogen bonds : angle 5.58198 ( 2409) SS BOND : bond 0.00572 ( 45) SS BOND : angle 1.55138 ( 90) covalent geometry : bond 0.00493 (29010) covalent geometry : angle 0.67952 (39489) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 518 time to evaluate : 2.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8734 (OUTLIER) cc_final: 0.8526 (t) REVERT: A 127 VAL cc_start: 0.8607 (t) cc_final: 0.8323 (m) REVERT: A 129 LYS cc_start: 0.8646 (mmtt) cc_final: 0.8269 (tppp) REVERT: A 184 PHE cc_start: 0.6057 (OUTLIER) cc_final: 0.5854 (m-10) REVERT: A 204 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8470 (tmtm) REVERT: A 277 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8786 (mt) REVERT: A 281 GLU cc_start: 0.7892 (pm20) cc_final: 0.7611 (pm20) REVERT: A 393 THR cc_start: 0.8873 (t) cc_final: 0.8195 (t) REVERT: A 394 ASN cc_start: 0.7499 (t0) cc_final: 0.6916 (m-40) REVERT: A 516 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.6662 (tm-30) REVERT: A 517 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7601 (pp) REVERT: A 776 LYS cc_start: 0.8913 (ttpt) cc_final: 0.8627 (ttpp) REVERT: A 796 TYR cc_start: 0.8641 (t80) cc_final: 0.8291 (t80) REVERT: A 902 MET cc_start: 0.8837 (mmm) cc_final: 0.8613 (tpt) REVERT: A 1002 GLN cc_start: 0.8581 (tt0) cc_final: 0.8352 (tp40) REVERT: A 1107 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7876 (mtt180) REVERT: A 1118 ASP cc_start: 0.8239 (t0) cc_final: 0.7979 (t70) REVERT: B 52 GLN cc_start: 0.8152 (tm-30) cc_final: 0.7576 (tm-30) REVERT: B 80 ASP cc_start: 0.7375 (t0) cc_final: 0.7050 (p0) REVERT: B 186 ASN cc_start: 0.8274 (p0) cc_final: 0.7470 (p0) REVERT: B 237 ARG cc_start: 0.8663 (mtp180) cc_final: 0.8296 (mtp-110) REVERT: B 338 PHE cc_start: 0.8109 (OUTLIER) cc_final: 0.7773 (t80) REVERT: B 340 GLU cc_start: 0.7848 (tm-30) cc_final: 0.7391 (tm-30) REVERT: B 378 LYS cc_start: 0.8545 (mptt) cc_final: 0.8297 (mppt) REVERT: B 391 CYS cc_start: 0.7067 (m) cc_final: 0.6752 (m) REVERT: B 449 TYR cc_start: 0.7497 (m-80) cc_final: 0.7240 (m-80) REVERT: B 558 LYS cc_start: 0.8846 (mtmt) cc_final: 0.8624 (mtmt) REVERT: B 660 TYR cc_start: 0.8593 (m-80) cc_final: 0.8266 (m-10) REVERT: B 762 GLN cc_start: 0.7944 (pp30) cc_final: 0.7546 (pp30) REVERT: B 765 ARG cc_start: 0.8302 (mtm-85) cc_final: 0.7369 (mtm-85) REVERT: B 947 LYS cc_start: 0.8612 (mtpp) cc_final: 0.8368 (mtmm) REVERT: B 1107 ARG cc_start: 0.7963 (mpt-90) cc_final: 0.7550 (mtt-85) REVERT: C 53 ASP cc_start: 0.8102 (t70) cc_final: 0.7900 (t70) REVERT: C 81 ASN cc_start: 0.8130 (t0) cc_final: 0.7199 (t0) REVERT: C 88 ASP cc_start: 0.7388 (m-30) cc_final: 0.7137 (m-30) REVERT: C 239 GLN cc_start: 0.8406 (pt0) cc_final: 0.8043 (tt0) REVERT: C 278 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8449 (ptmm) REVERT: C 425 LEU cc_start: 0.6505 (OUTLIER) cc_final: 0.6227 (pp) REVERT: C 549 THR cc_start: 0.8437 (t) cc_final: 0.8144 (m) REVERT: C 654 GLU cc_start: 0.8012 (mp0) cc_final: 0.7625 (pm20) REVERT: C 702 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7531 (tm-30) REVERT: C 751 ASN cc_start: 0.8414 (m-40) cc_final: 0.8190 (m110) REVERT: C 754 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7410 (mm) REVERT: C 779 GLN cc_start: 0.8608 (mm-40) cc_final: 0.8404 (tm-30) REVERT: C 814 LYS cc_start: 0.8162 (mmtm) cc_final: 0.7626 (mppt) REVERT: C 947 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8458 (mtpp) REVERT: C 950 ASP cc_start: 0.8074 (p0) cc_final: 0.7675 (p0) REVERT: C 957 GLN cc_start: 0.8245 (tt0) cc_final: 0.7827 (tt0) REVERT: C 1002 GLN cc_start: 0.8628 (tt0) cc_final: 0.8394 (tt0) REVERT: C 1107 ARG cc_start: 0.8012 (mpp80) cc_final: 0.7627 (mtt90) REVERT: D 51 MET cc_start: 0.8440 (tpt) cc_final: 0.8220 (tpt) REVERT: D 82 MET cc_start: 0.7412 (ppp) cc_final: 0.6694 (ppp) REVERT: E 4 LEU cc_start: -0.4589 (OUTLIER) cc_final: -0.4875 (tt) REVERT: E 31 ASP cc_start: 0.6561 (OUTLIER) cc_final: 0.6316 (p0) REVERT: E 92 MET cc_start: 0.4653 (tpp) cc_final: 0.4375 (tpp) REVERT: E 99 TRP cc_start: 0.5173 (OUTLIER) cc_final: 0.3668 (t60) REVERT: F 110 GLN cc_start: 0.3747 (OUTLIER) cc_final: 0.3299 (pm20) REVERT: G 28 TYR cc_start: 0.6529 (OUTLIER) cc_final: 0.3843 (p90) REVERT: G 32 TYR cc_start: 0.7597 (OUTLIER) cc_final: 0.6330 (m-80) REVERT: G 34 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7375 (tpt) REVERT: G 83 MET cc_start: 0.6865 (ptp) cc_final: 0.6438 (ptp) outliers start: 175 outliers final: 70 residues processed: 644 average time/residue: 1.2743 time to fit residues: 973.0067 Evaluate side-chains 570 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 481 time to evaluate : 2.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 969 LYS Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 960 ASN Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain D residue 1 GLU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 71 ARG Chi-restraints excluded: chain E residue 99 TRP Chi-restraints excluded: chain F residue 95 CYS Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain G residue 28 TYR Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 116 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 106 optimal weight: 5.9990 chunk 120 optimal weight: 0.0060 chunk 240 optimal weight: 9.9990 chunk 117 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 334 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 311 optimal weight: 0.3980 chunk 188 optimal weight: 2.9990 chunk 274 optimal weight: 2.9990 chunk 222 optimal weight: 0.5980 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 ASN A 658 ASN B 49 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN B 580 GLN B 907 ASN B 913 GLN B 957 GLN B1010 GLN C 30 ASN C 66 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS C 564 GLN C 901 GLN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1074 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.202026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.170013 restraints weight = 52969.679| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.48 r_work: 0.3505 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 29091 Z= 0.167 Angle : 0.636 9.749 39687 Z= 0.318 Chirality : 0.046 0.267 4562 Planarity : 0.005 0.054 5055 Dihedral : 6.654 82.466 4705 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.19 % Favored : 93.73 % Rotamer: Outliers : 5.54 % Allowed : 18.64 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.13), residues: 3522 helix: 0.67 (0.21), residues: 661 sheet: -1.36 (0.17), residues: 799 loop : -2.43 (0.12), residues: 2062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 47 HIS 0.010 0.001 HIS C 519 PHE 0.031 0.002 PHE C 541 TYR 0.035 0.001 TYR F 94 ARG 0.012 0.001 ARG B 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00381 ( 36) link_NAG-ASN : angle 2.32438 ( 108) hydrogen bonds : bond 0.03684 ( 879) hydrogen bonds : angle 5.34767 ( 2409) SS BOND : bond 0.00664 ( 45) SS BOND : angle 1.60601 ( 90) covalent geometry : bond 0.00388 (29010) covalent geometry : angle 0.62071 (39489) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 487 time to evaluate : 3.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ILE cc_start: 0.8328 (OUTLIER) cc_final: 0.8126 (pp) REVERT: A 127 VAL cc_start: 0.8540 (t) cc_final: 0.8280 (m) REVERT: A 128 ILE cc_start: 0.8336 (OUTLIER) cc_final: 0.8039 (mp) REVERT: A 129 LYS cc_start: 0.8491 (mmtt) cc_final: 0.8037 (tppp) REVERT: A 277 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8754 (mt) REVERT: A 281 GLU cc_start: 0.7754 (pm20) cc_final: 0.7452 (pm20) REVERT: A 393 THR cc_start: 0.8854 (t) cc_final: 0.8179 (t) REVERT: A 394 ASN cc_start: 0.7260 (t0) cc_final: 0.6610 (m-40) REVERT: A 516 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.6544 (tm-30) REVERT: A 517 LEU cc_start: 0.8103 (tm) cc_final: 0.7733 (pp) REVERT: A 574 ASP cc_start: 0.8054 (t0) cc_final: 0.7849 (t0) REVERT: A 773 GLU cc_start: 0.7899 (tp30) cc_final: 0.7651 (tp30) REVERT: A 776 LYS cc_start: 0.8748 (ttpt) cc_final: 0.8459 (ttpp) REVERT: A 790 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8146 (mmmm) REVERT: A 796 TYR cc_start: 0.8648 (t80) cc_final: 0.8303 (t80) REVERT: A 854 LYS cc_start: 0.8738 (tttm) cc_final: 0.8459 (ttmm) REVERT: A 990 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7810 (mp0) REVERT: A 1002 GLN cc_start: 0.8447 (tt0) cc_final: 0.8195 (tp40) REVERT: A 1107 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7736 (mtt180) REVERT: A 1118 ASP cc_start: 0.8024 (t0) cc_final: 0.7789 (t70) REVERT: B 46 SER cc_start: 0.8901 (OUTLIER) cc_final: 0.8608 (p) REVERT: B 52 GLN cc_start: 0.8074 (tm-30) cc_final: 0.7559 (tm-30) REVERT: B 186 ASN cc_start: 0.8089 (p0) cc_final: 0.7541 (p0) REVERT: B 237 ARG cc_start: 0.8518 (mtp180) cc_final: 0.8164 (mtp-110) REVERT: B 338 PHE cc_start: 0.7968 (OUTLIER) cc_final: 0.7619 (t80) REVERT: B 340 GLU cc_start: 0.7593 (tm-30) cc_final: 0.7077 (tm-30) REVERT: B 391 CYS cc_start: 0.6591 (m) cc_final: 0.6228 (m) REVERT: B 497 PHE cc_start: 0.8447 (m-10) cc_final: 0.8214 (m-80) REVERT: B 654 GLU cc_start: 0.7551 (mm-30) cc_final: 0.7323 (mp0) REVERT: B 660 TYR cc_start: 0.8557 (m-80) cc_final: 0.8272 (m-10) REVERT: B 762 GLN cc_start: 0.7655 (pp30) cc_final: 0.7280 (pp30) REVERT: B 765 ARG cc_start: 0.8199 (mtm-85) cc_final: 0.7217 (mtm-85) REVERT: B 933 LYS cc_start: 0.8677 (mtpp) cc_final: 0.8250 (mtmm) REVERT: B 1031 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7918 (mt-10) REVERT: B 1072 GLU cc_start: 0.8245 (pm20) cc_final: 0.8035 (pm20) REVERT: B 1091 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.7889 (ttp-110) REVERT: B 1107 ARG cc_start: 0.7852 (mpt-90) cc_final: 0.7571 (mtt-85) REVERT: C 88 ASP cc_start: 0.7253 (m-30) cc_final: 0.7015 (m-30) REVERT: C 129 LYS cc_start: 0.7957 (mmtm) cc_final: 0.7705 (mttp) REVERT: C 188 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7900 (mtp180) REVERT: C 218 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.8081 (mm-40) REVERT: C 239 GLN cc_start: 0.8234 (pt0) cc_final: 0.7907 (tt0) REVERT: C 278 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8424 (ptmm) REVERT: C 324 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7532 (mm-30) REVERT: C 425 LEU cc_start: 0.6591 (OUTLIER) cc_final: 0.6315 (pp) REVERT: C 654 GLU cc_start: 0.7863 (mp0) cc_final: 0.7475 (pm20) REVERT: C 745 ASP cc_start: 0.7188 (m-30) cc_final: 0.6909 (OUTLIER) REVERT: C 754 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7418 (mm) REVERT: C 779 GLN cc_start: 0.8477 (mm-40) cc_final: 0.8217 (tm-30) REVERT: C 790 LYS cc_start: 0.8799 (mtmm) cc_final: 0.8598 (mtmm) REVERT: C 814 LYS cc_start: 0.8070 (mmtm) cc_final: 0.7523 (mppt) REVERT: C 918 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7171 (mm-30) REVERT: C 950 ASP cc_start: 0.7861 (p0) cc_final: 0.7449 (p0) REVERT: C 957 GLN cc_start: 0.8074 (tt0) cc_final: 0.7549 (tt0) REVERT: C 1002 GLN cc_start: 0.8452 (tt0) cc_final: 0.8224 (tt0) REVERT: C 1072 GLU cc_start: 0.8456 (pm20) cc_final: 0.8126 (pm20) REVERT: C 1091 ARG cc_start: 0.8711 (ttm170) cc_final: 0.8445 (ttp-170) REVERT: C 1107 ARG cc_start: 0.7912 (mpp80) cc_final: 0.7674 (mtt90) REVERT: D 18 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7282 (mm) REVERT: D 33 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7488 (tm-30) REVERT: D 56 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.7447 (tpp80) REVERT: D 82 MET cc_start: 0.7127 (ppp) cc_final: 0.6361 (ppp) REVERT: E 31 ASP cc_start: 0.6611 (OUTLIER) cc_final: 0.6351 (p0) REVERT: E 92 MET cc_start: 0.4665 (tpp) cc_final: 0.4363 (tpp) REVERT: E 99 TRP cc_start: 0.5097 (OUTLIER) cc_final: 0.3571 (t60) REVERT: F 36 TRP cc_start: 0.4964 (t60) cc_final: 0.4689 (t60) REVERT: F 110 GLN cc_start: 0.3856 (OUTLIER) cc_final: 0.3337 (pm20) REVERT: G 28 TYR cc_start: 0.6536 (OUTLIER) cc_final: 0.3828 (p90) REVERT: G 32 TYR cc_start: 0.7529 (OUTLIER) cc_final: 0.6204 (m-80) REVERT: G 34 MET cc_start: 0.7853 (OUTLIER) cc_final: 0.7157 (tpt) REVERT: G 83 MET cc_start: 0.6933 (ptp) cc_final: 0.6452 (ptp) outliers start: 171 outliers final: 79 residues processed: 623 average time/residue: 1.4564 time to fit residues: 1075.7175 Evaluate side-chains 564 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 461 time to evaluate : 6.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 547 LYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 969 LYS Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1091 ARG Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 1 GLU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 71 ARG Chi-restraints excluded: chain E residue 99 TRP Chi-restraints excluded: chain F residue 95 CYS Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain G residue 28 TYR Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain G residue 116 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 119 optimal weight: 0.8980 chunk 128 optimal weight: 0.4980 chunk 280 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 177 optimal weight: 3.9990 chunk 211 optimal weight: 3.9990 chunk 325 optimal weight: 30.0000 chunk 236 optimal weight: 2.9990 chunk 353 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 320 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 ASN A 658 ASN B 49 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN B1010 GLN C 66 HIS C 121 ASN C 519 HIS C 564 GLN C 960 ASN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.201165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.166405 restraints weight = 52956.985| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 3.50 r_work: 0.3523 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 29091 Z= 0.174 Angle : 0.636 11.088 39687 Z= 0.317 Chirality : 0.046 0.246 4562 Planarity : 0.004 0.055 5055 Dihedral : 6.415 82.650 4697 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.90 % Favored : 93.07 % Rotamer: Outliers : 5.77 % Allowed : 19.29 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.14), residues: 3522 helix: 0.74 (0.21), residues: 673 sheet: -1.16 (0.17), residues: 791 loop : -2.30 (0.13), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP G 47 HIS 0.010 0.001 HIS C 519 PHE 0.034 0.002 PHE C 541 TYR 0.022 0.001 TYR F 94 ARG 0.014 0.001 ARG B 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00380 ( 36) link_NAG-ASN : angle 2.20038 ( 108) hydrogen bonds : bond 0.03646 ( 879) hydrogen bonds : angle 5.24790 ( 2409) SS BOND : bond 0.00408 ( 45) SS BOND : angle 1.61697 ( 90) covalent geometry : bond 0.00404 (29010) covalent geometry : angle 0.62242 (39489) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 481 time to evaluate : 2.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ILE cc_start: 0.8392 (pp) cc_final: 0.8162 (mt) REVERT: A 127 VAL cc_start: 0.8534 (t) cc_final: 0.8310 (m) REVERT: A 128 ILE cc_start: 0.8325 (OUTLIER) cc_final: 0.8038 (mp) REVERT: A 129 LYS cc_start: 0.8525 (mmtt) cc_final: 0.8118 (tppp) REVERT: A 281 GLU cc_start: 0.7802 (pm20) cc_final: 0.7468 (pm20) REVERT: A 393 THR cc_start: 0.8947 (t) cc_final: 0.8247 (t) REVERT: A 394 ASN cc_start: 0.7187 (t0) cc_final: 0.6592 (m-40) REVERT: A 516 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.6776 (tm-30) REVERT: A 517 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7483 (pp) REVERT: A 574 ASP cc_start: 0.8227 (t0) cc_final: 0.7886 (t0) REVERT: A 745 ASP cc_start: 0.7756 (p0) cc_final: 0.7387 (p0) REVERT: A 773 GLU cc_start: 0.7955 (tp30) cc_final: 0.7628 (tp30) REVERT: A 776 LYS cc_start: 0.8798 (ttpt) cc_final: 0.8524 (ttpp) REVERT: A 790 LYS cc_start: 0.8417 (tptt) cc_final: 0.8057 (mmmm) REVERT: A 854 LYS cc_start: 0.8768 (tttm) cc_final: 0.8529 (ttmm) REVERT: A 868 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7976 (mm-30) REVERT: A 990 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7908 (mp0) REVERT: A 1002 GLN cc_start: 0.8387 (tt0) cc_final: 0.8159 (tp40) REVERT: A 1072 GLU cc_start: 0.7957 (pm20) cc_final: 0.7736 (mp0) REVERT: A 1118 ASP cc_start: 0.8075 (t0) cc_final: 0.7854 (t70) REVERT: B 30 ASN cc_start: 0.8016 (t0) cc_final: 0.7601 (t0) REVERT: B 46 SER cc_start: 0.8988 (OUTLIER) cc_final: 0.8720 (p) REVERT: B 52 GLN cc_start: 0.8221 (tm-30) cc_final: 0.7740 (tm-30) REVERT: B 81 ASN cc_start: 0.8173 (OUTLIER) cc_final: 0.7924 (p0) REVERT: B 129 LYS cc_start: 0.8350 (mmmt) cc_final: 0.8030 (mmtt) REVERT: B 177 MET cc_start: 0.7261 (mpp) cc_final: 0.6949 (mpp) REVERT: B 186 ASN cc_start: 0.8089 (p0) cc_final: 0.7626 (p0) REVERT: B 224 GLU cc_start: 0.7375 (mm-30) cc_final: 0.7110 (mm-30) REVERT: B 237 ARG cc_start: 0.8615 (mtp180) cc_final: 0.8297 (mtp-110) REVERT: B 338 PHE cc_start: 0.8115 (OUTLIER) cc_final: 0.7805 (t80) REVERT: B 340 GLU cc_start: 0.7693 (tm-30) cc_final: 0.7123 (tm-30) REVERT: B 501 TYR cc_start: 0.7724 (m-80) cc_final: 0.7481 (m-10) REVERT: B 654 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7323 (mp0) REVERT: B 660 TYR cc_start: 0.8626 (m-80) cc_final: 0.8367 (m-10) REVERT: B 702 GLU cc_start: 0.7304 (tp30) cc_final: 0.7066 (tp30) REVERT: B 762 GLN cc_start: 0.7712 (pp30) cc_final: 0.7384 (pp30) REVERT: B 765 ARG cc_start: 0.8219 (mtm-85) cc_final: 0.7361 (mtm-85) REVERT: B 933 LYS cc_start: 0.8732 (mtpp) cc_final: 0.8458 (mtmm) REVERT: B 995 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.8234 (ttp80) REVERT: B 1031 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7877 (mt-10) REVERT: B 1072 GLU cc_start: 0.8320 (pm20) cc_final: 0.8103 (pm20) REVERT: B 1091 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.7969 (ttp-170) REVERT: B 1107 ARG cc_start: 0.7966 (mpt-90) cc_final: 0.7666 (mtt-85) REVERT: B 1141 LEU cc_start: 0.8031 (tm) cc_final: 0.7567 (tm) REVERT: B 1144 GLU cc_start: 0.7469 (pp20) cc_final: 0.7243 (pp20) REVERT: C 88 ASP cc_start: 0.7240 (m-30) cc_final: 0.7007 (m-30) REVERT: C 170 TYR cc_start: 0.7603 (t80) cc_final: 0.7189 (t80) REVERT: C 239 GLN cc_start: 0.8129 (pt0) cc_final: 0.7848 (tt0) REVERT: C 278 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8478 (ptmm) REVERT: C 324 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7445 (mm-30) REVERT: C 425 LEU cc_start: 0.7114 (OUTLIER) cc_final: 0.6786 (pp) REVERT: C 654 GLU cc_start: 0.7944 (mp0) cc_final: 0.7525 (pm20) REVERT: C 745 ASP cc_start: 0.7261 (m-30) cc_final: 0.6900 (OUTLIER) REVERT: C 751 ASN cc_start: 0.8427 (m-40) cc_final: 0.8164 (m110) REVERT: C 754 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7483 (mm) REVERT: C 779 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.8198 (tm-30) REVERT: C 814 LYS cc_start: 0.8062 (mmtm) cc_final: 0.7500 (mppt) REVERT: C 950 ASP cc_start: 0.7760 (p0) cc_final: 0.7457 (p0) REVERT: C 957 GLN cc_start: 0.8057 (tt0) cc_final: 0.7525 (tt0) REVERT: C 1091 ARG cc_start: 0.8732 (ttm170) cc_final: 0.8482 (ttp-170) REVERT: C 1107 ARG cc_start: 0.8030 (mpp80) cc_final: 0.7766 (mtt90) REVERT: D 18 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7321 (mm) REVERT: D 33 GLU cc_start: 0.7689 (tm-30) cc_final: 0.7412 (tm-30) REVERT: D 82 MET cc_start: 0.7210 (ppp) cc_final: 0.6408 (ppp) REVERT: E 4 LEU cc_start: -0.1226 (OUTLIER) cc_final: -0.2144 (tt) REVERT: E 99 TRP cc_start: 0.4943 (OUTLIER) cc_final: 0.3731 (t60) REVERT: F 36 TRP cc_start: 0.5481 (t60) cc_final: 0.5031 (t60) REVERT: F 82 MET cc_start: 0.7638 (tpt) cc_final: 0.6311 (pp-130) REVERT: F 110 GLN cc_start: 0.4376 (OUTLIER) cc_final: 0.3851 (pm20) REVERT: G 28 TYR cc_start: 0.6640 (OUTLIER) cc_final: 0.3944 (p90) REVERT: G 32 TYR cc_start: 0.7506 (OUTLIER) cc_final: 0.6151 (m-80) REVERT: G 34 MET cc_start: 0.7692 (OUTLIER) cc_final: 0.6892 (tpt) REVERT: G 47 TRP cc_start: 0.7972 (t60) cc_final: 0.7706 (t60) REVERT: G 83 MET cc_start: 0.6933 (ptp) cc_final: 0.6445 (ptp) outliers start: 178 outliers final: 90 residues processed: 615 average time/residue: 1.5141 time to fit residues: 1106.7367 Evaluate side-chains 579 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 469 time to evaluate : 3.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 969 LYS Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1091 ARG Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 1 GLU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 77 MET Chi-restraints excluded: chain E residue 95 CYS Chi-restraints excluded: chain E residue 99 TRP Chi-restraints excluded: chain F residue 95 CYS Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain G residue 28 TYR Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain G residue 116 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 181 optimal weight: 0.6980 chunk 233 optimal weight: 3.9990 chunk 334 optimal weight: 40.0000 chunk 308 optimal weight: 2.9990 chunk 196 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 218 optimal weight: 10.0000 chunk 160 optimal weight: 0.7980 chunk 305 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 ASN A 580 GLN A 641 ASN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN C 30 ASN C 66 HIS C 564 GLN C 762 GLN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.200358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.166586 restraints weight = 52657.764| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 3.00 r_work: 0.3489 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 29091 Z= 0.175 Angle : 0.636 14.928 39687 Z= 0.317 Chirality : 0.046 0.392 4562 Planarity : 0.005 0.081 5055 Dihedral : 6.138 82.923 4687 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.45 % Favored : 93.53 % Rotamer: Outliers : 5.67 % Allowed : 19.91 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.14), residues: 3522 helix: 0.81 (0.21), residues: 681 sheet: -1.02 (0.18), residues: 767 loop : -2.10 (0.13), residues: 2074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 436 HIS 0.004 0.001 HIS B1064 PHE 0.035 0.002 PHE C 541 TYR 0.021 0.001 TYR B1067 ARG 0.010 0.001 ARG B 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00347 ( 36) link_NAG-ASN : angle 2.18970 ( 108) hydrogen bonds : bond 0.03627 ( 879) hydrogen bonds : angle 5.18512 ( 2409) SS BOND : bond 0.00415 ( 45) SS BOND : angle 1.71018 ( 90) covalent geometry : bond 0.00409 (29010) covalent geometry : angle 0.62163 (39489) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 480 time to evaluate : 2.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 VAL cc_start: 0.8497 (t) cc_final: 0.8233 (m) REVERT: A 128 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.8104 (mp) REVERT: A 129 LYS cc_start: 0.8504 (mmtt) cc_final: 0.8135 (tppp) REVERT: A 169 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7640 (tm-30) REVERT: A 393 THR cc_start: 0.8867 (t) cc_final: 0.8190 (t) REVERT: A 394 ASN cc_start: 0.7150 (t0) cc_final: 0.6611 (m-40) REVERT: A 516 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.6635 (tm-30) REVERT: A 517 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7507 (pp) REVERT: A 574 ASP cc_start: 0.8159 (t0) cc_final: 0.7802 (t0) REVERT: A 745 ASP cc_start: 0.7854 (p0) cc_final: 0.7519 (p0) REVERT: A 773 GLU cc_start: 0.7903 (tp30) cc_final: 0.7514 (tp30) REVERT: A 776 LYS cc_start: 0.8746 (ttpt) cc_final: 0.8468 (ttpp) REVERT: A 790 LYS cc_start: 0.8391 (tptt) cc_final: 0.8008 (mmmm) REVERT: A 854 LYS cc_start: 0.8747 (tttm) cc_final: 0.8492 (ttmm) REVERT: A 868 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7921 (mm-30) REVERT: A 990 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7832 (mp0) REVERT: A 1072 GLU cc_start: 0.8022 (pm20) cc_final: 0.7822 (mp0) REVERT: B 52 GLN cc_start: 0.8197 (tm-30) cc_final: 0.7665 (tm-30) REVERT: B 81 ASN cc_start: 0.8194 (OUTLIER) cc_final: 0.7889 (p0) REVERT: B 96 GLU cc_start: 0.7344 (pm20) cc_final: 0.7133 (pm20) REVERT: B 177 MET cc_start: 0.7422 (mpp) cc_final: 0.6940 (mpp) REVERT: B 186 ASN cc_start: 0.8039 (p0) cc_final: 0.6198 (p0) REVERT: B 188 ARG cc_start: 0.8577 (ptp90) cc_final: 0.7931 (mtt-85) REVERT: B 224 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7232 (mm-30) REVERT: B 237 ARG cc_start: 0.8618 (mtp180) cc_final: 0.8344 (mtp-110) REVERT: B 338 PHE cc_start: 0.8270 (OUTLIER) cc_final: 0.8041 (t80) REVERT: B 340 GLU cc_start: 0.7659 (tm-30) cc_final: 0.7086 (tm-30) REVERT: B 571 ASP cc_start: 0.7439 (t0) cc_final: 0.7012 (t0) REVERT: B 588 THR cc_start: 0.8683 (OUTLIER) cc_final: 0.8469 (p) REVERT: B 654 GLU cc_start: 0.7540 (mm-30) cc_final: 0.7318 (mp0) REVERT: B 660 TYR cc_start: 0.8674 (m-80) cc_final: 0.8397 (m-10) REVERT: B 702 GLU cc_start: 0.7311 (tp30) cc_final: 0.7049 (tp30) REVERT: B 725 GLU cc_start: 0.8061 (tt0) cc_final: 0.7834 (tt0) REVERT: B 752 LEU cc_start: 0.8431 (tp) cc_final: 0.8164 (tt) REVERT: B 765 ARG cc_start: 0.8261 (mtm-85) cc_final: 0.7433 (mtm-85) REVERT: B 790 LYS cc_start: 0.8660 (mtmt) cc_final: 0.8407 (mtpp) REVERT: B 933 LYS cc_start: 0.8725 (mtpp) cc_final: 0.8396 (mtmm) REVERT: B 983 ARG cc_start: 0.7858 (ttm-80) cc_final: 0.7574 (mtm110) REVERT: B 995 ARG cc_start: 0.8515 (ttp80) cc_final: 0.8191 (ttp80) REVERT: B 1072 GLU cc_start: 0.8360 (pm20) cc_final: 0.8148 (pm20) REVERT: B 1091 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.7953 (ttp-110) REVERT: B 1107 ARG cc_start: 0.8011 (mpt-90) cc_final: 0.7758 (mtt-85) REVERT: C 88 ASP cc_start: 0.7157 (m-30) cc_final: 0.6916 (m-30) REVERT: C 170 TYR cc_start: 0.7655 (t80) cc_final: 0.7141 (t80) REVERT: C 239 GLN cc_start: 0.8263 (pt0) cc_final: 0.7939 (tt0) REVERT: C 320 VAL cc_start: 0.8740 (OUTLIER) cc_final: 0.8418 (m) REVERT: C 321 GLN cc_start: 0.8509 (mm-40) cc_final: 0.8122 (mm110) REVERT: C 324 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7470 (mm-30) REVERT: C 332 ILE cc_start: 0.7110 (OUTLIER) cc_final: 0.6898 (mt) REVERT: C 425 LEU cc_start: 0.7030 (OUTLIER) cc_final: 0.6709 (pp) REVERT: C 546 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7319 (mt) REVERT: C 654 GLU cc_start: 0.7920 (mp0) cc_final: 0.7537 (pm20) REVERT: C 745 ASP cc_start: 0.7211 (m-30) cc_final: 0.6930 (OUTLIER) REVERT: C 751 ASN cc_start: 0.8429 (m-40) cc_final: 0.8188 (m110) REVERT: C 754 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7508 (mm) REVERT: C 779 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.7929 (tm-30) REVERT: C 814 LYS cc_start: 0.8001 (mmtm) cc_final: 0.7402 (mppt) REVERT: C 856 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8847 (mptt) REVERT: C 918 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7241 (mm-30) REVERT: C 950 ASP cc_start: 0.7745 (p0) cc_final: 0.7421 (p0) REVERT: C 957 GLN cc_start: 0.8186 (tt0) cc_final: 0.7695 (tt0) REVERT: C 1041 ASP cc_start: 0.8102 (t0) cc_final: 0.7550 (t0) REVERT: D 18 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.6912 (mm) REVERT: D 82 MET cc_start: 0.7136 (ppp) cc_final: 0.6093 (ppp) REVERT: D 86 ARG cc_start: 0.7353 (mpp80) cc_final: 0.6885 (mpp80) REVERT: D 88 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7741 (pm20) REVERT: E 4 LEU cc_start: -0.2867 (OUTLIER) cc_final: -0.3485 (tt) REVERT: E 99 TRP cc_start: 0.5053 (OUTLIER) cc_final: 0.4057 (t60) REVERT: F 36 TRP cc_start: 0.5411 (t-100) cc_final: 0.4942 (t60) REVERT: F 82 MET cc_start: 0.7479 (tpt) cc_final: 0.6116 (pp-130) REVERT: F 110 GLN cc_start: 0.4626 (OUTLIER) cc_final: 0.4117 (pm20) REVERT: G 28 TYR cc_start: 0.6261 (OUTLIER) cc_final: 0.3827 (p90) REVERT: G 32 TYR cc_start: 0.7176 (OUTLIER) cc_final: 0.5918 (m-80) REVERT: G 34 MET cc_start: 0.7749 (OUTLIER) cc_final: 0.7019 (tpt) REVERT: G 47 TRP cc_start: 0.8279 (t60) cc_final: 0.7931 (t60) REVERT: G 83 MET cc_start: 0.6987 (ptp) cc_final: 0.6392 (ptp) outliers start: 175 outliers final: 87 residues processed: 614 average time/residue: 1.4020 time to fit residues: 1031.7727 Evaluate side-chains 574 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 463 time to evaluate : 2.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 969 LYS Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1091 ARG Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 1 GLU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 71 ARG Chi-restraints excluded: chain E residue 77 MET Chi-restraints excluded: chain E residue 95 CYS Chi-restraints excluded: chain E residue 99 TRP Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 95 CYS Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain G residue 28 TYR Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain G residue 116 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 267 optimal weight: 3.9990 chunk 240 optimal weight: 30.0000 chunk 44 optimal weight: 0.5980 chunk 144 optimal weight: 6.9990 chunk 181 optimal weight: 0.8980 chunk 153 optimal weight: 0.9980 chunk 155 optimal weight: 0.3980 chunk 196 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 62 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 HIS ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN A 580 GLN A 641 ASN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN B 913 GLN B1010 GLN C 66 HIS C 271 GLN C 564 GLN ** C 992 GLN ** 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 = 0.4171 r_free = 0.4171 target = 0.168582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.129403 restraints weight = 46630.251| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.77 r_work: 0.3408 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29091 Z= 0.133 Angle : 0.638 11.539 39687 Z= 0.316 Chirality : 0.045 0.334 4562 Planarity : 0.005 0.063 5055 Dihedral : 5.900 79.796 4678 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.30 % Favored : 93.67 % Rotamer: Outliers : 5.42 % Allowed : 21.04 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.14), residues: 3522 helix: 1.01 (0.21), residues: 681 sheet: -0.90 (0.18), residues: 778 loop : -1.98 (0.13), residues: 2063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 64 HIS 0.009 0.001 HIS A 205 PHE 0.037 0.001 PHE C 541 TYR 0.019 0.001 TYR B1067 ARG 0.017 0.001 ARG C1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00291 ( 36) link_NAG-ASN : angle 2.22787 ( 108) hydrogen bonds : bond 0.03308 ( 879) hydrogen bonds : angle 5.09332 ( 2409) SS BOND : bond 0.00337 ( 45) SS BOND : angle 1.86064 ( 90) covalent geometry : bond 0.00310 (29010) covalent geometry : angle 0.62283 (39489) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 480 time to evaluate : 4.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.6898 (OUTLIER) cc_final: 0.5942 (mm) REVERT: A 127 VAL cc_start: 0.8569 (t) cc_final: 0.8359 (m) REVERT: A 128 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.8170 (mp) REVERT: A 129 LYS cc_start: 0.8580 (mmtt) cc_final: 0.8267 (tppp) REVERT: A 177 MET cc_start: 0.5952 (OUTLIER) cc_final: 0.5673 (pmm) REVERT: A 393 THR cc_start: 0.8920 (t) cc_final: 0.8292 (t) REVERT: A 394 ASN cc_start: 0.7428 (t0) cc_final: 0.6704 (m-40) REVERT: A 516 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.6827 (tm-30) REVERT: A 517 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7908 (pp) REVERT: A 574 ASP cc_start: 0.8435 (t0) cc_final: 0.8103 (t0) REVERT: A 745 ASP cc_start: 0.8038 (p0) cc_final: 0.7742 (p0) REVERT: A 773 GLU cc_start: 0.8184 (tp30) cc_final: 0.7757 (OUTLIER) REVERT: A 776 LYS cc_start: 0.8812 (ttpt) cc_final: 0.8563 (ttpp) REVERT: A 780 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8240 (tp30) REVERT: A 790 LYS cc_start: 0.8461 (tptt) cc_final: 0.8074 (mmmm) REVERT: A 854 LYS cc_start: 0.8821 (tttm) cc_final: 0.8544 (ttmm) REVERT: A 868 GLU cc_start: 0.8285 (mm-30) cc_final: 0.8017 (mm-30) REVERT: A 921 LYS cc_start: 0.8479 (mmmm) cc_final: 0.8220 (mmmm) REVERT: A 990 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7879 (mp0) REVERT: A 1002 GLN cc_start: 0.8577 (tp40) cc_final: 0.8222 (tp40) REVERT: B 52 GLN cc_start: 0.8348 (tm-30) cc_final: 0.7867 (tm-30) REVERT: B 81 ASN cc_start: 0.8367 (OUTLIER) cc_final: 0.8053 (p0) REVERT: B 177 MET cc_start: 0.7389 (mpp) cc_final: 0.6942 (mpp) REVERT: B 186 ASN cc_start: 0.8119 (p0) cc_final: 0.7365 (p0) REVERT: B 224 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7508 (mm-30) REVERT: B 237 ARG cc_start: 0.8668 (mtp180) cc_final: 0.8413 (mtp-110) REVERT: B 338 PHE cc_start: 0.8264 (OUTLIER) cc_final: 0.8029 (t80) REVERT: B 340 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7275 (tm-30) REVERT: B 501 TYR cc_start: 0.7866 (m-10) cc_final: 0.7467 (m-10) REVERT: B 571 ASP cc_start: 0.7581 (t0) cc_final: 0.7134 (t0) REVERT: B 574 ASP cc_start: 0.8074 (t0) cc_final: 0.7824 (t0) REVERT: B 588 THR cc_start: 0.8762 (OUTLIER) cc_final: 0.8562 (p) REVERT: B 654 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7524 (mp0) REVERT: B 660 TYR cc_start: 0.8745 (m-80) cc_final: 0.8526 (m-10) REVERT: B 725 GLU cc_start: 0.8268 (tt0) cc_final: 0.8060 (tt0) REVERT: B 752 LEU cc_start: 0.8501 (tp) cc_final: 0.8224 (tt) REVERT: B 765 ARG cc_start: 0.8325 (mtm-85) cc_final: 0.7551 (mtm-85) REVERT: B 780 GLU cc_start: 0.8031 (pp20) cc_final: 0.7360 (pm20) REVERT: B 933 LYS cc_start: 0.8770 (mtpp) cc_final: 0.8374 (mtmm) REVERT: B 995 ARG cc_start: 0.8616 (ttp80) cc_final: 0.8238 (ttp80) REVERT: B 1031 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7836 (mt-10) REVERT: B 1072 GLU cc_start: 0.8560 (pm20) cc_final: 0.8335 (pm20) REVERT: B 1091 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.8062 (ttp-110) REVERT: B 1107 ARG cc_start: 0.8162 (mpt-90) cc_final: 0.7885 (mtt-85) REVERT: C 170 TYR cc_start: 0.7800 (t80) cc_final: 0.7212 (t80) REVERT: C 187 LEU cc_start: 0.9155 (tp) cc_final: 0.8902 (tm) REVERT: C 239 GLN cc_start: 0.8477 (pt0) cc_final: 0.8146 (tt0) REVERT: C 320 VAL cc_start: 0.8789 (OUTLIER) cc_final: 0.8492 (m) REVERT: C 321 GLN cc_start: 0.8641 (mm-40) cc_final: 0.8285 (mm110) REVERT: C 324 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7631 (mm-30) REVERT: C 425 LEU cc_start: 0.6603 (OUTLIER) cc_final: 0.6338 (pp) REVERT: C 546 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7466 (mt) REVERT: C 574 ASP cc_start: 0.8001 (t0) cc_final: 0.7767 (t0) REVERT: C 654 GLU cc_start: 0.8098 (mp0) cc_final: 0.7743 (pm20) REVERT: C 745 ASP cc_start: 0.7383 (m-30) cc_final: 0.7037 (OUTLIER) REVERT: C 751 ASN cc_start: 0.8441 (m-40) cc_final: 0.8194 (m110) REVERT: C 754 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7535 (mm) REVERT: C 779 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8048 (tm-30) REVERT: C 814 LYS cc_start: 0.8125 (mmtm) cc_final: 0.7521 (mppt) REVERT: C 918 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7401 (mm-30) REVERT: C 957 GLN cc_start: 0.8289 (tt0) cc_final: 0.7799 (tt0) REVERT: C 1002 GLN cc_start: 0.8548 (tt0) cc_final: 0.8291 (tp40) REVERT: C 1014 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.8568 (ttp80) REVERT: C 1041 ASP cc_start: 0.8314 (t0) cc_final: 0.7753 (t0) REVERT: D 18 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7509 (mm) REVERT: D 82 MET cc_start: 0.7348 (ppp) cc_final: 0.6744 (ppp) REVERT: D 86 ARG cc_start: 0.7427 (mpp80) cc_final: 0.7038 (mpp80) REVERT: E 4 LEU cc_start: -0.4164 (OUTLIER) cc_final: -0.4549 (tt) REVERT: E 99 TRP cc_start: 0.5033 (OUTLIER) cc_final: 0.3691 (t60) REVERT: F 82 MET cc_start: 0.6851 (tpt) cc_final: 0.5816 (pp-130) REVERT: F 89 ASP cc_start: 0.4822 (OUTLIER) cc_final: 0.4507 (m-30) REVERT: F 110 GLN cc_start: 0.3954 (OUTLIER) cc_final: 0.3417 (pm20) REVERT: G 28 TYR cc_start: 0.6532 (OUTLIER) cc_final: 0.3813 (p90) REVERT: G 32 TYR cc_start: 0.7741 (OUTLIER) cc_final: 0.6403 (m-80) REVERT: G 34 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.7443 (tpt) REVERT: G 47 TRP cc_start: 0.8359 (t60) cc_final: 0.8047 (t60) REVERT: G 83 MET cc_start: 0.7063 (ptp) cc_final: 0.6502 (ptp) outliers start: 167 outliers final: 82 residues processed: 605 average time/residue: 1.4057 time to fit residues: 1010.6988 Evaluate side-chains 561 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 455 time to evaluate : 2.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 969 LYS Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1091 ARG Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1014 ARG Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 1 GLU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 71 ARG Chi-restraints excluded: chain E residue 77 MET Chi-restraints excluded: chain E residue 95 CYS Chi-restraints excluded: chain E residue 99 TRP Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain F residue 95 CYS Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain G residue 28 TYR Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain G residue 116 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 168 optimal weight: 0.5980 chunk 235 optimal weight: 9.9990 chunk 56 optimal weight: 0.7980 chunk 282 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 310 optimal weight: 7.9990 chunk 144 optimal weight: 6.9990 chunk 175 optimal weight: 0.8980 chunk 170 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 143 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 HIS ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 641 ASN A 901 GLN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN B 955 ASN C 30 ASN C 66 HIS C 81 ASN C 542 ASN C 564 GLN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.200142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.165463 restraints weight = 52531.667| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 3.23 r_work: 0.3513 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 29091 Z= 0.168 Angle : 0.666 12.472 39687 Z= 0.329 Chirality : 0.046 0.424 4562 Planarity : 0.005 0.067 5055 Dihedral : 5.869 81.325 4670 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.39 % Favored : 93.58 % Rotamer: Outliers : 5.29 % Allowed : 21.53 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.14), residues: 3522 helix: 0.99 (0.21), residues: 685 sheet: -0.79 (0.18), residues: 777 loop : -1.93 (0.13), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP A 436 HIS 0.008 0.001 HIS A 205 PHE 0.038 0.002 PHE C 541 TYR 0.021 0.001 TYR B1067 ARG 0.013 0.001 ARG B 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00417 ( 36) link_NAG-ASN : angle 2.55887 ( 108) hydrogen bonds : bond 0.03518 ( 879) hydrogen bonds : angle 5.13009 ( 2409) SS BOND : bond 0.00392 ( 45) SS BOND : angle 1.95961 ( 90) covalent geometry : bond 0.00392 (29010) covalent geometry : angle 0.64735 (39489) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 480 time to evaluate : 3.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ASN cc_start: 0.4117 (OUTLIER) cc_final: 0.3865 (p0) REVERT: A 127 VAL cc_start: 0.8497 (t) cc_final: 0.8263 (m) REVERT: A 128 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.7980 (mp) REVERT: A 129 LYS cc_start: 0.8457 (mmtt) cc_final: 0.8036 (tppp) REVERT: A 188 ARG cc_start: 0.8209 (mtt90) cc_final: 0.8007 (mtt90) REVERT: A 364 ASP cc_start: 0.8102 (t0) cc_final: 0.7860 (OUTLIER) REVERT: A 393 THR cc_start: 0.8739 (t) cc_final: 0.7996 (t) REVERT: A 394 ASN cc_start: 0.6964 (t0) cc_final: 0.6131 (m-40) REVERT: A 516 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6162 (tm-30) REVERT: A 517 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7255 (pp) REVERT: A 574 ASP cc_start: 0.8258 (t0) cc_final: 0.7873 (t0) REVERT: A 745 ASP cc_start: 0.7945 (p0) cc_final: 0.7663 (p0) REVERT: A 773 GLU cc_start: 0.7993 (tp30) cc_final: 0.7526 (OUTLIER) REVERT: A 776 LYS cc_start: 0.8751 (ttpt) cc_final: 0.8483 (ttpp) REVERT: A 790 LYS cc_start: 0.8371 (tptt) cc_final: 0.8011 (mmmm) REVERT: A 854 LYS cc_start: 0.8722 (tttm) cc_final: 0.8455 (ttmm) REVERT: A 868 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7848 (mm-30) REVERT: A 921 LYS cc_start: 0.8319 (mmmm) cc_final: 0.8081 (mmmm) REVERT: A 990 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7770 (mp0) REVERT: B 52 GLN cc_start: 0.8211 (tm-30) cc_final: 0.7699 (tm-30) REVERT: B 104 TRP cc_start: 0.8395 (m-90) cc_final: 0.8113 (m-90) REVERT: B 127 VAL cc_start: 0.8763 (OUTLIER) cc_final: 0.8384 (m) REVERT: B 177 MET cc_start: 0.7289 (mpp) cc_final: 0.6957 (mpp) REVERT: B 186 ASN cc_start: 0.8046 (p0) cc_final: 0.6190 (p0) REVERT: B 188 ARG cc_start: 0.8581 (ptp90) cc_final: 0.7883 (mtt-85) REVERT: B 224 GLU cc_start: 0.7558 (mm-30) cc_final: 0.7189 (mm-30) REVERT: B 237 ARG cc_start: 0.8591 (mtp180) cc_final: 0.8264 (mtp-110) REVERT: B 338 PHE cc_start: 0.8320 (OUTLIER) cc_final: 0.8077 (t80) REVERT: B 340 GLU cc_start: 0.7698 (tm-30) cc_final: 0.7135 (tm-30) REVERT: B 546 LEU cc_start: 0.8228 (tp) cc_final: 0.8009 (tt) REVERT: B 571 ASP cc_start: 0.7466 (t0) cc_final: 0.6993 (t0) REVERT: B 574 ASP cc_start: 0.7896 (t0) cc_final: 0.7573 (t0) REVERT: B 588 THR cc_start: 0.8687 (OUTLIER) cc_final: 0.8484 (p) REVERT: B 654 GLU cc_start: 0.7479 (mm-30) cc_final: 0.7239 (mp0) REVERT: B 660 TYR cc_start: 0.8633 (m-80) cc_final: 0.8346 (m-10) REVERT: B 780 GLU cc_start: 0.7941 (pp20) cc_final: 0.7213 (pm20) REVERT: B 790 LYS cc_start: 0.8664 (mtmt) cc_final: 0.8429 (mtmm) REVERT: B 868 GLU cc_start: 0.7847 (mp0) cc_final: 0.7622 (mm-30) REVERT: B 933 LYS cc_start: 0.8733 (mtpp) cc_final: 0.8355 (mtmm) REVERT: B 995 ARG cc_start: 0.8467 (ttp80) cc_final: 0.8032 (ttp80) REVERT: B 1031 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7743 (mt-10) REVERT: B 1072 GLU cc_start: 0.8400 (pm20) cc_final: 0.8187 (pm20) REVERT: B 1091 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.8010 (ttp-170) REVERT: B 1107 ARG cc_start: 0.8072 (mpt-90) cc_final: 0.7848 (mtt-85) REVERT: C 102 ARG cc_start: 0.8046 (mmm-85) cc_final: 0.7789 (mmm-85) REVERT: C 170 TYR cc_start: 0.7676 (t80) cc_final: 0.6895 (t80) REVERT: C 187 LEU cc_start: 0.9079 (tp) cc_final: 0.8817 (tm) REVERT: C 239 GLN cc_start: 0.8267 (pt0) cc_final: 0.7932 (tt0) REVERT: C 320 VAL cc_start: 0.8700 (OUTLIER) cc_final: 0.8390 (m) REVERT: C 324 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7441 (mm-30) REVERT: C 328 ARG cc_start: 0.7589 (tpp-160) cc_final: 0.7374 (tpp-160) REVERT: C 425 LEU cc_start: 0.7154 (OUTLIER) cc_final: 0.6823 (pp) REVERT: C 546 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7560 (mt) REVERT: C 574 ASP cc_start: 0.7772 (t0) cc_final: 0.7435 (t0) REVERT: C 654 GLU cc_start: 0.7874 (mp0) cc_final: 0.7496 (pm20) REVERT: C 745 ASP cc_start: 0.7208 (m-30) cc_final: 0.6904 (OUTLIER) REVERT: C 751 ASN cc_start: 0.8490 (m-40) cc_final: 0.8216 (m110) REVERT: C 754 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7489 (mm) REVERT: C 773 GLU cc_start: 0.8197 (tt0) cc_final: 0.7995 (tt0) REVERT: C 779 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.7971 (tm-30) REVERT: C 814 LYS cc_start: 0.8028 (mmtm) cc_final: 0.7446 (mppt) REVERT: C 825 LYS cc_start: 0.8987 (mtmm) cc_final: 0.8765 (mtpp) REVERT: C 918 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7255 (mm-30) REVERT: C 976 VAL cc_start: 0.8610 (t) cc_final: 0.8314 (m) REVERT: C 990 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7550 (mp0) REVERT: C 1002 GLN cc_start: 0.8287 (tt0) cc_final: 0.7970 (tp40) REVERT: C 1014 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8309 (ttp80) REVERT: C 1041 ASP cc_start: 0.8130 (t0) cc_final: 0.7580 (t0) REVERT: C 1107 ARG cc_start: 0.8039 (mtm180) cc_final: 0.7794 (mmt90) REVERT: D 18 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7443 (mm) REVERT: D 56 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.8042 (tpp80) REVERT: D 82 MET cc_start: 0.7122 (ppp) cc_final: 0.6470 (ppp) REVERT: D 86 ARG cc_start: 0.7520 (mpp80) cc_final: 0.7088 (mpp80) REVERT: E 4 LEU cc_start: -0.1425 (OUTLIER) cc_final: -0.2441 (tt) REVERT: E 99 TRP cc_start: 0.4935 (OUTLIER) cc_final: 0.3914 (t60) REVERT: F 82 MET cc_start: 0.7212 (tpt) cc_final: 0.5928 (pp-130) REVERT: F 89 ASP cc_start: 0.4502 (OUTLIER) cc_final: 0.4240 (m-30) REVERT: F 110 GLN cc_start: 0.4718 (OUTLIER) cc_final: 0.4243 (pm20) REVERT: G 28 TYR cc_start: 0.6434 (OUTLIER) cc_final: 0.5619 (p90) REVERT: G 34 MET cc_start: 0.7510 (OUTLIER) cc_final: 0.6788 (tpt) REVERT: G 47 TRP cc_start: 0.7921 (t60) cc_final: 0.7604 (t60) REVERT: G 83 MET cc_start: 0.7045 (ptp) cc_final: 0.6467 (ptp) outliers start: 163 outliers final: 91 residues processed: 605 average time/residue: 1.4157 time to fit residues: 1017.5067 Evaluate side-chains 576 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 463 time to evaluate : 2.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 969 LYS Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1091 ARG Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1014 ARG Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 1 GLU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 71 ARG Chi-restraints excluded: chain E residue 77 MET Chi-restraints excluded: chain E residue 95 CYS Chi-restraints excluded: chain E residue 99 TRP Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain F residue 95 CYS Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain G residue 28 TYR Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain G residue 116 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 109 optimal weight: 0.8980 chunk 96 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 287 optimal weight: 0.5980 chunk 247 optimal weight: 4.9990 chunk 245 optimal weight: 20.0000 chunk 211 optimal weight: 0.0980 chunk 45 optimal weight: 0.7980 chunk 90 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 ASN A 205 HIS ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 641 ASN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN C 66 HIS ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.200955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.165576 restraints weight = 52694.994| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 3.53 r_work: 0.3550 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29091 Z= 0.132 Angle : 0.659 15.137 39687 Z= 0.325 Chirality : 0.045 0.225 4562 Planarity : 0.005 0.063 5055 Dihedral : 5.815 80.858 4667 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.05 % Favored : 93.92 % Rotamer: Outliers : 4.47 % Allowed : 22.47 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.14), residues: 3522 helix: 1.00 (0.21), residues: 697 sheet: -0.63 (0.19), residues: 769 loop : -1.87 (0.13), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 436 HIS 0.006 0.001 HIS A 205 PHE 0.039 0.001 PHE C 541 TYR 0.019 0.001 TYR B1067 ARG 0.012 0.001 ARG B 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00311 ( 36) link_NAG-ASN : angle 2.10949 ( 108) hydrogen bonds : bond 0.03317 ( 879) hydrogen bonds : angle 5.11198 ( 2409) SS BOND : bond 0.00344 ( 45) SS BOND : angle 1.76173 ( 90) covalent geometry : bond 0.00310 (29010) covalent geometry : angle 0.64638 (39489) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 471 time to evaluate : 2.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ASN cc_start: 0.4008 (OUTLIER) cc_final: 0.3756 (p0) REVERT: A 66 HIS cc_start: 0.7586 (t-170) cc_final: 0.7297 (t-90) REVERT: A 102 ARG cc_start: 0.6688 (mtp180) cc_final: 0.6461 (mtp180) REVERT: A 117 LEU cc_start: 0.6686 (OUTLIER) cc_final: 0.5720 (mm) REVERT: A 127 VAL cc_start: 0.8459 (t) cc_final: 0.8181 (m) REVERT: A 128 ILE cc_start: 0.8313 (mt) cc_final: 0.8099 (mp) REVERT: A 129 LYS cc_start: 0.8480 (mmtt) cc_final: 0.8121 (tppp) REVERT: A 364 ASP cc_start: 0.8167 (t0) cc_final: 0.7881 (OUTLIER) REVERT: A 393 THR cc_start: 0.8780 (t) cc_final: 0.7942 (t) REVERT: A 394 ASN cc_start: 0.7088 (t0) cc_final: 0.6156 (m-40) REVERT: A 516 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.6156 (tm-30) REVERT: A 517 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7507 (pp) REVERT: A 574 ASP cc_start: 0.8165 (t0) cc_final: 0.7806 (t0) REVERT: A 745 ASP cc_start: 0.7935 (p0) cc_final: 0.7677 (p0) REVERT: A 773 GLU cc_start: 0.7927 (tp30) cc_final: 0.7470 (OUTLIER) REVERT: A 776 LYS cc_start: 0.8771 (ttpt) cc_final: 0.8536 (ttpp) REVERT: A 790 LYS cc_start: 0.8373 (tptt) cc_final: 0.8002 (mmmm) REVERT: A 854 LYS cc_start: 0.8728 (tttm) cc_final: 0.8476 (ttmm) REVERT: A 868 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7883 (mm-30) REVERT: A 921 LYS cc_start: 0.8348 (mmmm) cc_final: 0.8109 (mmmm) REVERT: A 988 GLU cc_start: 0.7838 (pp20) cc_final: 0.7523 (tm-30) REVERT: A 990 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7675 (mp0) REVERT: A 1002 GLN cc_start: 0.8318 (tp40) cc_final: 0.7896 (tp40) REVERT: B 52 GLN cc_start: 0.8206 (tm-30) cc_final: 0.7688 (tm-30) REVERT: B 81 ASN cc_start: 0.8130 (OUTLIER) cc_final: 0.7792 (p0) REVERT: B 104 TRP cc_start: 0.8369 (m-90) cc_final: 0.8000 (m-90) REVERT: B 117 LEU cc_start: 0.7856 (tt) cc_final: 0.7650 (tm) REVERT: B 126 VAL cc_start: 0.8307 (OUTLIER) cc_final: 0.7982 (m) REVERT: B 127 VAL cc_start: 0.8725 (OUTLIER) cc_final: 0.8292 (m) REVERT: B 164 ASN cc_start: 0.7483 (t0) cc_final: 0.7163 (t0) REVERT: B 177 MET cc_start: 0.7294 (mpp) cc_final: 0.6959 (mpp) REVERT: B 186 ASN cc_start: 0.8006 (p0) cc_final: 0.7201 (p0) REVERT: B 224 GLU cc_start: 0.7511 (mm-30) cc_final: 0.7202 (mm-30) REVERT: B 237 ARG cc_start: 0.8552 (mtp180) cc_final: 0.8271 (mtp-110) REVERT: B 340 GLU cc_start: 0.7681 (tm-30) cc_final: 0.7087 (tm-30) REVERT: B 501 TYR cc_start: 0.7702 (m-10) cc_final: 0.7341 (m-10) REVERT: B 546 LEU cc_start: 0.8159 (tp) cc_final: 0.7937 (tt) REVERT: B 571 ASP cc_start: 0.7452 (t0) cc_final: 0.6991 (t0) REVERT: B 574 ASP cc_start: 0.7874 (t0) cc_final: 0.7566 (t0) REVERT: B 588 THR cc_start: 0.8703 (OUTLIER) cc_final: 0.8500 (p) REVERT: B 654 GLU cc_start: 0.7451 (mm-30) cc_final: 0.7192 (mp0) REVERT: B 660 TYR cc_start: 0.8659 (m-80) cc_final: 0.8345 (m-10) REVERT: B 790 LYS cc_start: 0.8670 (mtmt) cc_final: 0.8318 (mtmm) REVERT: B 868 GLU cc_start: 0.7881 (mp0) cc_final: 0.7578 (mm-30) REVERT: B 933 LYS cc_start: 0.8646 (mtpp) cc_final: 0.8229 (mtmm) REVERT: B 995 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.8041 (ttp80) REVERT: B 1014 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.8029 (mtp180) REVERT: B 1072 GLU cc_start: 0.8360 (pm20) cc_final: 0.8135 (pm20) REVERT: B 1107 ARG cc_start: 0.8010 (mpt-90) cc_final: 0.7790 (mtt-85) REVERT: C 132 GLU cc_start: 0.6177 (pm20) cc_final: 0.5759 (pm20) REVERT: C 170 TYR cc_start: 0.7506 (t80) cc_final: 0.6695 (t80) REVERT: C 187 LEU cc_start: 0.9131 (tp) cc_final: 0.8920 (tm) REVERT: C 239 GLN cc_start: 0.8177 (pt0) cc_final: 0.7868 (tt0) REVERT: C 320 VAL cc_start: 0.8733 (OUTLIER) cc_final: 0.8440 (m) REVERT: C 324 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7548 (mm-30) REVERT: C 574 ASP cc_start: 0.7751 (t0) cc_final: 0.7517 (t0) REVERT: C 654 GLU cc_start: 0.7894 (mp0) cc_final: 0.7489 (pm20) REVERT: C 745 ASP cc_start: 0.7177 (m-30) cc_final: 0.6908 (OUTLIER) REVERT: C 751 ASN cc_start: 0.8403 (m-40) cc_final: 0.8181 (m110) REVERT: C 754 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7538 (mm) REVERT: C 814 LYS cc_start: 0.7893 (mmtm) cc_final: 0.7267 (mppt) REVERT: C 918 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7218 (mm-30) REVERT: C 976 VAL cc_start: 0.8790 (t) cc_final: 0.8516 (m) REVERT: C 990 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7481 (mp0) REVERT: C 1002 GLN cc_start: 0.8364 (tt0) cc_final: 0.8094 (tp40) REVERT: C 1014 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8348 (ttp80) REVERT: C 1041 ASP cc_start: 0.8107 (t0) cc_final: 0.7577 (t0) REVERT: C 1107 ARG cc_start: 0.8136 (mtm180) cc_final: 0.7910 (mmt90) REVERT: D 18 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7268 (mm) REVERT: D 82 MET cc_start: 0.7210 (ppp) cc_final: 0.6504 (ppp) REVERT: D 86 ARG cc_start: 0.7341 (mpp80) cc_final: 0.6843 (mpp80) REVERT: E 4 LEU cc_start: -0.0505 (OUTLIER) cc_final: -0.1746 (tt) REVERT: E 99 TRP cc_start: 0.4710 (OUTLIER) cc_final: 0.3860 (t60) REVERT: F 82 MET cc_start: 0.7134 (tpt) cc_final: 0.5855 (pp-130) REVERT: F 89 ASP cc_start: 0.4456 (OUTLIER) cc_final: 0.4218 (m-30) REVERT: F 110 GLN cc_start: 0.4544 (OUTLIER) cc_final: 0.4097 (pm20) REVERT: G 28 TYR cc_start: 0.6439 (OUTLIER) cc_final: 0.4070 (p90) REVERT: G 32 TYR cc_start: 0.7260 (OUTLIER) cc_final: 0.6030 (m-80) REVERT: G 34 MET cc_start: 0.7592 (OUTLIER) cc_final: 0.6930 (tpt) REVERT: G 47 TRP cc_start: 0.8260 (t60) cc_final: 0.7980 (t60) REVERT: G 83 MET cc_start: 0.7009 (ptp) cc_final: 0.6409 (ptp) outliers start: 138 outliers final: 87 residues processed: 576 average time/residue: 1.3152 time to fit residues: 893.5799 Evaluate side-chains 557 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 450 time to evaluate : 2.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 969 LYS Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 1014 ARG Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1014 ARG Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 1 GLU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 71 ARG Chi-restraints excluded: chain E residue 77 MET Chi-restraints excluded: chain E residue 95 CYS Chi-restraints excluded: chain E residue 99 TRP Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain F residue 95 CYS Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain G residue 28 TYR Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain G residue 116 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 186 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 274 optimal weight: 1.9990 chunk 157 optimal weight: 0.3980 chunk 211 optimal weight: 0.1980 chunk 51 optimal weight: 3.9990 chunk 139 optimal weight: 0.7980 chunk 346 optimal weight: 9.9990 chunk 161 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 341 optimal weight: 10.0000 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 HIS A 580 GLN A 641 ASN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN B 935 GLN B 949 GLN B 955 ASN C 66 HIS C 564 GLN C 992 GLN G 39 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.200839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.166186 restraints weight = 52578.669| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 3.63 r_work: 0.3539 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29091 Z= 0.139 Angle : 0.673 14.819 39687 Z= 0.331 Chirality : 0.046 0.191 4562 Planarity : 0.005 0.062 5055 Dihedral : 5.722 80.512 4664 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.22 % Favored : 93.75 % Rotamer: Outliers : 3.76 % Allowed : 23.93 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.14), residues: 3522 helix: 1.04 (0.21), residues: 691 sheet: -0.60 (0.18), residues: 781 loop : -1.82 (0.13), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 436 HIS 0.006 0.001 HIS A 205 PHE 0.037 0.001 PHE C 541 TYR 0.021 0.001 TYR C 266 ARG 0.013 0.001 ARG C 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00337 ( 36) link_NAG-ASN : angle 2.04338 ( 108) hydrogen bonds : bond 0.03321 ( 879) hydrogen bonds : angle 5.08813 ( 2409) SS BOND : bond 0.00368 ( 45) SS BOND : angle 1.70675 ( 90) covalent geometry : bond 0.00328 (29010) covalent geometry : angle 0.66090 (39489) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 461 time to evaluate : 2.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ASN cc_start: 0.4200 (OUTLIER) cc_final: 0.3951 (p0) REVERT: A 66 HIS cc_start: 0.7664 (t-170) cc_final: 0.7312 (t-90) REVERT: A 102 ARG cc_start: 0.6634 (mtp180) cc_final: 0.6381 (mtp180) REVERT: A 117 LEU cc_start: 0.6653 (OUTLIER) cc_final: 0.5602 (mm) REVERT: A 127 VAL cc_start: 0.8451 (t) cc_final: 0.8151 (m) REVERT: A 128 ILE cc_start: 0.8267 (mt) cc_final: 0.8016 (mp) REVERT: A 129 LYS cc_start: 0.8474 (mmtt) cc_final: 0.8062 (tppp) REVERT: A 364 ASP cc_start: 0.8136 (t0) cc_final: 0.7837 (OUTLIER) REVERT: A 393 THR cc_start: 0.8397 (t) cc_final: 0.7371 (t) REVERT: A 394 ASN cc_start: 0.6263 (t0) cc_final: 0.5444 (m-40) REVERT: A 516 GLU cc_start: 0.6552 (OUTLIER) cc_final: 0.5467 (tm-30) REVERT: A 517 LEU cc_start: 0.7209 (OUTLIER) cc_final: 0.6884 (pp) REVERT: A 574 ASP cc_start: 0.8163 (t0) cc_final: 0.7859 (t0) REVERT: A 745 ASP cc_start: 0.8001 (p0) cc_final: 0.7762 (p0) REVERT: A 773 GLU cc_start: 0.7957 (tp30) cc_final: 0.7509 (OUTLIER) REVERT: A 776 LYS cc_start: 0.8800 (ttpt) cc_final: 0.8560 (ttpp) REVERT: A 790 LYS cc_start: 0.8399 (tptt) cc_final: 0.8031 (mmmm) REVERT: A 854 LYS cc_start: 0.8768 (tttm) cc_final: 0.8491 (ttmm) REVERT: A 868 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7892 (mm-30) REVERT: A 921 LYS cc_start: 0.8365 (mmmm) cc_final: 0.8120 (mmmm) REVERT: A 988 GLU cc_start: 0.7832 (pp20) cc_final: 0.7558 (tm-30) REVERT: A 990 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7728 (mp0) REVERT: A 1002 GLN cc_start: 0.8411 (tp40) cc_final: 0.7994 (tp40) REVERT: B 52 GLN cc_start: 0.8229 (tm-30) cc_final: 0.7709 (tm-30) REVERT: B 81 ASN cc_start: 0.8153 (OUTLIER) cc_final: 0.7810 (p0) REVERT: B 96 GLU cc_start: 0.7937 (pm20) cc_final: 0.7335 (pm20) REVERT: B 104 TRP cc_start: 0.8390 (m-90) cc_final: 0.7985 (m-90) REVERT: B 126 VAL cc_start: 0.8247 (OUTLIER) cc_final: 0.7887 (m) REVERT: B 127 VAL cc_start: 0.8756 (OUTLIER) cc_final: 0.8383 (m) REVERT: B 164 ASN cc_start: 0.7499 (t0) cc_final: 0.7204 (t0) REVERT: B 177 MET cc_start: 0.7235 (tpp) cc_final: 0.6884 (mpp) REVERT: B 186 ASN cc_start: 0.7998 (p0) cc_final: 0.6510 (p0) REVERT: B 188 ARG cc_start: 0.8608 (ptp90) cc_final: 0.7939 (mtt-85) REVERT: B 224 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7229 (mm-30) REVERT: B 237 ARG cc_start: 0.8583 (mtp180) cc_final: 0.8277 (mtp-110) REVERT: B 324 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7645 (mp0) REVERT: B 340 GLU cc_start: 0.7709 (tm-30) cc_final: 0.7099 (tm-30) REVERT: B 501 TYR cc_start: 0.7753 (m-10) cc_final: 0.7372 (m-10) REVERT: B 546 LEU cc_start: 0.8160 (tp) cc_final: 0.7928 (tt) REVERT: B 571 ASP cc_start: 0.7502 (t0) cc_final: 0.7067 (t0) REVERT: B 574 ASP cc_start: 0.7920 (t0) cc_final: 0.7612 (t0) REVERT: B 588 THR cc_start: 0.8711 (OUTLIER) cc_final: 0.8510 (p) REVERT: B 654 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7254 (mp0) REVERT: B 660 TYR cc_start: 0.8657 (m-80) cc_final: 0.8361 (m-10) REVERT: B 780 GLU cc_start: 0.7905 (pp20) cc_final: 0.7443 (pm20) REVERT: B 790 LYS cc_start: 0.8702 (mtmt) cc_final: 0.8455 (mtmm) REVERT: B 868 GLU cc_start: 0.7921 (mp0) cc_final: 0.7595 (mm-30) REVERT: B 933 LYS cc_start: 0.8655 (mtpp) cc_final: 0.8415 (mtmm) REVERT: B 995 ARG cc_start: 0.8435 (ttp80) cc_final: 0.7983 (ttp80) REVERT: B 1014 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.8058 (mtp180) REVERT: B 1072 GLU cc_start: 0.8430 (pm20) cc_final: 0.8209 (pm20) REVERT: C 237 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.7489 (mtp85) REVERT: C 239 GLN cc_start: 0.8324 (pt0) cc_final: 0.7974 (tt0) REVERT: C 320 VAL cc_start: 0.8729 (OUTLIER) cc_final: 0.8446 (m) REVERT: C 324 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7501 (mm-30) REVERT: C 558 LYS cc_start: 0.8404 (pttm) cc_final: 0.7903 (pttm) REVERT: C 574 ASP cc_start: 0.7712 (t0) cc_final: 0.7385 (t0) REVERT: C 654 GLU cc_start: 0.7902 (mp0) cc_final: 0.7461 (pm20) REVERT: C 702 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7659 (tm-30) REVERT: C 745 ASP cc_start: 0.7249 (m-30) cc_final: 0.6945 (p0) REVERT: C 751 ASN cc_start: 0.8436 (m-40) cc_final: 0.8202 (m110) REVERT: C 754 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7581 (mm) REVERT: C 814 LYS cc_start: 0.8024 (mmtm) cc_final: 0.7415 (mppt) REVERT: C 872 GLN cc_start: 0.8406 (tt0) cc_final: 0.8091 (mt0) REVERT: C 964 LYS cc_start: 0.8624 (tmtt) cc_final: 0.8312 (tmtt) REVERT: C 976 VAL cc_start: 0.8736 (t) cc_final: 0.8472 (m) REVERT: C 1002 GLN cc_start: 0.8434 (tt0) cc_final: 0.8133 (tp40) REVERT: C 1014 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.8318 (ttp80) REVERT: C 1041 ASP cc_start: 0.8165 (t0) cc_final: 0.7619 (t0) REVERT: D 18 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7216 (mm) REVERT: D 82 MET cc_start: 0.7246 (ppp) cc_final: 0.6517 (ppp) REVERT: D 86 ARG cc_start: 0.7313 (mpp80) cc_final: 0.6872 (mpp80) REVERT: E 4 LEU cc_start: -0.2525 (OUTLIER) cc_final: -0.3359 (tt) REVERT: E 99 TRP cc_start: 0.5012 (OUTLIER) cc_final: 0.3927 (t60) REVERT: F 82 MET cc_start: 0.7067 (tpt) cc_final: 0.5755 (pp-130) REVERT: F 89 ASP cc_start: 0.4353 (OUTLIER) cc_final: 0.4133 (m-30) REVERT: F 110 GLN cc_start: 0.4459 (OUTLIER) cc_final: 0.3959 (pm20) REVERT: G 28 TYR cc_start: 0.6019 (OUTLIER) cc_final: 0.5300 (p90) REVERT: G 34 MET cc_start: 0.7173 (OUTLIER) cc_final: 0.6578 (tpt) REVERT: G 47 TRP cc_start: 0.8013 (t60) cc_final: 0.7762 (t60) REVERT: G 83 MET cc_start: 0.7007 (ptp) cc_final: 0.6370 (ptp) outliers start: 116 outliers final: 82 residues processed: 551 average time/residue: 1.3065 time to fit residues: 850.2334 Evaluate side-chains 556 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 455 time to evaluate : 3.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 969 LYS Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1014 ARG Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1014 ARG Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 1 GLU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 71 ARG Chi-restraints excluded: chain E residue 77 MET Chi-restraints excluded: chain E residue 95 CYS Chi-restraints excluded: chain E residue 99 TRP Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain F residue 95 CYS Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain G residue 28 TYR Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain G residue 116 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 216 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 157 optimal weight: 0.5980 chunk 210 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 71 optimal weight: 0.1980 chunk 246 optimal weight: 0.3980 chunk 18 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 269 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS A 580 GLN A 641 ASN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN B 913 GLN B 949 GLN B 955 ASN C 66 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.201276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.166675 restraints weight = 52837.273| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 3.24 r_work: 0.3536 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29091 Z= 0.130 Angle : 0.678 13.919 39687 Z= 0.333 Chirality : 0.046 0.259 4562 Planarity : 0.005 0.079 5055 Dihedral : 5.733 80.107 4664 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.65 % Favored : 94.32 % Rotamer: Outliers : 3.63 % Allowed : 24.22 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.14), residues: 3522 helix: 1.10 (0.21), residues: 691 sheet: -0.52 (0.19), residues: 766 loop : -1.78 (0.13), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP A 436 HIS 0.005 0.001 HIS A 205 PHE 0.040 0.001 PHE C 541 TYR 0.020 0.001 TYR C 266 ARG 0.013 0.001 ARG C 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00388 ( 36) link_NAG-ASN : angle 2.20120 ( 108) hydrogen bonds : bond 0.03217 ( 879) hydrogen bonds : angle 5.06103 ( 2409) SS BOND : bond 0.00345 ( 45) SS BOND : angle 1.60713 ( 90) covalent geometry : bond 0.00307 (29010) covalent geometry : angle 0.66541 (39489) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 472 time to evaluate : 3.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ASN cc_start: 0.3904 (OUTLIER) cc_final: 0.3662 (p0) REVERT: A 66 HIS cc_start: 0.7731 (t-170) cc_final: 0.7419 (t-90) REVERT: A 96 GLU cc_start: 0.6939 (mt-10) cc_final: 0.6430 (mt-10) REVERT: A 102 ARG cc_start: 0.6594 (mtp180) cc_final: 0.6346 (mtp180) REVERT: A 117 LEU cc_start: 0.6701 (OUTLIER) cc_final: 0.5746 (mm) REVERT: A 127 VAL cc_start: 0.8439 (t) cc_final: 0.8157 (m) REVERT: A 128 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.8057 (mp) REVERT: A 129 LYS cc_start: 0.8486 (mmtt) cc_final: 0.8168 (tppp) REVERT: A 393 THR cc_start: 0.8865 (t) cc_final: 0.8119 (t) REVERT: A 394 ASN cc_start: 0.7224 (t0) cc_final: 0.6405 (m-40) REVERT: A 516 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.6517 (tm-30) REVERT: A 517 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7458 (pp) REVERT: A 574 ASP cc_start: 0.8072 (t0) cc_final: 0.7835 (t0) REVERT: A 773 GLU cc_start: 0.8044 (tp30) cc_final: 0.7611 (tp30) REVERT: A 776 LYS cc_start: 0.8747 (ttpt) cc_final: 0.8500 (ttpp) REVERT: A 790 LYS cc_start: 0.8414 (tptt) cc_final: 0.8032 (mmmm) REVERT: A 854 LYS cc_start: 0.8765 (tttm) cc_final: 0.8518 (ttmm) REVERT: A 868 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7876 (mm-30) REVERT: A 921 LYS cc_start: 0.8350 (mmmm) cc_final: 0.8137 (mmmm) REVERT: A 990 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7787 (mp0) REVERT: A 1002 GLN cc_start: 0.8280 (tp40) cc_final: 0.7853 (tp40) REVERT: B 52 GLN cc_start: 0.8271 (tm-30) cc_final: 0.7771 (tm-30) REVERT: B 81 ASN cc_start: 0.8084 (OUTLIER) cc_final: 0.7720 (p0) REVERT: B 96 GLU cc_start: 0.7888 (pm20) cc_final: 0.7398 (pm20) REVERT: B 104 TRP cc_start: 0.8351 (m-90) cc_final: 0.7634 (m-90) REVERT: B 126 VAL cc_start: 0.8300 (OUTLIER) cc_final: 0.7935 (m) REVERT: B 127 VAL cc_start: 0.8750 (OUTLIER) cc_final: 0.8356 (m) REVERT: B 164 ASN cc_start: 0.7569 (t0) cc_final: 0.7320 (t0) REVERT: B 177 MET cc_start: 0.6622 (tpp) cc_final: 0.6359 (mpp) REVERT: B 186 ASN cc_start: 0.7982 (p0) cc_final: 0.7355 (p0) REVERT: B 188 ARG cc_start: 0.8589 (ptp90) cc_final: 0.8146 (mtt-85) REVERT: B 224 GLU cc_start: 0.7397 (mm-30) cc_final: 0.7121 (mm-30) REVERT: B 237 ARG cc_start: 0.8563 (mtp180) cc_final: 0.8273 (mtp-110) REVERT: B 340 GLU cc_start: 0.7668 (tm-30) cc_final: 0.7084 (tm-30) REVERT: B 501 TYR cc_start: 0.7628 (m-10) cc_final: 0.7360 (m-10) REVERT: B 546 LEU cc_start: 0.8085 (tp) cc_final: 0.7880 (tt) REVERT: B 571 ASP cc_start: 0.7491 (t0) cc_final: 0.7062 (t0) REVERT: B 574 ASP cc_start: 0.7918 (t0) cc_final: 0.7572 (t0) REVERT: B 588 THR cc_start: 0.8687 (OUTLIER) cc_final: 0.8482 (p) REVERT: B 654 GLU cc_start: 0.7463 (mm-30) cc_final: 0.7224 (mp0) REVERT: B 933 LYS cc_start: 0.8697 (mtpp) cc_final: 0.8455 (mtmm) REVERT: B 995 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.8070 (ttp80) REVERT: B 1014 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.7982 (mtp180) REVERT: B 1072 GLU cc_start: 0.8366 (pm20) cc_final: 0.8166 (pm20) REVERT: C 237 ARG cc_start: 0.7656 (OUTLIER) cc_final: 0.7422 (mtp85) REVERT: C 239 GLN cc_start: 0.8091 (pt0) cc_final: 0.7834 (tt0) REVERT: C 319 ARG cc_start: 0.7795 (ptp90) cc_final: 0.7591 (ttp-170) REVERT: C 320 VAL cc_start: 0.8547 (OUTLIER) cc_final: 0.8274 (m) REVERT: C 324 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7471 (mm-30) REVERT: C 558 LYS cc_start: 0.8441 (pttm) cc_final: 0.7943 (pttm) REVERT: C 574 ASP cc_start: 0.7814 (t0) cc_final: 0.7333 (t0) REVERT: C 745 ASP cc_start: 0.7225 (m-30) cc_final: 0.6908 (p0) REVERT: C 751 ASN cc_start: 0.8487 (m-40) cc_final: 0.8225 (m110) REVERT: C 754 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7565 (mm) REVERT: C 814 LYS cc_start: 0.8104 (mmtm) cc_final: 0.7508 (mppt) REVERT: C 902 MET cc_start: 0.8596 (mmm) cc_final: 0.8350 (mmt) REVERT: C 976 VAL cc_start: 0.8708 (t) cc_final: 0.8466 (m) REVERT: C 1002 GLN cc_start: 0.8318 (tt0) cc_final: 0.8064 (tp40) REVERT: C 1014 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.8302 (ttp80) REVERT: C 1041 ASP cc_start: 0.8212 (t0) cc_final: 0.7663 (t0) REVERT: D 18 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7349 (mm) REVERT: D 33 GLU cc_start: 0.7716 (tm-30) cc_final: 0.7452 (tm-30) REVERT: D 34 MET cc_start: 0.8188 (ttm) cc_final: 0.7577 (ttm) REVERT: D 82 MET cc_start: 0.7115 (ppp) cc_final: 0.6479 (ppp) REVERT: D 86 ARG cc_start: 0.7480 (mpp80) cc_final: 0.7084 (mpp80) REVERT: E 4 LEU cc_start: -0.1946 (OUTLIER) cc_final: -0.2851 (tt) REVERT: E 99 TRP cc_start: 0.4857 (OUTLIER) cc_final: 0.3928 (t60) REVERT: F 82 MET cc_start: 0.6903 (tpt) cc_final: 0.5762 (pp-130) REVERT: F 89 ASP cc_start: 0.4516 (OUTLIER) cc_final: 0.4266 (m-30) REVERT: F 110 GLN cc_start: 0.4402 (OUTLIER) cc_final: 0.3910 (pm20) REVERT: G 28 TYR cc_start: 0.6642 (OUTLIER) cc_final: 0.5827 (p90) REVERT: G 34 MET cc_start: 0.7572 (OUTLIER) cc_final: 0.6856 (tpt) REVERT: G 47 TRP cc_start: 0.8004 (t60) cc_final: 0.7748 (t60) REVERT: G 83 MET cc_start: 0.7018 (ptp) cc_final: 0.6463 (ptp) outliers start: 112 outliers final: 74 residues processed: 553 average time/residue: 1.3298 time to fit residues: 867.7055 Evaluate side-chains 558 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 461 time to evaluate : 2.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 969 LYS Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 1014 ARG Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1014 ARG Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 1 GLU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 71 ARG Chi-restraints excluded: chain E residue 77 MET Chi-restraints excluded: chain E residue 95 CYS Chi-restraints excluded: chain E residue 99 TRP Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain F residue 95 CYS Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain G residue 28 TYR Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain G residue 116 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 209 optimal weight: 0.0070 chunk 230 optimal weight: 0.0980 chunk 341 optimal weight: 0.9990 chunk 344 optimal weight: 10.0000 chunk 329 optimal weight: 5.9990 chunk 156 optimal weight: 3.9990 chunk 177 optimal weight: 0.5980 chunk 250 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 overall best weight: 0.4600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS A 580 GLN A 641 ASN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN B 955 ASN C 66 HIS C 564 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.201418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.167204 restraints weight = 52792.499| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 3.40 r_work: 0.3533 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29091 Z= 0.127 Angle : 0.683 14.392 39687 Z= 0.336 Chirality : 0.046 0.234 4562 Planarity : 0.005 0.088 5055 Dihedral : 5.646 80.005 4662 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.68 % Favored : 94.29 % Rotamer: Outliers : 3.66 % Allowed : 24.38 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.14), residues: 3522 helix: 1.10 (0.21), residues: 697 sheet: -0.51 (0.19), residues: 753 loop : -1.70 (0.13), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP A 436 HIS 0.005 0.001 HIS A 205 PHE 0.040 0.001 PHE C 541 TYR 0.033 0.001 TYR A 160 ARG 0.020 0.001 ARG B 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00320 ( 36) link_NAG-ASN : angle 2.15607 ( 108) hydrogen bonds : bond 0.03158 ( 879) hydrogen bonds : angle 5.02277 ( 2409) SS BOND : bond 0.00312 ( 45) SS BOND : angle 1.54411 ( 90) covalent geometry : bond 0.00299 (29010) covalent geometry : angle 0.67146 (39489) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 34221.47 seconds wall clock time: 596 minutes 22.53 seconds (35782.53 seconds total)