Starting phenix.real_space_refine on Mon Jul 6 00:44:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wos_32657/07_2026/7wos_32657.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wos_32657/07_2026/7wos_32657.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wos_32657/07_2026/7wos_32657.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wos_32657/07_2026/7wos_32657.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7wos_32657/07_2026/7wos_32657.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wos_32657/07_2026/7wos_32657.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wos_32657/07_2026/7wos_32657.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wos_32657/07_2026/7wos_32657.map" } resolution = 3.91 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.028 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 141 5.16 5 C 19987 2.51 5 N 5212 2.21 5 O 6071 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31411 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 8047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8047 Classifications: {'peptide': 1033} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 58, 'TRANS': 974} 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: {'ARG:plan': 2, 'GLU:plan': 6, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "B" Number of atoms: 8043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8043 Classifications: {'peptide': 1033} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 58, 'TRANS': 974} Chain breaks: 7 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 6, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "C" Number of atoms: 7989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 7989 Classifications: {'peptide': 1026} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 56, 'TRANS': 969} Chain breaks: 7 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 6, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "D" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1754 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 225} Chain breaks: 1 Chain: "E" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1765 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "F" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1754 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 225} Chain breaks: 1 Chain: "G" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1765 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 5.94, per 1000 atoms: 0.19 Number of scatterers: 31411 At special positions: 0 Unit cell: (146.832, 169.176, 202.16, 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 141 16.00 O 6071 8.00 N 5212 7.00 C 19987 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=47, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.01 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 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 90 " distance=2.03 Simple disulfide: pdb=" SG CYS D 148 " - pdb=" SG CYS D 221 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS E 146 " - pdb=" SG CYS E 220 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 90 " distance=2.03 Simple disulfide: pdb=" SG CYS F 148 " - pdb=" SG CYS F 221 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 89 " distance=2.03 Simple disulfide: pdb=" SG CYS G 146 " - pdb=" SG CYS G 220 " 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 709 " " NAG A1302 " - " ASN A 717 " " NAG A1303 " - " ASN A 801 " " NAG A1304 " - " ASN A1098 " " NAG A1305 " - " ASN A1134 " " NAG B1301 " - " ASN B 165 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 331 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B 717 " " NAG B1307 " - " ASN B 801 " " NAG B1308 " - " ASN B1098 " " NAG B1309 " - " ASN B1134 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 709 " " NAG C1304 " - " ASN C 717 " " NAG C1305 " - " ASN C 801 " " NAG C1306 " - " ASN C1098 " " NAG C1307 " - " ASN C1134 " Time building additional restraints: 2.37 Conformation dependent library (CDL) restraints added in 1.3 seconds 7940 Ramachandran restraints generated. 3970 Oldfield, 0 Emsley, 3970 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7450 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 63 sheets defined 17.4% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 367 through 371 removed outlier: 4.051A pdb=" N ASN A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.545A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 444 through 448 removed outlier: 3.810A pdb=" N GLY A 447 " --> pdb=" O LYS A 444 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN A 448 " --> pdb=" O VAL A 445 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 444 through 448' Processing helix chain 'A' and resid 746 through 757 removed outlier: 3.721A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 783 removed outlier: 3.744A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 848 through 855 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.093A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 removed outlier: 3.646A pdb=" N GLY A 908 " --> pdb=" O TYR A 904 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY A 910 " --> pdb=" O PHE A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 929 Processing helix chain 'A' and resid 930 through 941 removed outlier: 3.547A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.619A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 983 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.408A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 4.042A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 336 through 341 removed outlier: 4.133A pdb=" N ASP B 339 " --> pdb=" O CYS B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 370 Processing helix chain 'B' and resid 383 through 388 removed outlier: 3.825A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 756 Processing helix chain 'B' and resid 761 through 782 removed outlier: 3.711A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 848 through 857 Processing helix chain 'B' and resid 866 through 883 Processing helix chain 'B' and resid 897 through 907 removed outlier: 3.740A pdb=" N ASN B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 939 removed outlier: 4.436A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.525A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 983 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.238A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 366 through 370 Processing helix chain 'C' and resid 383 through 388 removed outlier: 3.854A pdb=" N ASN C 388 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.556A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 747 through 755 removed outlier: 3.543A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 778 removed outlier: 3.574A pdb=" N ARG C 765 " --> pdb=" O THR C 761 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 823 Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 907 removed outlier: 3.632A pdb=" N ALA C 903 " --> pdb=" O PRO C 899 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG C 905 " --> pdb=" O GLN C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 938 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.913A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU C 959 " --> pdb=" O ASN C 955 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU C 962 " --> pdb=" O ALA C 958 " (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 983 removed outlier: 3.524A pdb=" N ASP C 979 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE C 980 " --> pdb=" O LEU C 977 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N PHE C 981 " --> pdb=" O ASN C 978 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER C 982 " --> pdb=" O ASP C 979 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG C 983 " --> pdb=" O ILE C 980 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 976 through 983' Processing helix chain 'C' and resid 985 through 993 removed outlier: 4.423A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 1033 removed outlier: 3.577A pdb=" N GLY C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.737A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 84 Processing helix chain 'E' and resid 152 through 156 removed outlier: 3.516A pdb=" N HIS E 156 " --> pdb=" O PHE E 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 84 Processing helix chain 'G' and resid 152 through 156 removed outlier: 3.526A pdb=" N HIS G 156 " --> pdb=" O PHE G 153 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 29 removed outlier: 3.643A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.888A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.619A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU A 117 " --> pdb=" O PHE A 106 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 90 through 93 removed outlier: 7.576A pdb=" N ILE A 201 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER A 203 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU A 224 " --> pdb=" O SER A 203 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 128 through 129 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.903A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AA9, first strand: chain 'A' and resid 376 through 377 removed outlier: 3.939A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 565 through 566 removed outlier: 8.084A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.326A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB4, first strand: chain 'A' and resid 712 through 722 removed outlier: 6.709A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 725 through 728 Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 735 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1121 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 31 removed outlier: 3.635A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) 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 48 through 55 removed outlier: 3.971A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AC4, first strand: chain 'B' and resid 89 through 94 removed outlier: 3.873A pdb=" N LEU B 229 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE B 201 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL B 227 " --> pdb=" O ILE B 201 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N SER B 203 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 120 through 122 Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.657A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 325 through 326 removed outlier: 3.705A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 356 through 358 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.611A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.840A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 712 through 718 removed outlier: 7.114A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 721 through 728 removed outlier: 7.094A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 734 through 735 removed outlier: 3.589A pdb=" N THR B 859 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 788 through 789 removed outlier: 5.480A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD7, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.866A pdb=" N LYS C 278 " --> pdb=" O ASP C 287 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AD9, first strand: chain 'C' and resid 93 through 96 removed outlier: 4.008A pdb=" N SER C 94 " --> pdb=" O ARG C 188 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU C 96 " --> pdb=" O ASN C 186 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN C 186 " --> pdb=" O GLU C 96 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 192 through 194 removed outlier: 7.463A pdb=" N ILE C 201 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU C 224 " --> pdb=" O SER C 203 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.752A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 325 through 326 removed outlier: 3.664A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 356 through 358 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.611A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 660 removed outlier: 5.777A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.730A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 712 through 713 Processing sheet with id=AE8, first strand: chain 'C' and resid 717 through 718 Processing sheet with id=AE9, first strand: chain 'C' and resid 721 through 727 removed outlier: 3.766A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.615A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 3.875A pdb=" N SER C1123 " --> pdb=" O ALA C1087 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF4, first strand: chain 'D' and resid 47 through 50 removed outlier: 6.048A pdb=" N LEU D 48 " --> pdb=" O GLN D 39 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLN D 39 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE D 50 " --> pdb=" O TRP D 37 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 66 through 69 removed outlier: 3.806A pdb=" N SER D 67 " --> pdb=" O SER D 74 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 172 through 176 removed outlier: 6.039A pdb=" N TRP D 173 " --> pdb=" O ARG D 164 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ARG D 164 " --> pdb=" O TRP D 173 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 21 through 23 Processing sheet with id=AF8, first strand: chain 'E' and resid 46 through 49 removed outlier: 5.023A pdb=" N LEU E 47 " --> pdb=" O GLN E 38 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N GLN E 38 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASN E 97 " --> pdb=" O ASP E 93 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 46 through 49 removed outlier: 5.023A pdb=" N LEU E 47 " --> pdb=" O GLN E 38 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N GLN E 38 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR E 87 " --> pdb=" O THR E 104 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 130 through 131 removed outlier: 3.512A pdb=" N SER E 131 " --> pdb=" O SER E 145 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 182 through 184 removed outlier: 6.616A pdb=" N TRP E 160 " --> pdb=" O VAL E 172 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N VAL E 174 " --> pdb=" O MET E 158 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N MET E 158 " --> pdb=" O VAL E 174 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 47 through 50 removed outlier: 3.536A pdb=" N LYS F 47 " --> pdb=" O GLN F 39 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N TRP F 37 " --> pdb=" O MET F 49 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 66 through 69 removed outlier: 3.758A pdb=" N SER F 67 " --> pdb=" O SER F 74 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 172 through 176 removed outlier: 6.021A pdb=" N TRP F 173 " --> pdb=" O ARG F 164 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ARG F 164 " --> pdb=" O TRP F 173 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 4 through 5 removed outlier: 4.085A pdb=" N VAL G 18 " --> pdb=" O ILE G 76 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE G 76 " --> pdb=" O VAL G 18 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 46 through 49 removed outlier: 4.974A pdb=" N LEU G 47 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N GLN G 38 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASN G 97 " --> pdb=" O ASP G 93 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 130 through 131 Processing sheet with id=AG9, first strand: chain 'G' and resid 182 through 184 removed outlier: 3.571A pdb=" N TYR G 183 " --> pdb=" O VAL G 174 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N TRP G 160 " --> pdb=" O VAL G 172 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N VAL G 174 " --> pdb=" O MET G 158 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N MET G 158 " --> pdb=" O VAL G 174 " (cutoff:3.500A) 859 hydrogen bonds defined for protein. 2274 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: 6.59 Time building geometry restraints manager: 3.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5659 1.33 - 1.45: 8826 1.45 - 1.58: 17480 1.58 - 1.70: 0 1.70 - 1.82: 182 Bond restraints: 32147 Sorted by residual: bond pdb=" N CYS A 291 " pdb=" CA CYS A 291 " ideal model delta sigma weight residual 1.457 1.394 0.063 1.06e-02 8.90e+03 3.49e+01 bond pdb=" CA ASN C 801 " pdb=" C ASN C 801 " ideal model delta sigma weight residual 1.528 1.466 0.062 1.18e-02 7.18e+03 2.73e+01 bond pdb=" CA ASN B1134 " pdb=" C ASN B1134 " ideal model delta sigma weight residual 1.524 1.460 0.064 1.23e-02 6.61e+03 2.72e+01 bond pdb=" N ASN B 282 " pdb=" CA ASN B 282 " ideal model delta sigma weight residual 1.459 1.401 0.058 1.20e-02 6.94e+03 2.35e+01 bond pdb=" CA ASN B 801 " pdb=" C ASN B 801 " ideal model delta sigma weight residual 1.523 1.464 0.058 1.23e-02 6.61e+03 2.24e+01 ... (remaining 32142 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 42918 1.61 - 3.22: 694 3.22 - 4.82: 105 4.82 - 6.43: 22 6.43 - 8.04: 11 Bond angle restraints: 43750 Sorted by residual: angle pdb=" N ASN B 282 " pdb=" CA ASN B 282 " pdb=" C ASN B 282 " ideal model delta sigma weight residual 111.24 103.20 8.04 1.29e+00 6.01e-01 3.88e+01 angle pdb=" N ASN A1134 " pdb=" CA ASN A1134 " pdb=" C ASN A1134 " ideal model delta sigma weight residual 110.55 103.69 6.86 1.35e+00 5.49e-01 2.58e+01 angle pdb=" N ASN C1134 " pdb=" CA ASN C1134 " pdb=" C ASN C1134 " ideal model delta sigma weight residual 110.46 103.93 6.53 1.48e+00 4.57e-01 1.95e+01 angle pdb=" N ASN B1134 " pdb=" CA ASN B1134 " pdb=" C ASN B1134 " ideal model delta sigma weight residual 108.73 102.06 6.67 1.63e+00 3.76e-01 1.68e+01 angle pdb=" N VAL C1128 " pdb=" CA VAL C1128 " pdb=" C VAL C1128 " ideal model delta sigma weight residual 113.53 109.62 3.91 9.80e-01 1.04e+00 1.59e+01 ... (remaining 43745 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.70: 18007 16.70 - 33.41: 739 33.41 - 50.11: 129 50.11 - 66.82: 25 66.82 - 83.52: 4 Dihedral angle restraints: 18904 sinusoidal: 7256 harmonic: 11648 Sorted by residual: dihedral pdb=" CA SER A 708 " pdb=" C SER A 708 " pdb=" N ASN A 709 " pdb=" CA ASN A 709 " ideal model delta harmonic sigma weight residual 180.00 155.64 24.36 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" N CYS A 291 " pdb=" C CYS A 291 " pdb=" CA CYS A 291 " pdb=" CB CYS A 291 " ideal model delta harmonic sigma weight residual 122.80 111.71 11.09 0 2.50e+00 1.60e-01 1.97e+01 dihedral pdb=" CA ASN A 709 " pdb=" C ASN A 709 " pdb=" N ASN A 710 " pdb=" CA ASN A 710 " ideal model delta harmonic sigma weight residual 180.00 161.51 18.49 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 18901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 4458 0.072 - 0.143: 493 0.143 - 0.215: 7 0.215 - 0.287: 3 0.287 - 0.358: 1 Chirality restraints: 4962 Sorted by residual: chirality pdb=" C1 NAG C1307 " pdb=" ND2 ASN C1134 " pdb=" C2 NAG C1307 " pdb=" O5 NAG C1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" C1 NAG B1305 " pdb=" ND2 ASN B 709 " pdb=" C2 NAG B1305 " pdb=" O5 NAG B1305 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 4959 not shown) Planarity restraints: 5675 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1304 " 0.355 2.00e-02 2.50e+03 3.05e-01 1.16e+03 pdb=" C7 NAG A1304 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG A1304 " 0.104 2.00e-02 2.50e+03 pdb=" N2 NAG A1304 " -0.542 2.00e-02 2.50e+03 pdb=" O7 NAG A1304 " 0.166 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1306 " 0.351 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C7 NAG C1306 " -0.081 2.00e-02 2.50e+03 pdb=" C8 NAG C1306 " 0.114 2.00e-02 2.50e+03 pdb=" N2 NAG C1306 " -0.539 2.00e-02 2.50e+03 pdb=" O7 NAG C1306 " 0.155 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1301 " 0.347 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG B1301 " -0.079 2.00e-02 2.50e+03 pdb=" C8 NAG B1301 " 0.122 2.00e-02 2.50e+03 pdb=" N2 NAG B1301 " -0.533 2.00e-02 2.50e+03 pdb=" O7 NAG B1301 " 0.144 2.00e-02 2.50e+03 ... (remaining 5672 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2929 2.75 - 3.29: 31325 3.29 - 3.82: 51377 3.82 - 4.36: 58627 4.36 - 4.90: 101717 Nonbonded interactions: 245975 Sorted by model distance: nonbonded pdb=" OE1 GLN B 52 " pdb=" OG1 THR B 274 " model vdw 2.210 3.040 nonbonded pdb=" OG1 THR B 719 " pdb=" O VAL B1068 " model vdw 2.212 3.040 nonbonded pdb=" OG SER F 91 " pdb=" OE1 GLN F 227 " model vdw 2.215 3.040 nonbonded pdb=" OG SER C 735 " pdb=" OG1 THR C 859 " model vdw 2.219 3.040 nonbonded pdb=" OG SER D 91 " pdb=" OE1 GLN D 227 " model vdw 2.222 3.040 ... (remaining 245970 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 243 or resid 262 through 528 or (resid 529 and \ (name N or name CA or name C or name O or name CB )) or resid 530 through 1305)) \ selection = (chain 'B' and (resid 26 through 243 or resid 262 through 1305)) selection = (chain 'C' and resid 26 through 1305) } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'E' selection = chain 'G' } 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 group one per residue 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: 2.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 26.080 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 32215 Z= 0.202 Angle : 0.531 8.039 43907 Z= 0.289 Chirality : 0.042 0.358 4962 Planarity : 0.013 0.305 5654 Dihedral : 9.045 83.522 11313 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.98 % Favored : 92.90 % Rotamer: Outliers : 5.30 % Allowed : 8.10 % Favored : 86.60 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.97 (0.11), residues: 3970 helix: -0.55 (0.20), residues: 658 sheet: -2.37 (0.16), residues: 778 loop : -3.54 (0.10), residues: 2534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1014 TYR 0.010 0.001 TYR A1067 PHE 0.010 0.001 PHE A 375 TRP 0.007 0.001 TRP E 98 HIS 0.001 0.000 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.20 (32147) covalent geometry : angle 0.51846 / 0.29 (43750) SS BOND : bond 0.00342 / 0.18 ( 47) SS BOND : angle 0.68829 / 0.34 ( 94) hydrogen bonds : bond 0.14003 / 8.84 ( 851) hydrogen bonds : angle 6.33162 / 4.42 ( 2274) link_NAG-ASN : bond 0.00822 / 0.56 ( 21) link_NAG-ASN : angle 2.97903 / 1.82 ( 63) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7940 Ramachandran restraints generated. 3970 Oldfield, 0 Emsley, 3970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7940 Ramachandran restraints generated. 3970 Oldfield, 0 Emsley, 3970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1113 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 931 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.8886 (t) cc_final: 0.8671 (t) REVERT: A 61 ASN cc_start: 0.7321 (m-40) cc_final: 0.6834 (p0) REVERT: A 92 PHE cc_start: 0.8210 (t80) cc_final: 0.7852 (t80) REVERT: A 104 TRP cc_start: 0.6816 (m-90) cc_final: 0.6500 (m-10) REVERT: A 117 LEU cc_start: 0.7729 (mt) cc_final: 0.7479 (mt) REVERT: A 128 ILE cc_start: 0.8680 (mp) cc_final: 0.7919 (mm) REVERT: A 130 VAL cc_start: 0.7856 (OUTLIER) cc_final: 0.7468 (t) REVERT: A 135 PHE cc_start: 0.6728 (OUTLIER) cc_final: 0.6521 (p90) REVERT: A 168 PHE cc_start: 0.7526 (t80) cc_final: 0.6864 (t80) REVERT: A 192 PHE cc_start: 0.7551 (m-10) cc_final: 0.7209 (m-10) REVERT: A 193 LYS cc_start: 0.7328 (mtmt) cc_final: 0.6995 (ptpt) REVERT: A 235 ILE cc_start: 0.8885 (mt) cc_final: 0.8253 (tp) REVERT: A 265 TYR cc_start: 0.7736 (p90) cc_final: 0.7499 (p90) REVERT: A 276 LEU cc_start: 0.8655 (tp) cc_final: 0.8371 (tt) REVERT: A 278 LYS cc_start: 0.8654 (ttmt) cc_final: 0.8294 (tttp) REVERT: A 293 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8640 (mp) REVERT: A 300 LYS cc_start: 0.7961 (mtmt) cc_final: 0.7604 (mtmm) REVERT: A 326 ILE cc_start: 0.7922 (mt) cc_final: 0.7304 (mm) REVERT: A 557 LYS cc_start: 0.7986 (mmtm) cc_final: 0.7668 (mmtm) REVERT: A 559 PHE cc_start: 0.7177 (m-80) cc_final: 0.6909 (m-80) REVERT: A 587 ILE cc_start: 0.8508 (mt) cc_final: 0.8285 (tp) REVERT: A 591 SER cc_start: 0.7315 (p) cc_final: 0.6867 (m) REVERT: A 602 THR cc_start: 0.8172 (m) cc_final: 0.7779 (p) REVERT: A 619 GLU cc_start: 0.7035 (mt-10) cc_final: 0.6739 (mt-10) REVERT: A 644 GLN cc_start: 0.7720 (tp40) cc_final: 0.7441 (tp40) REVERT: A 664 ILE cc_start: 0.8769 (mt) cc_final: 0.8562 (mm) REVERT: A 666 ILE cc_start: 0.9223 (mt) cc_final: 0.8963 (mt) REVERT: A 697 MET cc_start: 0.7545 (ptm) cc_final: 0.6130 (ptm) REVERT: A 707 TYR cc_start: 0.7948 (t80) cc_final: 0.7545 (t80) REVERT: A 710 ASN cc_start: 0.7662 (p0) cc_final: 0.7456 (p0) REVERT: A 725 GLU cc_start: 0.7790 (tt0) cc_final: 0.6952 (tt0) REVERT: A 732 THR cc_start: 0.9171 (OUTLIER) cc_final: 0.8953 (p) REVERT: A 737 ASP cc_start: 0.7221 (t0) cc_final: 0.6396 (t0) REVERT: A 741 TYR cc_start: 0.7354 (t80) cc_final: 0.6842 (t80) REVERT: A 742 ILE cc_start: 0.7987 (mm) cc_final: 0.7635 (tp) REVERT: A 765 ARG cc_start: 0.7566 (ttp-170) cc_final: 0.7276 (ptm160) REVERT: A 768 THR cc_start: 0.8419 (m) cc_final: 0.8176 (p) REVERT: A 821 LEU cc_start: 0.8710 (tp) cc_final: 0.7949 (tp) REVERT: A 858 LEU cc_start: 0.8530 (mt) cc_final: 0.8318 (mp) REVERT: A 905 ARG cc_start: 0.8254 (mtt-85) cc_final: 0.6980 (mmt180) REVERT: A 914 ASN cc_start: 0.7494 (p0) cc_final: 0.6296 (p0) REVERT: A 927 PHE cc_start: 0.8288 (t80) cc_final: 0.7526 (t80) REVERT: A 949 GLN cc_start: 0.8195 (mm110) cc_final: 0.7303 (mm-40) REVERT: A 953 ASN cc_start: 0.7601 (m-40) cc_final: 0.7248 (m-40) REVERT: A 964 LYS cc_start: 0.8521 (tmtm) cc_final: 0.7997 (tmtm) REVERT: A 977 LEU cc_start: 0.8812 (mp) cc_final: 0.7385 (mm) REVERT: A 993 ILE cc_start: 0.7799 (tp) cc_final: 0.7527 (tp) REVERT: A 1002 GLN cc_start: 0.7846 (tp-100) cc_final: 0.7575 (tp40) REVERT: A 1028 LYS cc_start: 0.8541 (ttmm) cc_final: 0.7806 (tttt) REVERT: A 1103 PHE cc_start: 0.7897 (m-80) cc_final: 0.7607 (m-80) REVERT: A 1118 ASP cc_start: 0.7398 (t70) cc_final: 0.7060 (t0) REVERT: A 1138 TYR cc_start: 0.6983 (t80) cc_final: 0.6719 (t80) REVERT: B 41 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8332 (mttt) REVERT: B 43 PHE cc_start: 0.8420 (t80) cc_final: 0.8105 (t80) REVERT: B 44 ARG cc_start: 0.8184 (mtt90) cc_final: 0.7660 (mtt180) REVERT: B 55 PHE cc_start: 0.7680 (m-80) cc_final: 0.7454 (m-80) REVERT: B 92 PHE cc_start: 0.8310 (t80) cc_final: 0.8027 (t80) REVERT: B 104 TRP cc_start: 0.7156 (m-90) cc_final: 0.6810 (m-90) REVERT: B 168 PHE cc_start: 0.8029 (t80) cc_final: 0.7118 (t80) REVERT: B 187 LEU cc_start: 0.8648 (tp) cc_final: 0.8427 (tp) REVERT: B 200 LYS cc_start: 0.8734 (mttt) cc_final: 0.8244 (mtmt) REVERT: B 203 SER cc_start: 0.8252 (p) cc_final: 0.7904 (p) REVERT: B 228 ASP cc_start: 0.6643 (t70) cc_final: 0.6034 (t0) REVERT: B 237 ARG cc_start: 0.7894 (ttm110) cc_final: 0.7678 (mtp85) REVERT: B 241 LEU cc_start: 0.6070 (pt) cc_final: 0.5438 (pp) REVERT: B 271 GLN cc_start: 0.7789 (mt0) cc_final: 0.7473 (mp-120) REVERT: B 275 PHE cc_start: 0.7439 (m-80) cc_final: 0.7183 (m-80) REVERT: B 278 LYS cc_start: 0.8752 (ttmp) cc_final: 0.8309 (ttmm) REVERT: B 281 GLU cc_start: 0.7265 (pp20) cc_final: 0.7035 (pp20) REVERT: B 297 SER cc_start: 0.7730 (m) cc_final: 0.7223 (p) REVERT: B 298 GLU cc_start: 0.7711 (tt0) cc_final: 0.7341 (tt0) REVERT: B 307 THR cc_start: 0.7967 (m) cc_final: 0.7647 (p) REVERT: B 342 PHE cc_start: 0.8021 (m-80) cc_final: 0.7728 (m-10) REVERT: B 433 VAL cc_start: 0.8793 (p) cc_final: 0.8530 (p) REVERT: B 584 ILE cc_start: 0.8030 (OUTLIER) cc_final: 0.7657 (tt) REVERT: B 585 LEU cc_start: 0.8274 (mt) cc_final: 0.8061 (mp) REVERT: B 610 VAL cc_start: 0.8375 (t) cc_final: 0.8122 (m) REVERT: B 619 GLU cc_start: 0.7707 (tt0) cc_final: 0.7320 (tt0) REVERT: B 641 ASN cc_start: 0.6771 (m-40) cc_final: 0.6128 (t0) REVERT: B 731 MET cc_start: 0.8155 (ttt) cc_final: 0.7909 (ttt) REVERT: B 796 TYR cc_start: 0.7664 (t80) cc_final: 0.7171 (t80) REVERT: B 824 ASN cc_start: 0.8608 (m-40) cc_final: 0.8378 (m110) REVERT: B 868 GLU cc_start: 0.7676 (tp30) cc_final: 0.7457 (tp30) REVERT: B 869 MET cc_start: 0.8399 (mtt) cc_final: 0.8168 (mtm) REVERT: B 894 LEU cc_start: 0.8314 (mt) cc_final: 0.7714 (mt) REVERT: B 900 MET cc_start: 0.8027 (mtp) cc_final: 0.7787 (mtm) REVERT: B 905 ARG cc_start: 0.7860 (mtt-85) cc_final: 0.7516 (mtt-85) REVERT: B 914 ASN cc_start: 0.8498 (p0) cc_final: 0.8260 (p0) REVERT: B 921 LYS cc_start: 0.8402 (mmmt) cc_final: 0.8134 (mmmm) REVERT: B 922 LEU cc_start: 0.8736 (tp) cc_final: 0.8446 (tp) REVERT: B 929 SER cc_start: 0.8624 (m) cc_final: 0.8284 (p) REVERT: B 933 LYS cc_start: 0.8619 (mtmt) cc_final: 0.8139 (mtmm) REVERT: B 962 LEU cc_start: 0.8883 (tp) cc_final: 0.8629 (tp) REVERT: B 977 LEU cc_start: 0.7461 (mp) cc_final: 0.7210 (mp) REVERT: B 1081 ILE cc_start: 0.8811 (pt) cc_final: 0.8489 (mm) REVERT: B 1086 LYS cc_start: 0.7425 (mmmm) cc_final: 0.7118 (mppt) REVERT: B 1111 GLU cc_start: 0.7626 (tt0) cc_final: 0.7142 (tt0) REVERT: B 1113 GLN cc_start: 0.7905 (mt0) cc_final: 0.7639 (mp-120) REVERT: B 1118 ASP cc_start: 0.7037 (t70) cc_final: 0.6613 (t0) REVERT: C 43 PHE cc_start: 0.7894 (t80) cc_final: 0.7682 (t80) REVERT: C 66 HIS cc_start: 0.6756 (OUTLIER) cc_final: 0.6518 (t70) REVERT: C 117 LEU cc_start: 0.7397 (tp) cc_final: 0.6998 (mt) REVERT: C 127 VAL cc_start: 0.7221 (OUTLIER) cc_final: 0.6879 (m) REVERT: C 170 TYR cc_start: 0.7640 (t80) cc_final: 0.7430 (t80) REVERT: C 223 LEU cc_start: 0.7454 (mt) cc_final: 0.7149 (mm) REVERT: C 269 TYR cc_start: 0.6923 (m-10) cc_final: 0.6552 (m-80) REVERT: C 287 ASP cc_start: 0.7148 (p0) cc_final: 0.6878 (p0) REVERT: C 294 ASP cc_start: 0.8117 (p0) cc_final: 0.7760 (p0) REVERT: C 297 SER cc_start: 0.8216 (m) cc_final: 0.7743 (p) REVERT: C 298 GLU cc_start: 0.8078 (tt0) cc_final: 0.7404 (tp30) REVERT: C 300 LYS cc_start: 0.8968 (mttt) cc_final: 0.8723 (mtpt) REVERT: C 306 PHE cc_start: 0.7649 (m-80) cc_final: 0.7166 (m-80) REVERT: C 310 LYS cc_start: 0.8726 (ttpp) cc_final: 0.8452 (ttpp) REVERT: C 326 ILE cc_start: 0.8722 (mp) cc_final: 0.8239 (mp) REVERT: C 375 PHE cc_start: 0.7416 (m-10) cc_final: 0.7042 (m-10) REVERT: C 387 LEU cc_start: 0.8716 (tp) cc_final: 0.8258 (tp) REVERT: C 406 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7551 (mt-10) REVERT: C 425 LEU cc_start: 0.9041 (mp) cc_final: 0.8657 (tp) REVERT: C 433 VAL cc_start: 0.8488 (p) cc_final: 0.8057 (p) REVERT: C 539 VAL cc_start: 0.8567 (m) cc_final: 0.8094 (m) REVERT: C 542 ASN cc_start: 0.7417 (t0) cc_final: 0.7120 (t0) REVERT: C 547 LYS cc_start: 0.8330 (mtmm) cc_final: 0.8054 (mtmm) REVERT: C 553 THR cc_start: 0.8702 (p) cc_final: 0.8446 (p) REVERT: C 587 ILE cc_start: 0.8637 (mt) cc_final: 0.8185 (pt) REVERT: C 655 TYR cc_start: 0.7988 (t80) cc_final: 0.7534 (t80) REVERT: C 705 VAL cc_start: 0.8474 (t) cc_final: 0.8151 (m) REVERT: C 708 SER cc_start: 0.8866 (t) cc_final: 0.8518 (m) REVERT: C 764 LYS cc_start: 0.7888 (mtpp) cc_final: 0.7583 (mtpp) REVERT: C 765 ARG cc_start: 0.7470 (ttp-110) cc_final: 0.7221 (ttm110) REVERT: C 773 GLU cc_start: 0.6898 (tm-30) cc_final: 0.6041 (tm-30) REVERT: C 820 ASP cc_start: 0.7604 (m-30) cc_final: 0.7152 (m-30) REVERT: C 867 ASP cc_start: 0.7881 (m-30) cc_final: 0.7675 (m-30) REVERT: C 933 LYS cc_start: 0.8066 (mtmm) cc_final: 0.7760 (mtmm) REVERT: C 949 GLN cc_start: 0.7960 (mm110) cc_final: 0.7334 (mm-40) REVERT: C 953 ASN cc_start: 0.8142 (m-40) cc_final: 0.7820 (m-40) REVERT: C 960 ASN cc_start: 0.7887 (m110) cc_final: 0.7385 (m110) REVERT: C 973 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.8107 (pp) REVERT: C 1028 LYS cc_start: 0.8504 (mttt) cc_final: 0.7700 (mtpp) REVERT: C 1048 HIS cc_start: 0.8413 (t70) cc_final: 0.7716 (t70) REVERT: C 1049 LEU cc_start: 0.8289 (mt) cc_final: 0.7946 (mp) REVERT: C 1097 SER cc_start: 0.8977 (t) cc_final: 0.8735 (p) REVERT: D 6 GLN cc_start: 0.0908 (OUTLIER) cc_final: -0.0329 (tp40) REVERT: E 156 HIS cc_start: 0.7148 (m-70) cc_final: 0.6658 (m90) REVERT: E 158 MET cc_start: 0.5033 (mmm) cc_final: 0.4656 (mmm) REVERT: E 159 HIS cc_start: 0.7553 (m170) cc_final: 0.7319 (m170) REVERT: F 128 VAL cc_start: 0.6680 (OUTLIER) cc_final: 0.6265 (p) REVERT: F 159 TYR cc_start: 0.6631 (m-80) cc_final: 0.6203 (m-80) REVERT: G 4 LEU cc_start: 0.8693 (mt) cc_final: 0.8192 (tp) REVERT: G 32 ASN cc_start: 0.7043 (m110) cc_final: 0.6794 (m-40) outliers start: 182 outliers final: 70 residues processed: 1073 average time/residue: 0.1957 time to fit residues: 332.8684 Evaluate side-chains 820 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 739 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 129 GLN Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain F residue 153 PHE Chi-restraints excluded: chain F residue 205 TYR Chi-restraints excluded: chain F residue 214 GLU Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain F residue 234 MET Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 106 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 197 optimal weight: 0.0870 chunk 388 optimal weight: 30.0000 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 0.6980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN A 173 GLN A 321 GLN A 394 ASN A 409 GLN A 414 GLN A 422 ASN A 477 ASN A 563 GLN A 564 GLN A 690 GLN A 777 ASN A 784 GLN A 853 GLN A 901 GLN A 957 GLN A 960 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN B 173 GLN B 181 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS B 354 ASN B 388 ASN B 409 GLN B 422 ASN B 448 ASN B 487 ASN B 564 GLN B 606 ASN B 784 GLN B 853 GLN B 914 ASN B 949 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS B1119 ASN C 30 ASN C 164 ASN C 388 ASN C 409 GLN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN C 448 ASN C 450 ASN C 540 ASN C 580 GLN C 616 ASN C 755 GLN C 784 GLN C 853 GLN C 913 GLN C 920 GLN C 955 ASN C1011 GLN C1048 HIS C1054 GLN C1071 GLN C1083 HIS C1106 GLN C1119 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN D 39 GLN D 40 GLN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 GLN D 165 GLN D 202 ASN ** E 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 GLN E 97 ASN E 127 GLN E 137 GLN E 159 HIS E 206 GLN ** E 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 ASN F 39 GLN F 40 GLN F 81 GLN F 129 GLN F 165 GLN F 202 ASN G 16 GLN ** G 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 GLN G 137 GLN G 159 HIS G 201 ASN G 206 GLN Total number of N/Q/H flips: 84 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.174536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.131082 restraints weight = 66902.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.135274 restraints weight = 31743.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.137880 restraints weight = 18541.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.139527 restraints weight = 12552.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.140573 restraints weight = 9574.255| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 32215 Z= 0.129 Angle : 0.634 15.638 43907 Z= 0.307 Chirality : 0.045 0.340 4962 Planarity : 0.004 0.048 5654 Dihedral : 6.076 80.054 4521 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.83 % Favored : 92.14 % Rotamer: Outliers : 4.55 % Allowed : 14.54 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.30 (0.12), residues: 3970 helix: 0.38 (0.21), residues: 676 sheet: -1.95 (0.17), residues: 798 loop : -3.23 (0.10), residues: 2496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 273 TYR 0.020 0.001 TYR F 51 PHE 0.027 0.001 PHE B 65 TRP 0.023 0.001 TRP G 36 HIS 0.009 0.001 HIS E 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (32147) covalent geometry : angle 0.61868 / 0.30 (43750) SS BOND : bond 0.00462 / 0.35 ( 47) SS BOND : angle 2.31188 / 1.63 ( 94) hydrogen bonds : bond 0.03240 / 2.07 ( 851) hydrogen bonds : angle 4.75263 / 3.32 ( 2274) link_NAG-ASN : bond 0.00406 / 0.26 ( 21) link_NAG-ASN : angle 2.53489 / 1.68 ( 63) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7940 Ramachandran restraints generated. 3970 Oldfield, 0 Emsley, 3970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7940 Ramachandran restraints generated. 3970 Oldfield, 0 Emsley, 3970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 896 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 740 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 VAL cc_start: 0.8095 (t) cc_final: 0.7847 (m) REVERT: A 61 ASN cc_start: 0.7442 (m-40) cc_final: 0.6960 (p0) REVERT: A 92 PHE cc_start: 0.8189 (t80) cc_final: 0.7474 (t80) REVERT: A 106 PHE cc_start: 0.7679 (m-80) cc_final: 0.7460 (m-80) REVERT: A 193 LYS cc_start: 0.7596 (mtmt) cc_final: 0.7284 (mtmt) REVERT: A 235 ILE cc_start: 0.8879 (mt) cc_final: 0.8392 (tp) REVERT: A 238 PHE cc_start: 0.8946 (p90) cc_final: 0.8531 (p90) REVERT: A 276 LEU cc_start: 0.8600 (tp) cc_final: 0.8379 (tt) REVERT: A 278 LYS cc_start: 0.8639 (ttmt) cc_final: 0.8311 (tttt) REVERT: A 324 GLU cc_start: 0.7054 (tm-30) cc_final: 0.6481 (tm-30) REVERT: A 326 ILE cc_start: 0.7868 (mt) cc_final: 0.7461 (mm) REVERT: A 539 VAL cc_start: 0.8079 (m) cc_final: 0.7863 (m) REVERT: A 557 LYS cc_start: 0.7900 (mmtm) cc_final: 0.7621 (mmtp) REVERT: A 559 PHE cc_start: 0.7143 (m-80) cc_final: 0.6921 (m-80) REVERT: A 562 PHE cc_start: 0.6688 (p90) cc_final: 0.5990 (p90) REVERT: A 585 LEU cc_start: 0.8400 (mp) cc_final: 0.8185 (pp) REVERT: A 587 ILE cc_start: 0.8696 (mt) cc_final: 0.8305 (tp) REVERT: A 602 THR cc_start: 0.8249 (m) cc_final: 0.7781 (p) REVERT: A 664 ILE cc_start: 0.8751 (mt) cc_final: 0.8532 (mm) REVERT: A 666 ILE cc_start: 0.9190 (mt) cc_final: 0.8949 (mt) REVERT: A 697 MET cc_start: 0.7603 (ptm) cc_final: 0.7314 (ptm) REVERT: A 707 TYR cc_start: 0.7988 (t80) cc_final: 0.7515 (t80) REVERT: A 709 ASN cc_start: 0.7490 (OUTLIER) cc_final: 0.7104 (p0) REVERT: A 725 GLU cc_start: 0.7849 (tt0) cc_final: 0.7641 (tt0) REVERT: A 737 ASP cc_start: 0.7443 (t0) cc_final: 0.5398 (p0) REVERT: A 741 TYR cc_start: 0.7667 (t80) cc_final: 0.7229 (t80) REVERT: A 742 ILE cc_start: 0.8213 (mm) cc_final: 0.7755 (tp) REVERT: A 764 LYS cc_start: 0.8160 (ttpp) cc_final: 0.7885 (tppt) REVERT: A 765 ARG cc_start: 0.7888 (ttp-170) cc_final: 0.7230 (ttm-80) REVERT: A 768 THR cc_start: 0.8517 (m) cc_final: 0.8280 (p) REVERT: A 776 LYS cc_start: 0.8699 (tmmt) cc_final: 0.8448 (ttmm) REVERT: A 820 ASP cc_start: 0.7818 (m-30) cc_final: 0.7597 (m-30) REVERT: A 821 LEU cc_start: 0.8741 (tp) cc_final: 0.8513 (tt) REVERT: A 914 ASN cc_start: 0.7454 (p0) cc_final: 0.7250 (p0) REVERT: A 935 GLN cc_start: 0.8537 (pt0) cc_final: 0.8222 (pt0) REVERT: A 949 GLN cc_start: 0.8356 (mm110) cc_final: 0.7538 (mm-40) REVERT: A 953 ASN cc_start: 0.7729 (m-40) cc_final: 0.7208 (m-40) REVERT: A 957 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7831 (tt0) REVERT: A 964 LYS cc_start: 0.8538 (tmtm) cc_final: 0.8294 (mmmt) REVERT: A 977 LEU cc_start: 0.8567 (mp) cc_final: 0.7532 (mt) REVERT: A 981 PHE cc_start: 0.5987 (m-80) cc_final: 0.5430 (m-80) REVERT: A 1027 THR cc_start: 0.8861 (m) cc_final: 0.8380 (t) REVERT: A 1072 GLU cc_start: 0.8621 (pm20) cc_final: 0.8006 (pm20) REVERT: A 1073 LYS cc_start: 0.8549 (tttm) cc_final: 0.7882 (ttmm) REVERT: A 1081 ILE cc_start: 0.8799 (pt) cc_final: 0.8414 (mm) REVERT: A 1088 HIS cc_start: 0.8337 (m90) cc_final: 0.8071 (m90) REVERT: A 1103 PHE cc_start: 0.8046 (m-80) cc_final: 0.7711 (m-80) REVERT: A 1107 ARG cc_start: 0.7305 (mtt180) cc_final: 0.7095 (mtm-85) REVERT: A 1118 ASP cc_start: 0.7592 (t70) cc_final: 0.7331 (t0) REVERT: A 1138 TYR cc_start: 0.7047 (t80) cc_final: 0.6741 (t80) REVERT: B 41 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8122 (mttp) REVERT: B 55 PHE cc_start: 0.7647 (m-80) cc_final: 0.7358 (m-80) REVERT: B 66 HIS cc_start: 0.7191 (m90) cc_final: 0.6868 (m90) REVERT: B 129 LYS cc_start: 0.7684 (tppt) cc_final: 0.7426 (tppt) REVERT: B 193 LYS cc_start: 0.8391 (ttpt) cc_final: 0.8178 (mtpt) REVERT: B 200 LYS cc_start: 0.8725 (mttt) cc_final: 0.8178 (mtmt) REVERT: B 228 ASP cc_start: 0.6913 (t70) cc_final: 0.5973 (t0) REVERT: B 229 LEU cc_start: 0.8608 (mm) cc_final: 0.8352 (mm) REVERT: B 237 ARG cc_start: 0.7898 (ttm110) cc_final: 0.7688 (mtp85) REVERT: B 269 TYR cc_start: 0.7447 (m-10) cc_final: 0.6899 (m-10) REVERT: B 271 GLN cc_start: 0.7817 (mt0) cc_final: 0.7495 (mp10) REVERT: B 275 PHE cc_start: 0.7555 (m-80) cc_final: 0.7322 (m-80) REVERT: B 278 LYS cc_start: 0.8810 (ttmp) cc_final: 0.8252 (ttmm) REVERT: B 281 GLU cc_start: 0.6852 (pp20) cc_final: 0.6415 (pp20) REVERT: B 297 SER cc_start: 0.8243 (m) cc_final: 0.7762 (p) REVERT: B 298 GLU cc_start: 0.7724 (tt0) cc_final: 0.7311 (tt0) REVERT: B 307 THR cc_start: 0.7963 (m) cc_final: 0.7762 (m) REVERT: B 342 PHE cc_start: 0.8016 (m-80) cc_final: 0.7803 (m-10) REVERT: B 378 LYS cc_start: 0.8711 (tptt) cc_final: 0.8328 (tptt) REVERT: B 581 THR cc_start: 0.7602 (t) cc_final: 0.7373 (t) REVERT: B 584 ILE cc_start: 0.8055 (OUTLIER) cc_final: 0.7696 (tt) REVERT: B 612 TYR cc_start: 0.7838 (m-80) cc_final: 0.7587 (m-10) REVERT: B 619 GLU cc_start: 0.7285 (tt0) cc_final: 0.6900 (tt0) REVERT: B 663 ASP cc_start: 0.7515 (t70) cc_final: 0.7311 (t70) REVERT: B 695 TYR cc_start: 0.7917 (p90) cc_final: 0.7124 (p90) REVERT: B 737 ASP cc_start: 0.7760 (t0) cc_final: 0.7142 (p0) REVERT: B 740 MET cc_start: 0.7044 (ttp) cc_final: 0.6762 (ttp) REVERT: B 764 LYS cc_start: 0.8416 (tptt) cc_final: 0.8010 (tppt) REVERT: B 773 GLU cc_start: 0.7321 (tm-30) cc_final: 0.6959 (tm-30) REVERT: B 796 TYR cc_start: 0.8110 (t80) cc_final: 0.7823 (t80) REVERT: B 868 GLU cc_start: 0.7807 (tp30) cc_final: 0.7580 (tp30) REVERT: B 869 MET cc_start: 0.8522 (mtt) cc_final: 0.8309 (mtt) REVERT: B 894 LEU cc_start: 0.8207 (mt) cc_final: 0.7709 (mt) REVERT: B 900 MET cc_start: 0.7969 (mtp) cc_final: 0.7765 (mtm) REVERT: B 914 ASN cc_start: 0.8559 (p0) cc_final: 0.7968 (p0) REVERT: B 921 LYS cc_start: 0.8577 (mmmt) cc_final: 0.8216 (mmmm) REVERT: B 922 LEU cc_start: 0.9059 (tp) cc_final: 0.8804 (tp) REVERT: B 925 ASN cc_start: 0.8816 (m-40) cc_final: 0.8604 (m-40) REVERT: B 929 SER cc_start: 0.8611 (m) cc_final: 0.8329 (p) REVERT: B 933 LYS cc_start: 0.8631 (mtmt) cc_final: 0.8147 (mtmm) REVERT: B 949 GLN cc_start: 0.8440 (mm-40) cc_final: 0.8093 (mm110) REVERT: B 950 ASP cc_start: 0.7309 (m-30) cc_final: 0.6712 (m-30) REVERT: B 1031 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7528 (mt-10) REVERT: B 1038 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8401 (mmmm) REVERT: B 1081 ILE cc_start: 0.8871 (pt) cc_final: 0.8519 (mm) REVERT: B 1111 GLU cc_start: 0.7764 (tt0) cc_final: 0.7308 (tt0) REVERT: B 1118 ASP cc_start: 0.7114 (t70) cc_final: 0.6633 (t0) REVERT: C 43 PHE cc_start: 0.8055 (t80) cc_final: 0.7737 (t80) REVERT: C 101 ILE cc_start: 0.8369 (mt) cc_final: 0.8097 (mm) REVERT: C 127 VAL cc_start: 0.7287 (OUTLIER) cc_final: 0.6984 (m) REVERT: C 170 TYR cc_start: 0.7699 (t80) cc_final: 0.7480 (t80) REVERT: C 189 GLU cc_start: 0.7812 (tp30) cc_final: 0.6693 (tm-30) REVERT: C 218 GLN cc_start: 0.7687 (mt0) cc_final: 0.7339 (mm-40) REVERT: C 224 GLU cc_start: 0.7244 (pm20) cc_final: 0.6730 (mp0) REVERT: C 269 TYR cc_start: 0.7033 (m-10) cc_final: 0.6738 (m-10) REVERT: C 271 GLN cc_start: 0.7659 (tm-30) cc_final: 0.7202 (tm-30) REVERT: C 280 ASN cc_start: 0.8885 (t0) cc_final: 0.8680 (t0) REVERT: C 287 ASP cc_start: 0.7301 (p0) cc_final: 0.6875 (p0) REVERT: C 297 SER cc_start: 0.8392 (m) cc_final: 0.8041 (p) REVERT: C 298 GLU cc_start: 0.8191 (tt0) cc_final: 0.7590 (tp30) REVERT: C 390 LEU cc_start: 0.9046 (tp) cc_final: 0.8249 (tt) REVERT: C 392 PHE cc_start: 0.7130 (m-80) cc_final: 0.6161 (m-80) REVERT: C 406 GLU cc_start: 0.8341 (mt-10) cc_final: 0.7719 (mt-10) REVERT: C 421 TYR cc_start: 0.6980 (m-10) cc_final: 0.6686 (m-10) REVERT: C 425 LEU cc_start: 0.9009 (mp) cc_final: 0.8590 (tp) REVERT: C 454 ARG cc_start: 0.7527 (ttt180) cc_final: 0.7303 (ttm170) REVERT: C 455 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7386 (tm) REVERT: C 535 LYS cc_start: 0.8796 (ttmm) cc_final: 0.8483 (tppp) REVERT: C 542 ASN cc_start: 0.7710 (t0) cc_final: 0.7341 (t0) REVERT: C 547 LYS cc_start: 0.8473 (mtmm) cc_final: 0.8235 (mtmm) REVERT: C 587 ILE cc_start: 0.8673 (mt) cc_final: 0.8107 (pt) REVERT: C 655 TYR cc_start: 0.7938 (t80) cc_final: 0.7718 (t80) REVERT: C 663 ASP cc_start: 0.7545 (t0) cc_final: 0.7219 (t0) REVERT: C 664 ILE cc_start: 0.8382 (mt) cc_final: 0.8007 (mm) REVERT: C 675 GLN cc_start: 0.7802 (mm110) cc_final: 0.7505 (mm110) REVERT: C 708 SER cc_start: 0.8916 (t) cc_final: 0.8411 (m) REVERT: C 773 GLU cc_start: 0.7286 (tm-30) cc_final: 0.6479 (tm-30) REVERT: C 820 ASP cc_start: 0.7607 (m-30) cc_final: 0.7248 (m-30) REVERT: C 867 ASP cc_start: 0.7944 (m-30) cc_final: 0.7672 (m-30) REVERT: C 901 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8173 (tm-30) REVERT: C 902 MET cc_start: 0.8614 (tpp) cc_final: 0.8398 (tpp) REVERT: C 933 LYS cc_start: 0.8091 (mtmm) cc_final: 0.7714 (mmmm) REVERT: C 949 GLN cc_start: 0.8065 (mm110) cc_final: 0.7386 (mm-40) REVERT: C 953 ASN cc_start: 0.8323 (m-40) cc_final: 0.7973 (m-40) REVERT: C 960 ASN cc_start: 0.7858 (m110) cc_final: 0.7380 (m110) REVERT: C 962 LEU cc_start: 0.9273 (tp) cc_final: 0.9003 (tt) REVERT: C 964 LYS cc_start: 0.8581 (mtmp) cc_final: 0.8177 (mmmm) REVERT: C 1017 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7631 (tm-30) REVERT: C 1038 LYS cc_start: 0.7957 (mttp) cc_final: 0.7683 (mmmm) REVERT: C 1048 HIS cc_start: 0.8443 (t-90) cc_final: 0.7793 (t70) REVERT: C 1071 GLN cc_start: 0.8258 (mm-40) cc_final: 0.7585 (mm-40) REVERT: C 1111 GLU cc_start: 0.7245 (tt0) cc_final: 0.6812 (tm-30) REVERT: C 1136 THR cc_start: 0.8889 (OUTLIER) cc_final: 0.8264 (p) REVERT: D 6 GLN cc_start: 0.0660 (OUTLIER) cc_final: -0.0300 (tp40) REVERT: D 83 GLU cc_start: 0.2403 (OUTLIER) cc_final: 0.2093 (pp20) REVERT: E 158 MET cc_start: 0.5119 (mmm) cc_final: 0.4722 (mmm) REVERT: F 146 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.7967 (tp) REVERT: F 159 TYR cc_start: 0.6701 (m-80) cc_final: 0.5902 (m-80) REVERT: F 206 LEU cc_start: 0.8806 (tp) cc_final: 0.8392 (mp) REVERT: F 230 TYR cc_start: 0.6828 (t80) cc_final: 0.6517 (t80) REVERT: G 4 LEU cc_start: 0.8674 (mt) cc_final: 0.8256 (tp) REVERT: G 32 ASN cc_start: 0.6829 (m110) cc_final: 0.6543 (m-40) outliers start: 156 outliers final: 89 residues processed: 855 average time/residue: 0.1963 time to fit residues: 269.1046 Evaluate side-chains 761 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 660 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 153 PHE Chi-restraints excluded: chain F residue 214 GLU Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain G residue 249 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 374 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 303 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 354 optimal weight: 5.9990 chunk 198 optimal weight: 3.9990 chunk 116 optimal weight: 9.9990 chunk 158 optimal weight: 0.4980 chunk 54 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN A 519 HIS A 955 ASN A 957 GLN A 960 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS B 87 ASN B 234 ASN B 448 ASN B 690 GLN B 978 ASN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS C 205 HIS C 487 ASN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C 913 GLN C 949 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 ASN E 35 ASN ** E 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 GLN E 156 HIS ** E 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.167027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.121747 restraints weight = 67137.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.125946 restraints weight = 31693.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.128579 restraints weight = 18520.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.130251 restraints weight = 12588.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.131286 restraints weight = 9684.207| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 32215 Z= 0.208 Angle : 0.664 11.770 43907 Z= 0.334 Chirality : 0.046 0.251 4962 Planarity : 0.005 0.048 5654 Dihedral : 6.105 80.576 4483 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.34 % Favored : 91.64 % Rotamer: Outliers : 5.33 % Allowed : 15.36 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.94 (0.12), residues: 3970 helix: 0.71 (0.21), residues: 668 sheet: -1.55 (0.17), residues: 821 loop : -3.06 (0.11), residues: 2481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 765 TYR 0.027 0.002 TYR A1067 PHE 0.035 0.002 PHE B 981 TRP 0.042 0.002 TRP B 64 HIS 0.009 0.001 HIS B1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.21 (32147) covalent geometry : angle 0.65342 / 0.33 (43750) SS BOND : bond 0.00608 / 0.43 ( 47) SS BOND : angle 2.05668 / 1.41 ( 94) hydrogen bonds : bond 0.03687 / 2.41 ( 851) hydrogen bonds : angle 4.79231 / 3.34 ( 2274) link_NAG-ASN : bond 0.00379 / 0.28 ( 21) link_NAG-ASN : angle 2.06812 / 1.41 ( 63) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7940 Ramachandran restraints generated. 3970 Oldfield, 0 Emsley, 3970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7940 Ramachandran restraints generated. 3970 Oldfield, 0 Emsley, 3970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 917 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 734 time to evaluate : 1.193 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 36 VAL cc_start: 0.8318 (t) cc_final: 0.8036 (m) REVERT: A 61 ASN cc_start: 0.7675 (m-40) cc_final: 0.7135 (p0) REVERT: A 92 PHE cc_start: 0.8244 (t80) cc_final: 0.7652 (t80) REVERT: A 106 PHE cc_start: 0.7725 (m-80) cc_final: 0.7405 (m-80) REVERT: A 135 PHE cc_start: 0.6403 (p90) cc_final: 0.5637 (p90) REVERT: A 177 MET cc_start: 0.6613 (ppp) cc_final: 0.6373 (ppp) REVERT: A 193 LYS cc_start: 0.8286 (mtmt) cc_final: 0.7886 (mtmt) REVERT: A 224 GLU cc_start: 0.8573 (pm20) cc_final: 0.8337 (pm20) REVERT: A 228 ASP cc_start: 0.7338 (OUTLIER) cc_final: 0.7102 (t0) REVERT: A 235 ILE cc_start: 0.8924 (mt) cc_final: 0.8419 (tp) REVERT: A 270 LEU cc_start: 0.8247 (mp) cc_final: 0.7656 (mt) REVERT: A 271 GLN cc_start: 0.7648 (mm-40) cc_final: 0.7371 (mm-40) REVERT: A 278 LYS cc_start: 0.8782 (ttmt) cc_final: 0.8395 (tttt) REVERT: A 297 SER cc_start: 0.8616 (m) cc_final: 0.8258 (p) REVERT: A 304 LYS cc_start: 0.8703 (mtmm) cc_final: 0.8495 (mtpp) REVERT: A 498 ARG cc_start: 0.6808 (mmm160) cc_final: 0.6448 (mmm160) REVERT: A 533 LEU cc_start: 0.8836 (tt) cc_final: 0.8340 (pp) REVERT: A 537 LYS cc_start: 0.8009 (tptt) cc_final: 0.7758 (tptp) REVERT: A 562 PHE cc_start: 0.7237 (p90) cc_final: 0.6999 (p90) REVERT: A 587 ILE cc_start: 0.8715 (mt) cc_final: 0.8271 (tp) REVERT: A 602 THR cc_start: 0.8523 (OUTLIER) cc_final: 0.8080 (p) REVERT: A 617 CYS cc_start: 0.6297 (OUTLIER) cc_final: 0.5693 (p) REVERT: A 619 GLU cc_start: 0.7375 (mp0) cc_final: 0.7154 (mp0) REVERT: A 664 ILE cc_start: 0.8818 (mt) cc_final: 0.8468 (mm) REVERT: A 666 ILE cc_start: 0.9166 (mt) cc_final: 0.8959 (mt) REVERT: A 675 GLN cc_start: 0.7349 (tp40) cc_final: 0.7141 (tp-100) REVERT: A 731 MET cc_start: 0.8707 (ptt) cc_final: 0.8459 (ptp) REVERT: A 736 VAL cc_start: 0.8769 (m) cc_final: 0.8434 (p) REVERT: A 737 ASP cc_start: 0.7576 (t0) cc_final: 0.6387 (p0) REVERT: A 740 MET cc_start: 0.7748 (mpp) cc_final: 0.7542 (mpp) REVERT: A 741 TYR cc_start: 0.8104 (t80) cc_final: 0.7701 (t80) REVERT: A 742 ILE cc_start: 0.8425 (mm) cc_final: 0.7873 (tp) REVERT: A 764 LYS cc_start: 0.8276 (ttpp) cc_final: 0.7928 (tppt) REVERT: A 765 ARG cc_start: 0.7994 (ttp-170) cc_final: 0.7496 (ttm170) REVERT: A 768 THR cc_start: 0.8681 (m) cc_final: 0.8380 (p) REVERT: A 776 LYS cc_start: 0.8757 (tmmt) cc_final: 0.8512 (ttmm) REVERT: A 869 MET cc_start: 0.8404 (mpp) cc_final: 0.8146 (mpp) REVERT: A 886 TRP cc_start: 0.8653 (p90) cc_final: 0.7567 (p90) REVERT: A 911 VAL cc_start: 0.9009 (t) cc_final: 0.8684 (m) REVERT: A 914 ASN cc_start: 0.7849 (p0) cc_final: 0.7579 (p0) REVERT: A 957 GLN cc_start: 0.8392 (tt0) cc_final: 0.8169 (tt0) REVERT: A 960 ASN cc_start: 0.8353 (OUTLIER) cc_final: 0.7962 (t0) REVERT: A 962 LEU cc_start: 0.8956 (tp) cc_final: 0.8247 (tp) REVERT: A 964 LYS cc_start: 0.8670 (tmtm) cc_final: 0.8419 (mmmt) REVERT: A 977 LEU cc_start: 0.8476 (mp) cc_final: 0.7438 (mm) REVERT: A 981 PHE cc_start: 0.6078 (m-10) cc_final: 0.5762 (m-80) REVERT: A 1031 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7394 (mt-10) REVERT: A 1081 ILE cc_start: 0.8739 (pt) cc_final: 0.8429 (mm) REVERT: A 1103 PHE cc_start: 0.8231 (m-80) cc_final: 0.8031 (m-80) REVERT: A 1118 ASP cc_start: 0.7837 (t70) cc_final: 0.7610 (t0) REVERT: A 1138 TYR cc_start: 0.7245 (t80) cc_final: 0.6918 (t80) REVERT: A 1141 LEU cc_start: 0.8880 (mp) cc_final: 0.8082 (mm) REVERT: B 41 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8374 (mttp) REVERT: B 55 PHE cc_start: 0.7796 (m-80) cc_final: 0.7554 (m-80) REVERT: B 64 TRP cc_start: 0.7396 (t60) cc_final: 0.7166 (t-100) REVERT: B 65 PHE cc_start: 0.7347 (m-80) cc_final: 0.7100 (m-80) REVERT: B 66 HIS cc_start: 0.7412 (m90) cc_final: 0.7076 (m90) REVERT: B 95 ILE cc_start: 0.7417 (OUTLIER) cc_final: 0.6854 (pt) REVERT: B 104 TRP cc_start: 0.7782 (m-90) cc_final: 0.7066 (m-90) REVERT: B 129 LYS cc_start: 0.7908 (tppt) cc_final: 0.7579 (tppt) REVERT: B 132 GLU cc_start: 0.6109 (pm20) cc_final: 0.5375 (pm20) REVERT: B 141 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7760 (mm) REVERT: B 200 LYS cc_start: 0.8765 (mttt) cc_final: 0.8290 (mtmt) REVERT: B 224 GLU cc_start: 0.7558 (mm-30) cc_final: 0.7195 (mm-30) REVERT: B 228 ASP cc_start: 0.7070 (t70) cc_final: 0.6207 (t0) REVERT: B 271 GLN cc_start: 0.7857 (mt0) cc_final: 0.7537 (mm110) REVERT: B 278 LYS cc_start: 0.8877 (ttmp) cc_final: 0.8381 (ttmm) REVERT: B 297 SER cc_start: 0.8366 (m) cc_final: 0.7886 (p) REVERT: B 307 THR cc_start: 0.8251 (m) cc_final: 0.7918 (p) REVERT: B 378 LYS cc_start: 0.8353 (tptt) cc_final: 0.7864 (tptp) REVERT: B 534 VAL cc_start: 0.8349 (p) cc_final: 0.8143 (m) REVERT: B 663 ASP cc_start: 0.7603 (t70) cc_final: 0.7375 (t70) REVERT: B 695 TYR cc_start: 0.8077 (p90) cc_final: 0.7355 (p90) REVERT: B 730 SER cc_start: 0.8823 (t) cc_final: 0.8294 (p) REVERT: B 737 ASP cc_start: 0.7963 (t0) cc_final: 0.7263 (p0) REVERT: B 762 GLN cc_start: 0.8016 (mp10) cc_final: 0.7750 (mp10) REVERT: B 764 LYS cc_start: 0.8508 (tptt) cc_final: 0.8277 (tppt) REVERT: B 796 TYR cc_start: 0.8365 (t80) cc_final: 0.7986 (t80) REVERT: B 803 SER cc_start: 0.8379 (m) cc_final: 0.7932 (p) REVERT: B 804 GLN cc_start: 0.8358 (mp10) cc_final: 0.8036 (mp10) REVERT: B 820 ASP cc_start: 0.7531 (m-30) cc_final: 0.7133 (m-30) REVERT: B 824 ASN cc_start: 0.8604 (m-40) cc_final: 0.8404 (m110) REVERT: B 868 GLU cc_start: 0.8027 (tp30) cc_final: 0.7686 (mm-30) REVERT: B 869 MET cc_start: 0.8565 (mtt) cc_final: 0.8310 (mtt) REVERT: B 895 GLN cc_start: 0.7972 (pm20) cc_final: 0.7772 (pm20) REVERT: B 902 MET cc_start: 0.8507 (tpp) cc_final: 0.8107 (tpp) REVERT: B 914 ASN cc_start: 0.8573 (p0) cc_final: 0.7658 (p0) REVERT: B 918 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7472 (mt-10) REVERT: B 921 LYS cc_start: 0.8663 (mmmt) cc_final: 0.8271 (mmmm) REVERT: B 922 LEU cc_start: 0.9101 (tp) cc_final: 0.8890 (tp) REVERT: B 925 ASN cc_start: 0.8908 (m-40) cc_final: 0.8674 (m-40) REVERT: B 929 SER cc_start: 0.8817 (m) cc_final: 0.8491 (p) REVERT: B 933 LYS cc_start: 0.8676 (mtmt) cc_final: 0.8242 (mtpp) REVERT: B 947 LYS cc_start: 0.9226 (OUTLIER) cc_final: 0.8776 (mtmt) REVERT: B 949 GLN cc_start: 0.8549 (mm-40) cc_final: 0.8245 (mm110) REVERT: B 950 ASP cc_start: 0.7638 (m-30) cc_final: 0.7037 (m-30) REVERT: B 965 GLN cc_start: 0.8368 (mm-40) cc_final: 0.8129 (mm-40) REVERT: B 1031 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7597 (mt-10) REVERT: B 1038 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8529 (mmmm) REVERT: B 1072 GLU cc_start: 0.8576 (pm20) cc_final: 0.7574 (mp0) REVERT: B 1081 ILE cc_start: 0.8859 (pt) cc_final: 0.8524 (mm) REVERT: B 1107 ARG cc_start: 0.7324 (mtt90) cc_final: 0.7065 (mtt90) REVERT: B 1111 GLU cc_start: 0.7904 (tt0) cc_final: 0.7528 (tt0) REVERT: B 1118 ASP cc_start: 0.7387 (t70) cc_final: 0.6629 (t0) REVERT: C 41 LYS cc_start: 0.8553 (mtmm) cc_final: 0.7928 (mtmm) REVERT: C 53 ASP cc_start: 0.7853 (m-30) cc_final: 0.7645 (m-30) REVERT: C 56 LEU cc_start: 0.8758 (tp) cc_final: 0.8293 (tt) REVERT: C 101 ILE cc_start: 0.8545 (mt) cc_final: 0.8157 (tp) REVERT: C 117 LEU cc_start: 0.7769 (tp) cc_final: 0.7486 (mt) REVERT: C 127 VAL cc_start: 0.7323 (OUTLIER) cc_final: 0.7018 (m) REVERT: C 170 TYR cc_start: 0.7957 (t80) cc_final: 0.7648 (t80) REVERT: C 189 GLU cc_start: 0.7726 (tp30) cc_final: 0.6651 (tm-30) REVERT: C 218 GLN cc_start: 0.7752 (mt0) cc_final: 0.7335 (mm-40) REVERT: C 224 GLU cc_start: 0.7337 (pm20) cc_final: 0.6695 (mp0) REVERT: C 269 TYR cc_start: 0.7247 (m-10) cc_final: 0.6667 (m-80) REVERT: C 271 GLN cc_start: 0.7785 (tm-30) cc_final: 0.7383 (tm-30) REVERT: C 280 ASN cc_start: 0.8892 (t0) cc_final: 0.8644 (t0) REVERT: C 297 SER cc_start: 0.8442 (m) cc_final: 0.8037 (p) REVERT: C 298 GLU cc_start: 0.8245 (tt0) cc_final: 0.7732 (tp30) REVERT: C 328 ARG cc_start: 0.8193 (mtp180) cc_final: 0.7105 (mtp85) REVERT: C 354 ASN cc_start: 0.8518 (t0) cc_final: 0.8316 (t0) REVERT: C 375 PHE cc_start: 0.7461 (m-80) cc_final: 0.6751 (m-10) REVERT: C 392 PHE cc_start: 0.7268 (m-80) cc_final: 0.6717 (m-80) REVERT: C 406 GLU cc_start: 0.8411 (mt-10) cc_final: 0.7805 (mt-10) REVERT: C 421 TYR cc_start: 0.7109 (m-10) cc_final: 0.6845 (m-80) REVERT: C 425 LEU cc_start: 0.9027 (mp) cc_final: 0.8557 (tp) REVERT: C 436 TRP cc_start: 0.7402 (p90) cc_final: 0.6884 (p90) REVERT: C 454 ARG cc_start: 0.7474 (ttt180) cc_final: 0.7165 (ttm170) REVERT: C 455 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7530 (tm) REVERT: C 514 SER cc_start: 0.8878 (m) cc_final: 0.8632 (p) REVERT: C 535 LYS cc_start: 0.8819 (ttmm) cc_final: 0.8381 (tppp) REVERT: C 537 LYS cc_start: 0.8420 (tmtt) cc_final: 0.7988 (tmtt) REVERT: C 542 ASN cc_start: 0.7879 (t0) cc_final: 0.7524 (t0) REVERT: C 547 LYS cc_start: 0.8577 (mtmm) cc_final: 0.8348 (mtmm) REVERT: C 571 ASP cc_start: 0.5954 (t0) cc_final: 0.5617 (t0) REVERT: C 582 LEU cc_start: 0.7621 (mt) cc_final: 0.7269 (mp) REVERT: C 587 ILE cc_start: 0.8969 (mt) cc_final: 0.8571 (pt) REVERT: C 602 THR cc_start: 0.8844 (OUTLIER) cc_final: 0.8478 (p) REVERT: C 663 ASP cc_start: 0.7686 (t0) cc_final: 0.7454 (t0) REVERT: C 664 ILE cc_start: 0.8394 (mt) cc_final: 0.8083 (mm) REVERT: C 675 GLN cc_start: 0.7863 (mm110) cc_final: 0.7487 (mm110) REVERT: C 708 SER cc_start: 0.8942 (t) cc_final: 0.8427 (m) REVERT: C 773 GLU cc_start: 0.7506 (tm-30) cc_final: 0.6665 (tm-30) REVERT: C 816 SER cc_start: 0.8706 (p) cc_final: 0.6509 (m) REVERT: C 820 ASP cc_start: 0.7815 (m-30) cc_final: 0.7449 (m-30) REVERT: C 850 ILE cc_start: 0.9039 (mm) cc_final: 0.8809 (tp) REVERT: C 867 ASP cc_start: 0.8032 (m-30) cc_final: 0.7794 (m-30) REVERT: C 901 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8203 (tm-30) REVERT: C 902 MET cc_start: 0.8778 (tpp) cc_final: 0.8544 (tpp) REVERT: C 914 ASN cc_start: 0.8434 (p0) cc_final: 0.8129 (p0) REVERT: C 933 LYS cc_start: 0.8315 (mtmm) cc_final: 0.7882 (mmmm) REVERT: C 949 GLN cc_start: 0.8373 (mm-40) cc_final: 0.7479 (mm-40) REVERT: C 950 ASP cc_start: 0.7497 (t70) cc_final: 0.6923 (t0) REVERT: C 953 ASN cc_start: 0.8415 (m-40) cc_final: 0.7965 (m-40) REVERT: C 960 ASN cc_start: 0.8024 (m110) cc_final: 0.7578 (m110) REVERT: C 962 LEU cc_start: 0.9315 (tp) cc_final: 0.9104 (tp) REVERT: C 964 LYS cc_start: 0.8587 (mtmp) cc_final: 0.8178 (mmmm) REVERT: C 990 GLU cc_start: 0.6802 (OUTLIER) cc_final: 0.6510 (mp0) REVERT: C 1031 GLU cc_start: 0.8434 (mm-30) cc_final: 0.8107 (mm-30) REVERT: C 1038 LYS cc_start: 0.8080 (mtmp) cc_final: 0.7742 (mmmm) REVERT: C 1048 HIS cc_start: 0.8420 (t-90) cc_final: 0.7844 (t70) REVERT: C 1086 LYS cc_start: 0.7946 (mmmt) cc_final: 0.7706 (mmmt) REVERT: D 6 GLN cc_start: 0.1044 (OUTLIER) cc_final: 0.0159 (tp40) REVERT: D 83 GLU cc_start: 0.2421 (OUTLIER) cc_final: 0.2121 (pp20) REVERT: D 219 TYR cc_start: 0.1783 (m-80) cc_final: 0.1417 (m-80) REVERT: E 158 MET cc_start: 0.5296 (mmm) cc_final: 0.4912 (mmm) REVERT: F 146 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8027 (tp) REVERT: F 159 TYR cc_start: 0.7150 (m-80) cc_final: 0.6190 (m-80) REVERT: F 206 LEU cc_start: 0.8977 (tp) cc_final: 0.8682 (mp) REVERT: G 4 LEU cc_start: 0.8715 (mt) cc_final: 0.8186 (tp) REVERT: G 32 ASN cc_start: 0.6639 (m110) cc_final: 0.6285 (m-40) outliers start: 183 outliers final: 111 residues processed: 869 average time/residue: 0.1961 time to fit residues: 274.8909 Evaluate side-chains 805 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 677 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 718 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 659 SER Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 98 ASN Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 153 PHE Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 214 GLU Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain G residue 249 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 144 optimal weight: 8.9990 chunk 212 optimal weight: 10.0000 chunk 215 optimal weight: 0.9990 chunk 240 optimal weight: 0.6980 chunk 352 optimal weight: 9.9990 chunk 286 optimal weight: 3.9990 chunk 336 optimal weight: 6.9990 chunk 283 optimal weight: 0.7980 chunk 361 optimal weight: 20.0000 chunk 374 optimal weight: 2.9990 chunk 34 optimal weight: 20.0000 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 HIS A 644 GLN ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A 960 ASN A1002 GLN A1058 HIS A1119 ASN B 81 ASN B 703 ASN B1002 GLN B1005 GLN B1023 ASN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN E 156 HIS E 206 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.165781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.121067 restraints weight = 66513.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.125282 restraints weight = 31280.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.127904 restraints weight = 18311.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.129531 restraints weight = 12543.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.130652 restraints weight = 9726.704| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 32215 Z= 0.228 Angle : 0.684 10.528 43907 Z= 0.345 Chirality : 0.047 0.267 4962 Planarity : 0.005 0.051 5654 Dihedral : 6.304 81.216 4474 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.97 % Favored : 91.01 % Rotamer: Outliers : 5.30 % Allowed : 17.72 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.71 (0.13), residues: 3970 helix: 0.90 (0.21), residues: 662 sheet: -1.45 (0.17), residues: 829 loop : -2.89 (0.11), residues: 2479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 355 TYR 0.029 0.002 TYR A 91 PHE 0.038 0.002 PHE B 981 TRP 0.035 0.002 TRP G 36 HIS 0.007 0.001 HIS B1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.23 (32147) covalent geometry : angle 0.67301 / 0.34 (43750) SS BOND : bond 0.00592 / 0.42 ( 47) SS BOND : angle 2.13421 / 1.46 ( 94) hydrogen bonds : bond 0.03667 / 2.42 ( 851) hydrogen bonds : angle 4.91513 / 3.41 ( 2274) link_NAG-ASN : bond 0.00341 / 0.25 ( 21) link_NAG-ASN : angle 2.15037 / 1.49 ( 63) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7940 Ramachandran restraints generated. 3970 Oldfield, 0 Emsley, 3970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7940 Ramachandran restraints generated. 3970 Oldfield, 0 Emsley, 3970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 882 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 700 time to evaluate : 1.156 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 36 VAL cc_start: 0.8345 (t) cc_final: 0.8106 (m) REVERT: A 61 ASN cc_start: 0.7745 (m-40) cc_final: 0.7305 (p0) REVERT: A 92 PHE cc_start: 0.8218 (t80) cc_final: 0.7946 (t80) REVERT: A 121 ASN cc_start: 0.7083 (t0) cc_final: 0.6838 (t0) REVERT: A 135 PHE cc_start: 0.6661 (p90) cc_final: 0.5841 (p90) REVERT: A 193 LYS cc_start: 0.8417 (mtmt) cc_final: 0.8031 (mtmt) REVERT: A 224 GLU cc_start: 0.8491 (pm20) cc_final: 0.8247 (pm20) REVERT: A 228 ASP cc_start: 0.7451 (OUTLIER) cc_final: 0.7088 (t0) REVERT: A 235 ILE cc_start: 0.8909 (mt) cc_final: 0.8493 (tp) REVERT: A 238 PHE cc_start: 0.9028 (p90) cc_final: 0.8823 (p90) REVERT: A 271 GLN cc_start: 0.7637 (mm-40) cc_final: 0.7381 (mt0) REVERT: A 278 LYS cc_start: 0.8808 (ttmt) cc_final: 0.8443 (tttt) REVERT: A 297 SER cc_start: 0.8608 (m) cc_final: 0.8232 (p) REVERT: A 498 ARG cc_start: 0.6947 (mmm160) cc_final: 0.6550 (mmm160) REVERT: A 568 ASP cc_start: 0.7289 (t70) cc_final: 0.7037 (t70) REVERT: A 587 ILE cc_start: 0.8818 (mt) cc_final: 0.8421 (tp) REVERT: A 602 THR cc_start: 0.8700 (m) cc_final: 0.8246 (p) REVERT: A 642 VAL cc_start: 0.9199 (t) cc_final: 0.8972 (m) REVERT: A 664 ILE cc_start: 0.8907 (mt) cc_final: 0.8605 (mm) REVERT: A 666 ILE cc_start: 0.9186 (mt) cc_final: 0.8916 (mt) REVERT: A 737 ASP cc_start: 0.7620 (t0) cc_final: 0.7116 (t0) REVERT: A 741 TYR cc_start: 0.8296 (t80) cc_final: 0.7842 (t80) REVERT: A 742 ILE cc_start: 0.8493 (mm) cc_final: 0.7828 (tp) REVERT: A 764 LYS cc_start: 0.8252 (ttpp) cc_final: 0.7984 (tppt) REVERT: A 765 ARG cc_start: 0.7999 (ttp-170) cc_final: 0.7438 (ttm170) REVERT: A 768 THR cc_start: 0.8715 (m) cc_final: 0.8396 (p) REVERT: A 825 LYS cc_start: 0.9026 (ttmm) cc_final: 0.8708 (ttmm) REVERT: A 858 LEU cc_start: 0.8792 (mp) cc_final: 0.8541 (mm) REVERT: A 869 MET cc_start: 0.8414 (mpp) cc_final: 0.8002 (mpp) REVERT: A 902 MET cc_start: 0.8726 (mmt) cc_final: 0.8475 (mmt) REVERT: A 911 VAL cc_start: 0.9041 (t) cc_final: 0.8697 (m) REVERT: A 914 ASN cc_start: 0.7949 (p0) cc_final: 0.7645 (p0) REVERT: A 960 ASN cc_start: 0.8371 (OUTLIER) cc_final: 0.8003 (t0) REVERT: A 962 LEU cc_start: 0.8959 (tp) cc_final: 0.8387 (tp) REVERT: A 964 LYS cc_start: 0.8650 (tmtm) cc_final: 0.8449 (mmmt) REVERT: A 977 LEU cc_start: 0.8462 (mp) cc_final: 0.7336 (mm) REVERT: A 981 PHE cc_start: 0.6103 (m-10) cc_final: 0.5827 (m-80) REVERT: A 995 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7587 (ttm-80) REVERT: A 1031 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7249 (mt-10) REVERT: A 1073 LYS cc_start: 0.8252 (mmtt) cc_final: 0.7946 (mmtt) REVERT: A 1081 ILE cc_start: 0.8783 (pt) cc_final: 0.8462 (mm) REVERT: A 1118 ASP cc_start: 0.7808 (t70) cc_final: 0.7565 (t0) REVERT: A 1138 TYR cc_start: 0.7263 (t80) cc_final: 0.7022 (t80) REVERT: B 41 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8524 (mttp) REVERT: B 66 HIS cc_start: 0.7345 (m90) cc_final: 0.6974 (m90) REVERT: B 104 TRP cc_start: 0.7816 (m-90) cc_final: 0.7295 (m-90) REVERT: B 106 PHE cc_start: 0.7859 (m-80) cc_final: 0.7447 (m-80) REVERT: B 129 LYS cc_start: 0.7993 (tppt) cc_final: 0.7512 (tppt) REVERT: B 192 PHE cc_start: 0.8471 (m-80) cc_final: 0.7993 (m-10) REVERT: B 193 LYS cc_start: 0.8545 (ttpt) cc_final: 0.8090 (ttmm) REVERT: B 200 LYS cc_start: 0.8793 (mttt) cc_final: 0.8328 (mtmt) REVERT: B 204 LYS cc_start: 0.7694 (tppt) cc_final: 0.7264 (tptp) REVERT: B 224 GLU cc_start: 0.7505 (mm-30) cc_final: 0.7159 (mm-30) REVERT: B 228 ASP cc_start: 0.7023 (t70) cc_final: 0.6072 (t0) REVERT: B 229 LEU cc_start: 0.8737 (mm) cc_final: 0.8476 (mm) REVERT: B 271 GLN cc_start: 0.7814 (mt0) cc_final: 0.7404 (mm-40) REVERT: B 275 PHE cc_start: 0.7801 (m-80) cc_final: 0.7366 (m-80) REVERT: B 278 LYS cc_start: 0.8906 (ttmp) cc_final: 0.8391 (ttmm) REVERT: B 298 GLU cc_start: 0.7304 (mt-10) cc_final: 0.7093 (mt-10) REVERT: B 307 THR cc_start: 0.8246 (m) cc_final: 0.7950 (p) REVERT: B 324 GLU cc_start: 0.7530 (pm20) cc_final: 0.7139 (pm20) REVERT: B 663 ASP cc_start: 0.7637 (t70) cc_final: 0.7428 (t70) REVERT: B 695 TYR cc_start: 0.8137 (p90) cc_final: 0.7545 (p90) REVERT: B 712 ILE cc_start: 0.8691 (tp) cc_final: 0.8460 (tp) REVERT: B 725 GLU cc_start: 0.8191 (tt0) cc_final: 0.7901 (tp30) REVERT: B 730 SER cc_start: 0.9001 (t) cc_final: 0.8443 (p) REVERT: B 737 ASP cc_start: 0.8070 (t0) cc_final: 0.7795 (t70) REVERT: B 762 GLN cc_start: 0.7962 (mp10) cc_final: 0.7709 (mp10) REVERT: B 765 ARG cc_start: 0.7963 (tpp80) cc_final: 0.7762 (tpp80) REVERT: B 780 GLU cc_start: 0.7877 (pt0) cc_final: 0.7643 (tp30) REVERT: B 796 TYR cc_start: 0.8434 (t80) cc_final: 0.8131 (t80) REVERT: B 803 SER cc_start: 0.8420 (m) cc_final: 0.8031 (p) REVERT: B 804 GLN cc_start: 0.8394 (mp10) cc_final: 0.8122 (mp10) REVERT: B 819 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7607 (mt-10) REVERT: B 820 ASP cc_start: 0.7599 (m-30) cc_final: 0.7219 (m-30) REVERT: B 868 GLU cc_start: 0.8012 (tp30) cc_final: 0.7793 (mm-30) REVERT: B 869 MET cc_start: 0.8545 (mtt) cc_final: 0.8279 (mtt) REVERT: B 895 GLN cc_start: 0.8177 (pm20) cc_final: 0.7860 (pm20) REVERT: B 914 ASN cc_start: 0.8620 (p0) cc_final: 0.8019 (p0) REVERT: B 921 LYS cc_start: 0.8672 (mmmt) cc_final: 0.8283 (mmmm) REVERT: B 925 ASN cc_start: 0.8890 (m-40) cc_final: 0.8647 (m-40) REVERT: B 929 SER cc_start: 0.8834 (m) cc_final: 0.8520 (p) REVERT: B 933 LYS cc_start: 0.8685 (mtmt) cc_final: 0.8193 (mtpp) REVERT: B 949 GLN cc_start: 0.8571 (mm-40) cc_final: 0.8236 (mm-40) REVERT: B 950 ASP cc_start: 0.7714 (m-30) cc_final: 0.7136 (m-30) REVERT: B 965 GLN cc_start: 0.8370 (mm-40) cc_final: 0.8054 (mm-40) REVERT: B 1031 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7488 (mm-30) REVERT: B 1038 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8573 (mmmm) REVERT: B 1081 ILE cc_start: 0.8852 (pt) cc_final: 0.8493 (mm) REVERT: B 1111 GLU cc_start: 0.7969 (tt0) cc_final: 0.7658 (tt0) REVERT: B 1113 GLN cc_start: 0.7763 (mm110) cc_final: 0.7540 (mm110) REVERT: B 1118 ASP cc_start: 0.7245 (t70) cc_final: 0.6908 (t0) REVERT: C 91 TYR cc_start: 0.7082 (t80) cc_final: 0.6509 (t80) REVERT: C 101 ILE cc_start: 0.8566 (mt) cc_final: 0.8160 (tp) REVERT: C 170 TYR cc_start: 0.7834 (t80) cc_final: 0.7597 (t80) REVERT: C 189 GLU cc_start: 0.7842 (tp30) cc_final: 0.7603 (tp30) REVERT: C 224 GLU cc_start: 0.7428 (pm20) cc_final: 0.6838 (mp0) REVERT: C 228 ASP cc_start: 0.6933 (t70) cc_final: 0.6520 (t70) REVERT: C 269 TYR cc_start: 0.7231 (m-10) cc_final: 0.6698 (m-80) REVERT: C 271 GLN cc_start: 0.7815 (tm-30) cc_final: 0.7483 (tm-30) REVERT: C 297 SER cc_start: 0.8467 (m) cc_final: 0.8113 (p) REVERT: C 298 GLU cc_start: 0.8232 (tt0) cc_final: 0.7745 (tp30) REVERT: C 375 PHE cc_start: 0.7423 (m-80) cc_final: 0.6613 (m-10) REVERT: C 406 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7660 (mt-10) REVERT: C 421 TYR cc_start: 0.7137 (m-10) cc_final: 0.6409 (m-80) REVERT: C 436 TRP cc_start: 0.7432 (p90) cc_final: 0.6988 (p90) REVERT: C 454 ARG cc_start: 0.7447 (ttt180) cc_final: 0.7060 (ttm170) REVERT: C 455 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7494 (tm) REVERT: C 537 LYS cc_start: 0.8477 (tmtt) cc_final: 0.8215 (tmtt) REVERT: C 542 ASN cc_start: 0.7951 (t0) cc_final: 0.7609 (t0) REVERT: C 547 LYS cc_start: 0.8622 (mtmm) cc_final: 0.8388 (mtmm) REVERT: C 571 ASP cc_start: 0.6063 (t0) cc_final: 0.5758 (t0) REVERT: C 587 ILE cc_start: 0.9077 (mt) cc_final: 0.8606 (pt) REVERT: C 598 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8481 (tt) REVERT: C 602 THR cc_start: 0.8826 (OUTLIER) cc_final: 0.8430 (p) REVERT: C 675 GLN cc_start: 0.7842 (mm110) cc_final: 0.7536 (mm110) REVERT: C 705 VAL cc_start: 0.8675 (OUTLIER) cc_final: 0.8394 (m) REVERT: C 708 SER cc_start: 0.8970 (t) cc_final: 0.8452 (m) REVERT: C 726 ILE cc_start: 0.8645 (OUTLIER) cc_final: 0.7925 (mm) REVERT: C 740 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.8035 (mtm) REVERT: C 773 GLU cc_start: 0.7373 (tm-30) cc_final: 0.6606 (tm-30) REVERT: C 853 GLN cc_start: 0.8121 (mt0) cc_final: 0.7841 (mt0) REVERT: C 867 ASP cc_start: 0.8127 (m-30) cc_final: 0.7827 (m-30) REVERT: C 901 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.8201 (tm-30) REVERT: C 933 LYS cc_start: 0.8337 (mtmm) cc_final: 0.7874 (mmmm) REVERT: C 949 GLN cc_start: 0.8514 (mm-40) cc_final: 0.7839 (mm-40) REVERT: C 950 ASP cc_start: 0.7560 (t70) cc_final: 0.6975 (t0) REVERT: C 953 ASN cc_start: 0.8459 (m-40) cc_final: 0.8119 (m-40) REVERT: C 962 LEU cc_start: 0.9351 (tp) cc_final: 0.9016 (tp) REVERT: C 964 LYS cc_start: 0.8679 (mtmp) cc_final: 0.8252 (mmmm) REVERT: C 990 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.6469 (mp0) REVERT: C 1017 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7544 (tm-30) REVERT: C 1031 GLU cc_start: 0.8367 (mm-30) cc_final: 0.8132 (mm-30) REVERT: C 1038 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7762 (mmmm) REVERT: C 1048 HIS cc_start: 0.8457 (t-90) cc_final: 0.7928 (t70) REVERT: C 1111 GLU cc_start: 0.7204 (tm-30) cc_final: 0.6802 (tm-30) REVERT: D 6 GLN cc_start: 0.1065 (OUTLIER) cc_final: 0.0238 (tp40) REVERT: D 49 MET cc_start: 0.5268 (tpt) cc_final: 0.4287 (ptm) REVERT: D 83 GLU cc_start: 0.2510 (OUTLIER) cc_final: 0.2207 (pp20) REVERT: E 156 HIS cc_start: 0.7548 (m-70) cc_final: 0.7213 (m90) REVERT: E 158 MET cc_start: 0.5084 (mmm) cc_final: 0.4728 (mmm) REVERT: E 206 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7879 (tm-30) REVERT: F 39 GLN cc_start: 0.7931 (pp30) cc_final: 0.7436 (pm20) REVERT: F 146 LEU cc_start: 0.8743 (mp) cc_final: 0.8122 (tp) REVERT: F 159 TYR cc_start: 0.7065 (m-80) cc_final: 0.5506 (m-80) REVERT: F 178 TYR cc_start: 0.6662 (m-80) cc_final: 0.6154 (m-80) REVERT: F 206 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8689 (mp) REVERT: F 229 TYR cc_start: 0.6413 (t80) cc_final: 0.5812 (t80) REVERT: G 4 LEU cc_start: 0.8731 (mt) cc_final: 0.8205 (tp) REVERT: G 128 LEU cc_start: 0.7292 (mm) cc_final: 0.6929 (mm) outliers start: 182 outliers final: 121 residues processed: 825 average time/residue: 0.1931 time to fit residues: 256.9011 Evaluate side-chains 796 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 657 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 190 PHE Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 644 GLN Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 718 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 98 ASN Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 153 PHE Chi-restraints excluded: chain F residue 156 SER Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 182 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 275 optimal weight: 0.7980 chunk 268 optimal weight: 2.9990 chunk 250 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 348 optimal weight: 8.9990 chunk 67 optimal weight: 1.9990 chunk 241 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 361 optimal weight: 8.9990 chunk 160 optimal weight: 2.9990 chunk 144 optimal weight: 7.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 ASN A 321 GLN A 519 HIS A 644 GLN ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A 957 GLN A 960 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B 978 ASN B1005 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN C 913 GLN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 ASN G 127 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.162995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.117809 restraints weight = 66673.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.121954 restraints weight = 31272.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.124521 restraints weight = 18245.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.126171 restraints weight = 12462.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.127177 restraints weight = 9612.087| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 32215 Z= 0.228 Angle : 0.692 10.748 43907 Z= 0.348 Chirality : 0.047 0.258 4962 Planarity : 0.005 0.051 5654 Dihedral : 6.209 81.318 4462 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.72 % Favored : 90.23 % Rotamer: Outliers : 5.62 % Allowed : 18.36 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.59 (0.13), residues: 3970 helix: 0.94 (0.21), residues: 673 sheet: -1.27 (0.17), residues: 803 loop : -2.82 (0.11), residues: 2494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 212 TYR 0.031 0.002 TYR C 365 PHE 0.041 0.002 PHE B 981 TRP 0.037 0.002 TRP B 64 HIS 0.026 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.23 (32147) covalent geometry : angle 0.68287 / 0.34 (43750) SS BOND : bond 0.00407 / 0.32 ( 47) SS BOND : angle 1.96367 / 1.40 ( 94) hydrogen bonds : bond 0.03668 / 2.41 ( 851) hydrogen bonds : angle 4.93942 / 3.43 ( 2274) link_NAG-ASN : bond 0.00324 / 0.25 ( 21) link_NAG-ASN : angle 2.03794 / 1.38 ( 63) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7940 Ramachandran restraints generated. 3970 Oldfield, 0 Emsley, 3970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7940 Ramachandran restraints generated. 3970 Oldfield, 0 Emsley, 3970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 881 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 688 time to evaluate : 1.160 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 36 VAL cc_start: 0.8384 (t) cc_final: 0.8127 (m) REVERT: A 41 LYS cc_start: 0.8503 (mmmt) cc_final: 0.7930 (mmtp) REVERT: A 61 ASN cc_start: 0.7715 (m-40) cc_final: 0.7501 (p0) REVERT: A 121 ASN cc_start: 0.7237 (t0) cc_final: 0.6834 (t0) REVERT: A 224 GLU cc_start: 0.8468 (pm20) cc_final: 0.8180 (pm20) REVERT: A 235 ILE cc_start: 0.8861 (mt) cc_final: 0.8413 (tp) REVERT: A 237 ARG cc_start: 0.7875 (mtp180) cc_final: 0.7669 (mtp180) REVERT: A 270 LEU cc_start: 0.8297 (mt) cc_final: 0.7750 (mp) REVERT: A 271 GLN cc_start: 0.7596 (mm-40) cc_final: 0.7334 (mm-40) REVERT: A 278 LYS cc_start: 0.8762 (ttmt) cc_final: 0.8350 (tttt) REVERT: A 297 SER cc_start: 0.8581 (m) cc_final: 0.8235 (p) REVERT: A 498 ARG cc_start: 0.7072 (mmm160) cc_final: 0.6753 (mmm160) REVERT: A 532 ASN cc_start: 0.8487 (t0) cc_final: 0.8280 (t0) REVERT: A 537 LYS cc_start: 0.8165 (tptt) cc_final: 0.7958 (tptt) REVERT: A 568 ASP cc_start: 0.7385 (t70) cc_final: 0.7099 (t70) REVERT: A 587 ILE cc_start: 0.8831 (mt) cc_final: 0.8414 (tp) REVERT: A 602 THR cc_start: 0.8740 (OUTLIER) cc_final: 0.8328 (p) REVERT: A 642 VAL cc_start: 0.9209 (t) cc_final: 0.8971 (m) REVERT: A 655 TYR cc_start: 0.8298 (t80) cc_final: 0.7871 (t80) REVERT: A 664 ILE cc_start: 0.8971 (mt) cc_final: 0.8634 (mm) REVERT: A 725 GLU cc_start: 0.7939 (tt0) cc_final: 0.7304 (tm-30) REVERT: A 740 MET cc_start: 0.8110 (mpp) cc_final: 0.7649 (mpp) REVERT: A 741 TYR cc_start: 0.8516 (t80) cc_final: 0.8040 (t80) REVERT: A 742 ILE cc_start: 0.8553 (mm) cc_final: 0.7888 (tp) REVERT: A 764 LYS cc_start: 0.8242 (ttpp) cc_final: 0.8029 (tppt) REVERT: A 765 ARG cc_start: 0.8017 (ttp-170) cc_final: 0.7614 (ttm170) REVERT: A 781 VAL cc_start: 0.9146 (t) cc_final: 0.8925 (p) REVERT: A 858 LEU cc_start: 0.8792 (mp) cc_final: 0.8528 (mm) REVERT: A 911 VAL cc_start: 0.9047 (t) cc_final: 0.8678 (m) REVERT: A 914 ASN cc_start: 0.8003 (p0) cc_final: 0.7311 (p0) REVERT: A 918 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7652 (mt-10) REVERT: A 960 ASN cc_start: 0.8492 (OUTLIER) cc_final: 0.7686 (t0) REVERT: A 964 LYS cc_start: 0.8661 (tmtm) cc_final: 0.8412 (mmmt) REVERT: A 977 LEU cc_start: 0.8460 (mp) cc_final: 0.7251 (mm) REVERT: A 981 PHE cc_start: 0.6187 (m-10) cc_final: 0.5967 (m-80) REVERT: A 994 ASP cc_start: 0.7436 (m-30) cc_final: 0.7127 (m-30) REVERT: A 998 THR cc_start: 0.8056 (m) cc_final: 0.7766 (p) REVERT: A 1031 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7206 (mt-10) REVERT: A 1073 LYS cc_start: 0.8276 (mmtt) cc_final: 0.7897 (mmtt) REVERT: A 1081 ILE cc_start: 0.8560 (pt) cc_final: 0.8287 (mm) REVERT: A 1118 ASP cc_start: 0.7824 (t70) cc_final: 0.7577 (t0) REVERT: A 1138 TYR cc_start: 0.7353 (t80) cc_final: 0.7010 (t80) REVERT: B 41 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8552 (mttp) REVERT: B 44 ARG cc_start: 0.8426 (mtt90) cc_final: 0.7847 (mtt180) REVERT: B 53 ASP cc_start: 0.6952 (t0) cc_final: 0.6506 (t0) REVERT: B 104 TRP cc_start: 0.7866 (m-90) cc_final: 0.7530 (m-90) REVERT: B 106 PHE cc_start: 0.7727 (m-80) cc_final: 0.7475 (m-80) REVERT: B 129 LYS cc_start: 0.7917 (tppt) cc_final: 0.7550 (tmtt) REVERT: B 192 PHE cc_start: 0.8506 (m-80) cc_final: 0.8060 (m-10) REVERT: B 193 LYS cc_start: 0.8464 (ttpt) cc_final: 0.8259 (ttmt) REVERT: B 200 LYS cc_start: 0.8769 (mttt) cc_final: 0.8325 (mtmt) REVERT: B 204 LYS cc_start: 0.7742 (tppt) cc_final: 0.7345 (tptp) REVERT: B 224 GLU cc_start: 0.7475 (mm-30) cc_final: 0.7047 (mm-30) REVERT: B 228 ASP cc_start: 0.7065 (t70) cc_final: 0.6111 (t0) REVERT: B 229 LEU cc_start: 0.8769 (mm) cc_final: 0.8517 (mm) REVERT: B 271 GLN cc_start: 0.7849 (mt0) cc_final: 0.7403 (mm-40) REVERT: B 275 PHE cc_start: 0.7888 (m-80) cc_final: 0.7411 (m-80) REVERT: B 278 LYS cc_start: 0.8875 (ttmp) cc_final: 0.8373 (ttmm) REVERT: B 307 THR cc_start: 0.8291 (m) cc_final: 0.8022 (p) REVERT: B 324 GLU cc_start: 0.7625 (pm20) cc_final: 0.7224 (pm20) REVERT: B 565 PHE cc_start: 0.6700 (m-10) cc_final: 0.6423 (m-10) REVERT: B 663 ASP cc_start: 0.7676 (t70) cc_final: 0.7458 (t70) REVERT: B 695 TYR cc_start: 0.8176 (p90) cc_final: 0.7585 (p90) REVERT: B 712 ILE cc_start: 0.8758 (tp) cc_final: 0.8514 (tp) REVERT: B 725 GLU cc_start: 0.8131 (tt0) cc_final: 0.7890 (tp30) REVERT: B 730 SER cc_start: 0.9018 (t) cc_final: 0.8683 (p) REVERT: B 737 ASP cc_start: 0.7780 (t0) cc_final: 0.7495 (p0) REVERT: B 762 GLN cc_start: 0.8004 (mp10) cc_final: 0.7750 (mp10) REVERT: B 764 LYS cc_start: 0.8578 (tppt) cc_final: 0.8259 (tppt) REVERT: B 765 ARG cc_start: 0.8053 (tpp80) cc_final: 0.7647 (tpp80) REVERT: B 780 GLU cc_start: 0.7882 (pt0) cc_final: 0.7650 (tp30) REVERT: B 796 TYR cc_start: 0.8451 (t80) cc_final: 0.8183 (t80) REVERT: B 803 SER cc_start: 0.8547 (m) cc_final: 0.8177 (p) REVERT: B 804 GLN cc_start: 0.8430 (mp10) cc_final: 0.8159 (mp10) REVERT: B 819 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7566 (mt-10) REVERT: B 820 ASP cc_start: 0.7728 (m-30) cc_final: 0.7411 (m-30) REVERT: B 868 GLU cc_start: 0.8035 (tp30) cc_final: 0.7828 (mm-30) REVERT: B 869 MET cc_start: 0.8568 (mtt) cc_final: 0.8312 (mtt) REVERT: B 895 GLN cc_start: 0.8261 (pm20) cc_final: 0.7921 (pm20) REVERT: B 902 MET cc_start: 0.8613 (tpp) cc_final: 0.8219 (tpp) REVERT: B 916 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8669 (tp) REVERT: B 921 LYS cc_start: 0.8690 (mmmt) cc_final: 0.8294 (mmmm) REVERT: B 925 ASN cc_start: 0.8924 (m-40) cc_final: 0.8698 (m-40) REVERT: B 929 SER cc_start: 0.8815 (m) cc_final: 0.8479 (p) REVERT: B 933 LYS cc_start: 0.8654 (mtmt) cc_final: 0.8176 (mtpp) REVERT: B 949 GLN cc_start: 0.8623 (mm-40) cc_final: 0.8240 (mm110) REVERT: B 950 ASP cc_start: 0.7793 (m-30) cc_final: 0.7181 (m-30) REVERT: B 965 GLN cc_start: 0.8444 (mm-40) cc_final: 0.8057 (mm-40) REVERT: B 996 LEU cc_start: 0.8629 (mt) cc_final: 0.8396 (mm) REVERT: B 1031 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7481 (mm-30) REVERT: B 1038 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8591 (mmmm) REVERT: B 1081 ILE cc_start: 0.8852 (pt) cc_final: 0.8467 (mm) REVERT: B 1113 GLN cc_start: 0.7824 (mm110) cc_final: 0.7597 (mm-40) REVERT: B 1118 ASP cc_start: 0.7463 (t70) cc_final: 0.6972 (t0) REVERT: C 67 VAL cc_start: 0.7200 (OUTLIER) cc_final: 0.6935 (t) REVERT: C 91 TYR cc_start: 0.7047 (t80) cc_final: 0.6756 (t80) REVERT: C 101 ILE cc_start: 0.8657 (mt) cc_final: 0.8236 (tp) REVERT: C 170 TYR cc_start: 0.7943 (t80) cc_final: 0.7722 (t80) REVERT: C 198 TYR cc_start: 0.6527 (m-80) cc_final: 0.5913 (m-10) REVERT: C 224 GLU cc_start: 0.7341 (pm20) cc_final: 0.6656 (mp0) REVERT: C 228 ASP cc_start: 0.6877 (t70) cc_final: 0.5111 (t0) REVERT: C 269 TYR cc_start: 0.7364 (m-10) cc_final: 0.6853 (m-10) REVERT: C 271 GLN cc_start: 0.7816 (tm-30) cc_final: 0.7480 (tm-30) REVERT: C 297 SER cc_start: 0.8448 (m) cc_final: 0.8062 (p) REVERT: C 298 GLU cc_start: 0.8263 (tt0) cc_final: 0.7727 (tp30) REVERT: C 375 PHE cc_start: 0.7489 (m-80) cc_final: 0.6793 (m-10) REVERT: C 406 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7692 (mt-10) REVERT: C 421 TYR cc_start: 0.7221 (m-10) cc_final: 0.6545 (m-80) REVERT: C 436 TRP cc_start: 0.7445 (p90) cc_final: 0.6871 (p-90) REVERT: C 454 ARG cc_start: 0.7558 (ttt180) cc_final: 0.6999 (ttm170) REVERT: C 455 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7583 (tm) REVERT: C 535 LYS cc_start: 0.8696 (mmmm) cc_final: 0.8456 (mmmm) REVERT: C 537 LYS cc_start: 0.8584 (tmtt) cc_final: 0.8320 (tmtt) REVERT: C 542 ASN cc_start: 0.8013 (t0) cc_final: 0.7658 (t0) REVERT: C 547 LYS cc_start: 0.8607 (mtmm) cc_final: 0.8395 (mtmm) REVERT: C 571 ASP cc_start: 0.6232 (t0) cc_final: 0.5964 (t0) REVERT: C 587 ILE cc_start: 0.9072 (mt) cc_final: 0.8673 (pt) REVERT: C 598 ILE cc_start: 0.8825 (OUTLIER) cc_final: 0.8479 (tt) REVERT: C 602 THR cc_start: 0.8793 (OUTLIER) cc_final: 0.8384 (p) REVERT: C 663 ASP cc_start: 0.7674 (t0) cc_final: 0.7406 (t0) REVERT: C 664 ILE cc_start: 0.8504 (mt) cc_final: 0.8215 (mm) REVERT: C 675 GLN cc_start: 0.7862 (mm110) cc_final: 0.7470 (mm110) REVERT: C 705 VAL cc_start: 0.8719 (OUTLIER) cc_final: 0.8456 (m) REVERT: C 708 SER cc_start: 0.8922 (t) cc_final: 0.8414 (m) REVERT: C 726 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8222 (mm) REVERT: C 773 GLU cc_start: 0.7417 (tm-30) cc_final: 0.6843 (tm-30) REVERT: C 820 ASP cc_start: 0.7774 (m-30) cc_final: 0.7215 (m-30) REVERT: C 823 PHE cc_start: 0.7662 (m-80) cc_final: 0.7383 (m-80) REVERT: C 853 GLN cc_start: 0.8173 (mt0) cc_final: 0.7831 (mt0) REVERT: C 867 ASP cc_start: 0.8136 (m-30) cc_final: 0.7737 (m-30) REVERT: C 868 GLU cc_start: 0.7837 (tp30) cc_final: 0.7303 (tp30) REVERT: C 872 GLN cc_start: 0.8383 (tp40) cc_final: 0.8018 (tp40) REVERT: C 901 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8306 (tm-30) REVERT: C 914 ASN cc_start: 0.8501 (p0) cc_final: 0.8075 (p0) REVERT: C 918 GLU cc_start: 0.7467 (mp0) cc_final: 0.7015 (mp0) REVERT: C 933 LYS cc_start: 0.8278 (mtmm) cc_final: 0.7837 (mmmm) REVERT: C 949 GLN cc_start: 0.8580 (mm-40) cc_final: 0.7881 (mm-40) REVERT: C 950 ASP cc_start: 0.7609 (t70) cc_final: 0.7055 (t0) REVERT: C 953 ASN cc_start: 0.8527 (m-40) cc_final: 0.8147 (m110) REVERT: C 962 LEU cc_start: 0.9334 (tp) cc_final: 0.8962 (tp) REVERT: C 964 LYS cc_start: 0.8658 (mtmp) cc_final: 0.8281 (mmmm) REVERT: C 966 LEU cc_start: 0.9109 (tt) cc_final: 0.8889 (tp) REVERT: C 1014 ARG cc_start: 0.8024 (tpp80) cc_final: 0.7741 (tpp80) REVERT: C 1017 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7613 (tm-30) REVERT: C 1038 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7824 (mmmm) REVERT: C 1048 HIS cc_start: 0.8463 (t-90) cc_final: 0.7993 (t-170) REVERT: C 1103 PHE cc_start: 0.8528 (m-10) cc_final: 0.8317 (m-10) REVERT: C 1111 GLU cc_start: 0.7183 (tm-30) cc_final: 0.6712 (tm-30) REVERT: D 6 GLN cc_start: 0.1216 (OUTLIER) cc_final: 0.0162 (tp40) REVERT: D 49 MET cc_start: 0.5231 (tpt) cc_final: 0.4259 (ptm) REVERT: D 83 GLU cc_start: 0.2506 (OUTLIER) cc_final: 0.2189 (pp20) REVERT: D 160 MET cc_start: 0.2878 (mmm) cc_final: 0.2421 (mmp) REVERT: E 156 HIS cc_start: 0.7503 (m-70) cc_final: 0.7179 (m90) REVERT: E 158 MET cc_start: 0.5113 (mmm) cc_final: 0.4755 (mmm) REVERT: F 146 LEU cc_start: 0.8778 (mp) cc_final: 0.8142 (tp) REVERT: F 159 TYR cc_start: 0.7140 (m-80) cc_final: 0.5577 (m-80) REVERT: F 178 TYR cc_start: 0.6733 (m-80) cc_final: 0.6280 (m-80) REVERT: F 206 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8621 (mp) REVERT: G 4 LEU cc_start: 0.8699 (mt) cc_final: 0.8291 (tp) REVERT: G 36 TRP cc_start: 0.5186 (m100) cc_final: 0.4826 (m100) REVERT: G 191 ARG cc_start: 0.7104 (ptt90) cc_final: 0.6617 (ptt90) REVERT: G 238 MET cc_start: 0.6586 (mmm) cc_final: 0.6357 (mmm) outliers start: 193 outliers final: 129 residues processed: 823 average time/residue: 0.2025 time to fit residues: 267.0199 Evaluate side-chains 801 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 655 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 659 SER Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 960 ASN Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 98 ASN Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 153 PHE Chi-restraints excluded: chain F residue 156 SER Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain G residue 197 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 319 optimal weight: 30.0000 chunk 345 optimal weight: 9.9990 chunk 69 optimal weight: 0.3980 chunk 158 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 281 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN A 519 HIS A 957 GLN A 960 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 GLN ** G 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.163473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.118531 restraints weight = 66591.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.122694 restraints weight = 31261.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.125315 restraints weight = 18226.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.126996 restraints weight = 12421.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.128015 restraints weight = 9563.096| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 32215 Z= 0.183 Angle : 0.681 11.780 43907 Z= 0.339 Chirality : 0.046 0.262 4962 Planarity : 0.005 0.086 5654 Dihedral : 6.206 81.410 4461 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.52 % Favored : 90.43 % Rotamer: Outliers : 5.36 % Allowed : 19.26 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.45 (0.13), residues: 3970 helix: 0.96 (0.21), residues: 681 sheet: -1.15 (0.18), residues: 806 loop : -2.73 (0.11), residues: 2483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 328 TYR 0.036 0.001 TYR A 170 PHE 0.041 0.002 PHE B 981 TRP 0.037 0.002 TRP B 64 HIS 0.024 0.002 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 (32147) covalent geometry : angle 0.67136 / 0.34 (43750) SS BOND : bond 0.00381 / 0.28 ( 47) SS BOND : angle 2.05454 / 1.47 ( 94) hydrogen bonds : bond 0.03440 / 2.26 ( 851) hydrogen bonds : angle 4.84825 / 3.37 ( 2274) link_NAG-ASN : bond 0.00269 / 0.21 ( 21) link_NAG-ASN : angle 1.96530 / 1.34 ( 63) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7940 Ramachandran restraints generated. 3970 Oldfield, 0 Emsley, 3970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7940 Ramachandran restraints generated. 3970 Oldfield, 0 Emsley, 3970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 857 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 673 time to evaluate : 1.134 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 36 VAL cc_start: 0.8385 (t) cc_final: 0.8119 (m) REVERT: A 41 LYS cc_start: 0.8520 (mmmt) cc_final: 0.7910 (mmtp) REVERT: A 117 LEU cc_start: 0.7302 (mt) cc_final: 0.6844 (mt) REVERT: A 121 ASN cc_start: 0.7143 (t0) cc_final: 0.6679 (t0) REVERT: A 224 GLU cc_start: 0.8454 (pm20) cc_final: 0.8162 (pm20) REVERT: A 235 ILE cc_start: 0.8819 (mt) cc_final: 0.8568 (mm) REVERT: A 238 PHE cc_start: 0.8857 (p90) cc_final: 0.8553 (p90) REVERT: A 271 GLN cc_start: 0.7562 (mm-40) cc_final: 0.7323 (mt0) REVERT: A 278 LYS cc_start: 0.8742 (ttmt) cc_final: 0.8386 (tttt) REVERT: A 293 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8257 (mt) REVERT: A 297 SER cc_start: 0.8559 (m) cc_final: 0.8191 (p) REVERT: A 498 ARG cc_start: 0.7088 (mmm160) cc_final: 0.6747 (mmm160) REVERT: A 532 ASN cc_start: 0.8569 (t0) cc_final: 0.8359 (t0) REVERT: A 568 ASP cc_start: 0.7447 (t70) cc_final: 0.7117 (t70) REVERT: A 587 ILE cc_start: 0.8837 (mt) cc_final: 0.8404 (tp) REVERT: A 602 THR cc_start: 0.8736 (OUTLIER) cc_final: 0.8311 (p) REVERT: A 642 VAL cc_start: 0.9177 (t) cc_final: 0.8964 (m) REVERT: A 655 TYR cc_start: 0.8260 (t80) cc_final: 0.7901 (t80) REVERT: A 664 ILE cc_start: 0.8982 (mt) cc_final: 0.8654 (mm) REVERT: A 740 MET cc_start: 0.8119 (mpp) cc_final: 0.7754 (mpp) REVERT: A 742 ILE cc_start: 0.8562 (mm) cc_final: 0.8244 (tp) REVERT: A 764 LYS cc_start: 0.8234 (ttpp) cc_final: 0.7998 (tppt) REVERT: A 765 ARG cc_start: 0.8006 (ttp-170) cc_final: 0.7587 (ttm170) REVERT: A 858 LEU cc_start: 0.8742 (mp) cc_final: 0.8537 (mm) REVERT: A 902 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.8331 (tpp) REVERT: A 911 VAL cc_start: 0.9036 (t) cc_final: 0.8664 (m) REVERT: A 914 ASN cc_start: 0.8007 (p0) cc_final: 0.7303 (p0) REVERT: A 918 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7623 (mt-10) REVERT: A 960 ASN cc_start: 0.8546 (OUTLIER) cc_final: 0.8136 (t0) REVERT: A 977 LEU cc_start: 0.8533 (mp) cc_final: 0.7140 (mm) REVERT: A 981 PHE cc_start: 0.6228 (m-10) cc_final: 0.5990 (m-80) REVERT: A 994 ASP cc_start: 0.7401 (m-30) cc_final: 0.7107 (m-30) REVERT: A 998 THR cc_start: 0.8037 (m) cc_final: 0.7744 (p) REVERT: A 1031 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7218 (mt-10) REVERT: A 1073 LYS cc_start: 0.8314 (mmtt) cc_final: 0.7902 (mmtt) REVERT: A 1081 ILE cc_start: 0.8618 (pt) cc_final: 0.8304 (mm) REVERT: A 1107 ARG cc_start: 0.7510 (mtt180) cc_final: 0.7135 (mtm-85) REVERT: A 1118 ASP cc_start: 0.7797 (t70) cc_final: 0.7580 (t0) REVERT: A 1138 TYR cc_start: 0.7306 (t80) cc_final: 0.6973 (t80) REVERT: B 41 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8503 (mttp) REVERT: B 64 TRP cc_start: 0.7795 (t60) cc_final: 0.7530 (t-100) REVERT: B 104 TRP cc_start: 0.7850 (m-90) cc_final: 0.7420 (m-90) REVERT: B 106 PHE cc_start: 0.7754 (m-80) cc_final: 0.7446 (m-80) REVERT: B 129 LYS cc_start: 0.7977 (tppt) cc_final: 0.7629 (tmtt) REVERT: B 192 PHE cc_start: 0.8518 (m-80) cc_final: 0.8056 (m-10) REVERT: B 200 LYS cc_start: 0.8762 (mttt) cc_final: 0.8258 (mtmt) REVERT: B 204 LYS cc_start: 0.7783 (tppt) cc_final: 0.7419 (tptp) REVERT: B 205 HIS cc_start: 0.7767 (t70) cc_final: 0.7539 (t-90) REVERT: B 224 GLU cc_start: 0.7487 (mm-30) cc_final: 0.7020 (mm-30) REVERT: B 228 ASP cc_start: 0.7032 (t70) cc_final: 0.6136 (t0) REVERT: B 229 LEU cc_start: 0.8701 (mm) cc_final: 0.8428 (mm) REVERT: B 269 TYR cc_start: 0.7479 (m-80) cc_final: 0.6888 (m-80) REVERT: B 271 GLN cc_start: 0.7893 (mt0) cc_final: 0.7485 (mp-120) REVERT: B 275 PHE cc_start: 0.7900 (m-80) cc_final: 0.7359 (m-80) REVERT: B 277 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8533 (mp) REVERT: B 278 LYS cc_start: 0.8906 (ttmp) cc_final: 0.8401 (ttmm) REVERT: B 324 GLU cc_start: 0.7679 (pm20) cc_final: 0.7265 (pm20) REVERT: B 353 TRP cc_start: 0.5747 (OUTLIER) cc_final: 0.5051 (p-90) REVERT: B 565 PHE cc_start: 0.6723 (m-10) cc_final: 0.6481 (m-10) REVERT: B 663 ASP cc_start: 0.7684 (t70) cc_final: 0.7463 (t70) REVERT: B 695 TYR cc_start: 0.8171 (p90) cc_final: 0.7550 (p90) REVERT: B 712 ILE cc_start: 0.8693 (tp) cc_final: 0.8490 (tp) REVERT: B 725 GLU cc_start: 0.8076 (tt0) cc_final: 0.7823 (tp30) REVERT: B 726 ILE cc_start: 0.9185 (OUTLIER) cc_final: 0.8300 (mm) REVERT: B 730 SER cc_start: 0.9052 (t) cc_final: 0.8819 (t) REVERT: B 737 ASP cc_start: 0.7870 (t0) cc_final: 0.7381 (p0) REVERT: B 740 MET cc_start: 0.7658 (OUTLIER) cc_final: 0.6902 (tmm) REVERT: B 762 GLN cc_start: 0.7980 (mp10) cc_final: 0.7744 (mp10) REVERT: B 764 LYS cc_start: 0.8537 (tppt) cc_final: 0.8208 (tppt) REVERT: B 780 GLU cc_start: 0.7919 (pt0) cc_final: 0.7640 (tp30) REVERT: B 796 TYR cc_start: 0.8452 (t80) cc_final: 0.8210 (t80) REVERT: B 803 SER cc_start: 0.8524 (m) cc_final: 0.8238 (p) REVERT: B 804 GLN cc_start: 0.8404 (mp10) cc_final: 0.8149 (mp10) REVERT: B 819 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7568 (mt-10) REVERT: B 820 ASP cc_start: 0.7636 (m-30) cc_final: 0.7322 (m-30) REVERT: B 869 MET cc_start: 0.8558 (mtt) cc_final: 0.8301 (mtt) REVERT: B 895 GLN cc_start: 0.8299 (pm20) cc_final: 0.7966 (pm20) REVERT: B 900 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.7962 (mpp) REVERT: B 916 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8677 (tp) REVERT: B 921 LYS cc_start: 0.8720 (mmmt) cc_final: 0.8308 (mmmm) REVERT: B 925 ASN cc_start: 0.8942 (m-40) cc_final: 0.8693 (m-40) REVERT: B 929 SER cc_start: 0.8802 (m) cc_final: 0.8486 (p) REVERT: B 933 LYS cc_start: 0.8615 (mtmt) cc_final: 0.8219 (mtpp) REVERT: B 949 GLN cc_start: 0.8637 (mm-40) cc_final: 0.8231 (mm110) REVERT: B 950 ASP cc_start: 0.7825 (m-30) cc_final: 0.7214 (m-30) REVERT: B 965 GLN cc_start: 0.8417 (mm-40) cc_final: 0.8023 (mm-40) REVERT: B 996 LEU cc_start: 0.8631 (mt) cc_final: 0.8394 (mm) REVERT: B 1031 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7488 (mm-30) REVERT: B 1038 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8555 (mmmm) REVERT: B 1081 ILE cc_start: 0.8809 (pt) cc_final: 0.8435 (mm) REVERT: B 1118 ASP cc_start: 0.7434 (t70) cc_final: 0.6964 (t0) REVERT: C 101 ILE cc_start: 0.8637 (mt) cc_final: 0.8174 (tp) REVERT: C 198 TYR cc_start: 0.6506 (m-80) cc_final: 0.5841 (m-10) REVERT: C 224 GLU cc_start: 0.7276 (pm20) cc_final: 0.6595 (mp0) REVERT: C 228 ASP cc_start: 0.6882 (t70) cc_final: 0.5230 (t0) REVERT: C 269 TYR cc_start: 0.7348 (m-10) cc_final: 0.6800 (m-10) REVERT: C 271 GLN cc_start: 0.7827 (tm-30) cc_final: 0.7493 (tm-30) REVERT: C 297 SER cc_start: 0.8412 (m) cc_final: 0.8040 (p) REVERT: C 298 GLU cc_start: 0.8239 (tt0) cc_final: 0.7706 (tp30) REVERT: C 357 ARG cc_start: 0.7639 (ttt90) cc_final: 0.7306 (ttt-90) REVERT: C 375 PHE cc_start: 0.7545 (m-80) cc_final: 0.7009 (m-10) REVERT: C 394 ASN cc_start: 0.8255 (t0) cc_final: 0.6767 (t0) REVERT: C 406 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7617 (mt-10) REVERT: C 421 TYR cc_start: 0.7237 (m-10) cc_final: 0.6573 (m-80) REVERT: C 436 TRP cc_start: 0.7382 (p90) cc_final: 0.6875 (p-90) REVERT: C 454 ARG cc_start: 0.7576 (ttt180) cc_final: 0.6997 (ttm170) REVERT: C 455 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7614 (tm) REVERT: C 535 LYS cc_start: 0.8818 (mmmm) cc_final: 0.8535 (mmmt) REVERT: C 542 ASN cc_start: 0.8020 (t0) cc_final: 0.7669 (t0) REVERT: C 547 LYS cc_start: 0.8621 (mtmm) cc_final: 0.8407 (mtmm) REVERT: C 571 ASP cc_start: 0.6198 (t0) cc_final: 0.5934 (t0) REVERT: C 587 ILE cc_start: 0.9067 (mt) cc_final: 0.8653 (pt) REVERT: C 602 THR cc_start: 0.8734 (OUTLIER) cc_final: 0.8307 (p) REVERT: C 643 PHE cc_start: 0.7826 (t80) cc_final: 0.7618 (t80) REVERT: C 663 ASP cc_start: 0.7648 (t0) cc_final: 0.7414 (t0) REVERT: C 664 ILE cc_start: 0.8510 (mt) cc_final: 0.8169 (mm) REVERT: C 675 GLN cc_start: 0.7810 (mm110) cc_final: 0.7401 (mm110) REVERT: C 705 VAL cc_start: 0.8729 (t) cc_final: 0.8443 (m) REVERT: C 708 SER cc_start: 0.8928 (t) cc_final: 0.8384 (m) REVERT: C 726 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8434 (mm) REVERT: C 773 GLU cc_start: 0.7355 (tm-30) cc_final: 0.6815 (tm-30) REVERT: C 816 SER cc_start: 0.8522 (OUTLIER) cc_final: 0.7000 (m) REVERT: C 820 ASP cc_start: 0.7722 (m-30) cc_final: 0.7170 (m-30) REVERT: C 823 PHE cc_start: 0.7613 (m-80) cc_final: 0.7374 (m-80) REVERT: C 853 GLN cc_start: 0.8173 (mt0) cc_final: 0.7879 (mt0) REVERT: C 867 ASP cc_start: 0.8113 (m-30) cc_final: 0.7761 (m-30) REVERT: C 868 GLU cc_start: 0.7895 (tp30) cc_final: 0.7298 (tp30) REVERT: C 872 GLN cc_start: 0.8378 (tp40) cc_final: 0.7990 (tp40) REVERT: C 901 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8290 (tm-30) REVERT: C 914 ASN cc_start: 0.8448 (p0) cc_final: 0.8044 (p0) REVERT: C 918 GLU cc_start: 0.7516 (mp0) cc_final: 0.7032 (mp0) REVERT: C 933 LYS cc_start: 0.8240 (mtmm) cc_final: 0.7798 (mmmm) REVERT: C 949 GLN cc_start: 0.8512 (mm-40) cc_final: 0.7869 (mm-40) REVERT: C 950 ASP cc_start: 0.7559 (t70) cc_final: 0.7002 (t0) REVERT: C 953 ASN cc_start: 0.8518 (m-40) cc_final: 0.8135 (m110) REVERT: C 964 LYS cc_start: 0.8663 (mtmp) cc_final: 0.8266 (mmmm) REVERT: C 966 LEU cc_start: 0.9150 (tt) cc_final: 0.8877 (tp) REVERT: C 979 ASP cc_start: 0.8483 (m-30) cc_final: 0.8010 (m-30) REVERT: C 1017 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7642 (tm-30) REVERT: C 1038 LYS cc_start: 0.8097 (OUTLIER) cc_final: 0.7770 (mmmm) REVERT: C 1048 HIS cc_start: 0.8421 (t-90) cc_final: 0.7951 (t70) REVERT: C 1111 GLU cc_start: 0.7184 (tm-30) cc_final: 0.6911 (tm-30) REVERT: D 6 GLN cc_start: 0.1011 (OUTLIER) cc_final: 0.0490 (tp40) REVERT: D 83 GLU cc_start: 0.2509 (OUTLIER) cc_final: 0.2190 (pp20) REVERT: E 156 HIS cc_start: 0.7454 (m-70) cc_final: 0.7095 (m90) REVERT: E 158 MET cc_start: 0.5042 (mmm) cc_final: 0.4662 (mmm) REVERT: F 39 GLN cc_start: 0.7858 (pp30) cc_final: 0.7489 (pp30) REVERT: F 146 LEU cc_start: 0.8756 (mp) cc_final: 0.8081 (tp) REVERT: F 159 TYR cc_start: 0.7191 (m-80) cc_final: 0.5602 (m-80) REVERT: F 178 TYR cc_start: 0.6704 (m-80) cc_final: 0.6218 (m-80) REVERT: F 206 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8616 (mt) REVERT: G 4 LEU cc_start: 0.8628 (mt) cc_final: 0.8305 (tp) REVERT: G 28 ASN cc_start: 0.8582 (p0) cc_final: 0.8317 (p0) REVERT: G 36 TRP cc_start: 0.5238 (m100) cc_final: 0.4876 (m100) REVERT: G 54 GLN cc_start: 0.8004 (mm-40) cc_final: 0.7521 (mm-40) REVERT: G 128 LEU cc_start: 0.7497 (mm) cc_final: 0.7159 (mm) REVERT: G 191 ARG cc_start: 0.7063 (ptt90) cc_final: 0.6541 (ptt90) REVERT: G 238 MET cc_start: 0.6613 (mmm) cc_final: 0.6402 (mmm) outliers start: 184 outliers final: 135 residues processed: 802 average time/residue: 0.2018 time to fit residues: 260.8101 Evaluate side-chains 809 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 652 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 160 TYR Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 659 SER Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 960 ASN Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 207 MET Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 98 ASN Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 153 PHE Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain G residue 197 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 349 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 304 optimal weight: 2.9990 chunk 224 optimal weight: 3.9990 chunk 265 optimal weight: 3.9990 chunk 243 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 162 optimal weight: 0.3980 chunk 160 optimal weight: 3.9990 chunk 141 optimal weight: 0.1980 chunk 100 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 HIS A 61 ASN ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN A 519 HIS A 957 GLN A 960 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 ASN F 209 ASN ** G 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.163201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.118758 restraints weight = 67397.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.122994 restraints weight = 31407.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.125649 restraints weight = 18185.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.127322 restraints weight = 12312.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.128474 restraints weight = 9415.701| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.4791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 32215 Z= 0.156 Angle : 0.682 14.287 43907 Z= 0.338 Chirality : 0.046 0.280 4962 Planarity : 0.004 0.062 5654 Dihedral : 6.149 81.398 4457 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.42 % Favored : 90.55 % Rotamer: Outliers : 5.39 % Allowed : 19.38 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.13), residues: 3970 helix: 1.04 (0.21), residues: 677 sheet: -1.07 (0.18), residues: 808 loop : -2.65 (0.11), residues: 2485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 577 TYR 0.028 0.001 TYR E 204 PHE 0.042 0.002 PHE B 981 TRP 0.031 0.002 TRP B 64 HIS 0.016 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 (32147) covalent geometry : angle 0.67192 / 0.33 (43750) SS BOND : bond 0.00347 / 0.28 ( 47) SS BOND : angle 2.15845 / 1.51 ( 94) hydrogen bonds : bond 0.03311 / 2.17 ( 851) hydrogen bonds : angle 4.83016 / 3.36 ( 2274) link_NAG-ASN : bond 0.00301 / 0.20 ( 21) link_NAG-ASN : angle 1.99078 / 1.37 ( 63) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7940 Ramachandran restraints generated. 3970 Oldfield, 0 Emsley, 3970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7940 Ramachandran restraints generated. 3970 Oldfield, 0 Emsley, 3970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 874 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 689 time to evaluate : 1.180 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 36 VAL cc_start: 0.8412 (t) cc_final: 0.8142 (m) REVERT: A 117 LEU cc_start: 0.7190 (mt) cc_final: 0.6717 (mt) REVERT: A 121 ASN cc_start: 0.7267 (t0) cc_final: 0.6843 (t0) REVERT: A 224 GLU cc_start: 0.8448 (pm20) cc_final: 0.8131 (pm20) REVERT: A 235 ILE cc_start: 0.8816 (mt) cc_final: 0.8574 (mm) REVERT: A 238 PHE cc_start: 0.8821 (p90) cc_final: 0.8442 (p90) REVERT: A 271 GLN cc_start: 0.7526 (mm-40) cc_final: 0.7305 (mt0) REVERT: A 278 LYS cc_start: 0.8709 (ttmt) cc_final: 0.8366 (tttt) REVERT: A 293 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8327 (mt) REVERT: A 294 ASP cc_start: 0.7834 (t70) cc_final: 0.7557 (p0) REVERT: A 297 SER cc_start: 0.8546 (m) cc_final: 0.7974 (p) REVERT: A 498 ARG cc_start: 0.7086 (mmm160) cc_final: 0.6744 (mmm160) REVERT: A 532 ASN cc_start: 0.8591 (t0) cc_final: 0.8375 (t0) REVERT: A 577 ARG cc_start: 0.6421 (tpt170) cc_final: 0.6156 (tpt170) REVERT: A 587 ILE cc_start: 0.8853 (mt) cc_final: 0.8441 (tp) REVERT: A 602 THR cc_start: 0.8713 (OUTLIER) cc_final: 0.8312 (p) REVERT: A 642 VAL cc_start: 0.9183 (t) cc_final: 0.8980 (m) REVERT: A 655 TYR cc_start: 0.8269 (t80) cc_final: 0.7953 (t80) REVERT: A 664 ILE cc_start: 0.8925 (mt) cc_final: 0.8556 (mm) REVERT: A 740 MET cc_start: 0.8066 (mpp) cc_final: 0.7603 (mpp) REVERT: A 742 ILE cc_start: 0.8521 (mm) cc_final: 0.8172 (tp) REVERT: A 764 LYS cc_start: 0.8210 (ttpp) cc_final: 0.7984 (tppt) REVERT: A 765 ARG cc_start: 0.7977 (ttp-170) cc_final: 0.7571 (ttm170) REVERT: A 790 LYS cc_start: 0.8199 (mttp) cc_final: 0.7753 (mmtm) REVERT: A 902 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.8344 (tpp) REVERT: A 911 VAL cc_start: 0.9026 (t) cc_final: 0.8624 (m) REVERT: A 914 ASN cc_start: 0.8035 (p0) cc_final: 0.7334 (p0) REVERT: A 918 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7620 (mt-10) REVERT: A 960 ASN cc_start: 0.8399 (OUTLIER) cc_final: 0.8147 (t0) REVERT: A 964 LYS cc_start: 0.8880 (mmmt) cc_final: 0.8549 (mmmt) REVERT: A 977 LEU cc_start: 0.8489 (mp) cc_final: 0.7159 (mm) REVERT: A 998 THR cc_start: 0.8012 (m) cc_final: 0.7744 (p) REVERT: A 1031 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7200 (mt-10) REVERT: A 1073 LYS cc_start: 0.8328 (mmtt) cc_final: 0.7926 (mmtt) REVERT: A 1081 ILE cc_start: 0.8667 (pt) cc_final: 0.8351 (mm) REVERT: A 1118 ASP cc_start: 0.7783 (t70) cc_final: 0.7524 (t0) REVERT: A 1138 TYR cc_start: 0.7281 (t80) cc_final: 0.6966 (t80) REVERT: B 41 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8512 (mttp) REVERT: B 44 ARG cc_start: 0.8443 (mtt90) cc_final: 0.8054 (mtt180) REVERT: B 104 TRP cc_start: 0.7783 (m-90) cc_final: 0.7421 (m-90) REVERT: B 106 PHE cc_start: 0.7709 (m-80) cc_final: 0.7452 (m-80) REVERT: B 129 LYS cc_start: 0.7953 (tppt) cc_final: 0.7583 (tmtt) REVERT: B 192 PHE cc_start: 0.8485 (m-80) cc_final: 0.8052 (m-10) REVERT: B 193 LYS cc_start: 0.8594 (ttmt) cc_final: 0.8299 (mtpt) REVERT: B 200 LYS cc_start: 0.8794 (mttt) cc_final: 0.8199 (mtmt) REVERT: B 204 LYS cc_start: 0.7802 (tppt) cc_final: 0.7453 (tptp) REVERT: B 205 HIS cc_start: 0.7762 (t70) cc_final: 0.7430 (t-170) REVERT: B 224 GLU cc_start: 0.7474 (mm-30) cc_final: 0.6984 (mm-30) REVERT: B 228 ASP cc_start: 0.7051 (t70) cc_final: 0.6153 (t0) REVERT: B 229 LEU cc_start: 0.8707 (mm) cc_final: 0.8459 (mm) REVERT: B 269 TYR cc_start: 0.7502 (m-80) cc_final: 0.6883 (m-80) REVERT: B 271 GLN cc_start: 0.7868 (mt0) cc_final: 0.7491 (mp-120) REVERT: B 275 PHE cc_start: 0.7887 (m-80) cc_final: 0.7325 (m-80) REVERT: B 278 LYS cc_start: 0.8894 (ttmp) cc_final: 0.8386 (ttmm) REVERT: B 298 GLU cc_start: 0.7372 (mt-10) cc_final: 0.6784 (mm-30) REVERT: B 324 GLU cc_start: 0.7736 (pm20) cc_final: 0.7294 (pm20) REVERT: B 353 TRP cc_start: 0.5743 (OUTLIER) cc_final: 0.5090 (p-90) REVERT: B 434 ILE cc_start: 0.8662 (mt) cc_final: 0.8454 (mt) REVERT: B 565 PHE cc_start: 0.6688 (m-10) cc_final: 0.6458 (m-10) REVERT: B 695 TYR cc_start: 0.8149 (p90) cc_final: 0.7525 (p90) REVERT: B 712 ILE cc_start: 0.8688 (tp) cc_final: 0.8471 (tp) REVERT: B 725 GLU cc_start: 0.8064 (tt0) cc_final: 0.7789 (tp30) REVERT: B 726 ILE cc_start: 0.9168 (OUTLIER) cc_final: 0.8268 (mm) REVERT: B 730 SER cc_start: 0.9045 (t) cc_final: 0.8824 (t) REVERT: B 737 ASP cc_start: 0.7890 (t0) cc_final: 0.7479 (p0) REVERT: B 740 MET cc_start: 0.7675 (OUTLIER) cc_final: 0.7016 (tmm) REVERT: B 764 LYS cc_start: 0.8497 (tppt) cc_final: 0.8191 (tppt) REVERT: B 780 GLU cc_start: 0.7925 (pt0) cc_final: 0.7633 (tp30) REVERT: B 796 TYR cc_start: 0.8442 (t80) cc_final: 0.8231 (t80) REVERT: B 803 SER cc_start: 0.8530 (m) cc_final: 0.8256 (p) REVERT: B 804 GLN cc_start: 0.8390 (mp10) cc_final: 0.8129 (mp10) REVERT: B 819 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7559 (mt-10) REVERT: B 820 ASP cc_start: 0.7613 (m-30) cc_final: 0.7320 (m-30) REVERT: B 869 MET cc_start: 0.8555 (mtt) cc_final: 0.8267 (mtt) REVERT: B 895 GLN cc_start: 0.8314 (pm20) cc_final: 0.7963 (pm20) REVERT: B 900 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.7982 (mpp) REVERT: B 914 ASN cc_start: 0.8542 (p0) cc_final: 0.8117 (p0) REVERT: B 921 LYS cc_start: 0.8710 (mmmt) cc_final: 0.8307 (mmmm) REVERT: B 925 ASN cc_start: 0.8922 (m-40) cc_final: 0.8684 (m-40) REVERT: B 929 SER cc_start: 0.8789 (m) cc_final: 0.8453 (p) REVERT: B 933 LYS cc_start: 0.8637 (mtmt) cc_final: 0.8178 (mtpp) REVERT: B 949 GLN cc_start: 0.8654 (mm-40) cc_final: 0.8226 (mm-40) REVERT: B 950 ASP cc_start: 0.7822 (m-30) cc_final: 0.7201 (m-30) REVERT: B 965 GLN cc_start: 0.8420 (mm-40) cc_final: 0.7978 (mm-40) REVERT: B 996 LEU cc_start: 0.8641 (mt) cc_final: 0.8433 (mm) REVERT: B 1031 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7469 (mm-30) REVERT: B 1038 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8562 (mmmm) REVERT: B 1081 ILE cc_start: 0.8797 (pt) cc_final: 0.8425 (mm) REVERT: B 1107 ARG cc_start: 0.7467 (mtt90) cc_final: 0.7096 (mtm-85) REVERT: B 1118 ASP cc_start: 0.7425 (t70) cc_final: 0.6951 (t0) REVERT: B 1144 GLU cc_start: 0.8103 (mp0) cc_final: 0.7507 (mp0) REVERT: C 101 ILE cc_start: 0.8584 (mt) cc_final: 0.8108 (tp) REVERT: C 195 ILE cc_start: 0.8394 (mm) cc_final: 0.8084 (tp) REVERT: C 198 TYR cc_start: 0.6395 (m-80) cc_final: 0.5796 (m-10) REVERT: C 224 GLU cc_start: 0.7287 (pm20) cc_final: 0.6572 (mp0) REVERT: C 228 ASP cc_start: 0.6897 (t70) cc_final: 0.5223 (t0) REVERT: C 269 TYR cc_start: 0.7310 (m-10) cc_final: 0.6727 (m-80) REVERT: C 271 GLN cc_start: 0.7825 (tm-30) cc_final: 0.7496 (tm-30) REVERT: C 297 SER cc_start: 0.8396 (m) cc_final: 0.7997 (p) REVERT: C 298 GLU cc_start: 0.8237 (tt0) cc_final: 0.7697 (tp30) REVERT: C 357 ARG cc_start: 0.7597 (ttt90) cc_final: 0.7245 (ttt-90) REVERT: C 375 PHE cc_start: 0.7484 (m-80) cc_final: 0.6971 (m-10) REVERT: C 394 ASN cc_start: 0.8121 (t0) cc_final: 0.7268 (t0) REVERT: C 400 PHE cc_start: 0.7706 (p90) cc_final: 0.7096 (p90) REVERT: C 406 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7425 (mt-10) REVERT: C 408 ARG cc_start: 0.9041 (tmm160) cc_final: 0.8710 (ttp80) REVERT: C 421 TYR cc_start: 0.7210 (m-10) cc_final: 0.6917 (m-80) REVERT: C 436 TRP cc_start: 0.7319 (p90) cc_final: 0.6779 (p-90) REVERT: C 454 ARG cc_start: 0.7567 (ttt180) cc_final: 0.7008 (ttm170) REVERT: C 455 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7582 (tm) REVERT: C 535 LYS cc_start: 0.8802 (mmmm) cc_final: 0.8580 (mmmm) REVERT: C 537 LYS cc_start: 0.8597 (tptt) cc_final: 0.8346 (tptp) REVERT: C 542 ASN cc_start: 0.7994 (t0) cc_final: 0.7648 (t0) REVERT: C 547 LYS cc_start: 0.8619 (mtmm) cc_final: 0.8378 (mtmm) REVERT: C 571 ASP cc_start: 0.6207 (t0) cc_final: 0.5937 (t0) REVERT: C 587 ILE cc_start: 0.9041 (mt) cc_final: 0.8642 (pt) REVERT: C 602 THR cc_start: 0.8720 (OUTLIER) cc_final: 0.8285 (p) REVERT: C 643 PHE cc_start: 0.7609 (t80) cc_final: 0.7404 (t80) REVERT: C 664 ILE cc_start: 0.8525 (mt) cc_final: 0.8140 (mm) REVERT: C 675 GLN cc_start: 0.7775 (mm110) cc_final: 0.7364 (mm110) REVERT: C 705 VAL cc_start: 0.8715 (t) cc_final: 0.8442 (m) REVERT: C 708 SER cc_start: 0.8949 (t) cc_final: 0.8421 (m) REVERT: C 726 ILE cc_start: 0.8936 (OUTLIER) cc_final: 0.8424 (pt) REVERT: C 773 GLU cc_start: 0.7383 (tm-30) cc_final: 0.6611 (tm-30) REVERT: C 820 ASP cc_start: 0.7750 (m-30) cc_final: 0.7187 (m-30) REVERT: C 823 PHE cc_start: 0.7600 (m-80) cc_final: 0.7331 (m-80) REVERT: C 853 GLN cc_start: 0.8178 (mt0) cc_final: 0.7849 (mt0) REVERT: C 867 ASP cc_start: 0.8111 (m-30) cc_final: 0.7751 (m-30) REVERT: C 868 GLU cc_start: 0.7873 (tp30) cc_final: 0.7418 (tp30) REVERT: C 872 GLN cc_start: 0.8339 (tp40) cc_final: 0.7966 (tp40) REVERT: C 901 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8362 (tm-30) REVERT: C 914 ASN cc_start: 0.8442 (p0) cc_final: 0.8075 (p0) REVERT: C 918 GLU cc_start: 0.7509 (mp0) cc_final: 0.7001 (mp0) REVERT: C 933 LYS cc_start: 0.8192 (mtmm) cc_final: 0.7741 (mmmm) REVERT: C 949 GLN cc_start: 0.8547 (mm-40) cc_final: 0.7841 (mm-40) REVERT: C 950 ASP cc_start: 0.7565 (t70) cc_final: 0.6997 (t0) REVERT: C 953 ASN cc_start: 0.8471 (m-40) cc_final: 0.8079 (m110) REVERT: C 964 LYS cc_start: 0.8706 (mtmp) cc_final: 0.8272 (mmmm) REVERT: C 966 LEU cc_start: 0.9136 (tt) cc_final: 0.8861 (tp) REVERT: C 1014 ARG cc_start: 0.7878 (tpp80) cc_final: 0.7673 (tpp80) REVERT: C 1017 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7670 (tm-30) REVERT: C 1031 GLU cc_start: 0.8317 (mm-30) cc_final: 0.8116 (mm-30) REVERT: C 1038 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7802 (mmmm) REVERT: C 1048 HIS cc_start: 0.8457 (t-90) cc_final: 0.7924 (t-170) REVERT: C 1111 GLU cc_start: 0.7150 (tm-30) cc_final: 0.6872 (tm-30) REVERT: D 6 GLN cc_start: 0.0828 (OUTLIER) cc_final: 0.0343 (tp40) REVERT: D 83 GLU cc_start: 0.2537 (OUTLIER) cc_final: 0.2205 (pp20) REVERT: D 160 MET cc_start: 0.2806 (mmm) cc_final: 0.2449 (mmp) REVERT: E 156 HIS cc_start: 0.7430 (m-70) cc_final: 0.7053 (m90) REVERT: E 158 MET cc_start: 0.4929 (mmm) cc_final: 0.4569 (mmm) REVERT: F 51 TYR cc_start: 0.7080 (p90) cc_final: 0.6828 (p90) REVERT: F 146 LEU cc_start: 0.8714 (mp) cc_final: 0.8085 (tp) REVERT: F 159 TYR cc_start: 0.7129 (m-80) cc_final: 0.5779 (m-80) REVERT: F 206 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8577 (mp) REVERT: G 4 LEU cc_start: 0.8611 (mt) cc_final: 0.8335 (tp) REVERT: G 28 ASN cc_start: 0.8574 (p0) cc_final: 0.8310 (p0) REVERT: G 36 TRP cc_start: 0.5302 (m100) cc_final: 0.5047 (m100) REVERT: G 54 GLN cc_start: 0.7877 (mm-40) cc_final: 0.7407 (mm-40) REVERT: G 191 ARG cc_start: 0.6956 (ptt90) cc_final: 0.6494 (ptt90) REVERT: G 238 MET cc_start: 0.6553 (mmm) cc_final: 0.6353 (mmm) outliers start: 185 outliers final: 128 residues processed: 820 average time/residue: 0.2017 time to fit residues: 264.9829 Evaluate side-chains 813 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 666 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 659 SER Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 960 ASN Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 98 ASN Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 153 PHE Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain G residue 197 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 288 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 234 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 338 optimal weight: 30.0000 chunk 16 optimal weight: 0.8980 chunk 228 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 346 optimal weight: 8.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 ASN A 66 HIS ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN A 519 HIS A 957 GLN A 960 ASN A 965 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS B 919 ASN B1005 GLN B1023 ASN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 GLN ** G 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.163680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.119711 restraints weight = 67672.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.123944 restraints weight = 31403.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.126615 restraints weight = 18170.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.128381 restraints weight = 12275.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.129478 restraints weight = 9323.723| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.4968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 32215 Z= 0.161 Angle : 0.697 13.462 43907 Z= 0.347 Chirality : 0.047 0.320 4962 Planarity : 0.005 0.052 5654 Dihedral : 6.145 81.300 4455 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.55 % Favored : 90.43 % Rotamer: Outliers : 5.01 % Allowed : 20.43 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.13), residues: 3970 helix: 1.06 (0.21), residues: 676 sheet: -1.04 (0.18), residues: 813 loop : -2.60 (0.12), residues: 2481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 328 TYR 0.037 0.001 TYR E 204 PHE 0.039 0.002 PHE B 981 TRP 0.043 0.002 TRP B 64 HIS 0.010 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 (32147) covalent geometry : angle 0.68720 / 0.34 (43750) SS BOND : bond 0.00350 / 0.28 ( 47) SS BOND : angle 2.16549 / 1.50 ( 94) hydrogen bonds : bond 0.03291 / 2.17 ( 851) hydrogen bonds : angle 4.81146 / 3.35 ( 2274) link_NAG-ASN : bond 0.00289 / 0.19 ( 21) link_NAG-ASN : angle 1.98203 / 1.37 ( 63) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7940 Ramachandran restraints generated. 3970 Oldfield, 0 Emsley, 3970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7940 Ramachandran restraints generated. 3970 Oldfield, 0 Emsley, 3970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 842 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 670 time to evaluate : 1.133 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 36 VAL cc_start: 0.8419 (t) cc_final: 0.8170 (m) REVERT: A 117 LEU cc_start: 0.7196 (mt) cc_final: 0.6743 (mt) REVERT: A 121 ASN cc_start: 0.7305 (t0) cc_final: 0.6829 (t0) REVERT: A 224 GLU cc_start: 0.8335 (pm20) cc_final: 0.7998 (pm20) REVERT: A 235 ILE cc_start: 0.8820 (mt) cc_final: 0.8562 (mm) REVERT: A 238 PHE cc_start: 0.8816 (p90) cc_final: 0.8588 (p90) REVERT: A 278 LYS cc_start: 0.8663 (ttmt) cc_final: 0.8328 (tttt) REVERT: A 294 ASP cc_start: 0.7837 (t70) cc_final: 0.7549 (p0) REVERT: A 297 SER cc_start: 0.8546 (m) cc_final: 0.7973 (p) REVERT: A 498 ARG cc_start: 0.7063 (mmm160) cc_final: 0.6702 (mmm160) REVERT: A 532 ASN cc_start: 0.8637 (t0) cc_final: 0.8431 (t0) REVERT: A 587 ILE cc_start: 0.8853 (mt) cc_final: 0.8434 (tp) REVERT: A 602 THR cc_start: 0.8664 (OUTLIER) cc_final: 0.8284 (p) REVERT: A 655 TYR cc_start: 0.8268 (t80) cc_final: 0.7977 (t80) REVERT: A 664 ILE cc_start: 0.8951 (mt) cc_final: 0.8707 (mm) REVERT: A 697 MET cc_start: 0.8070 (mtm) cc_final: 0.7595 (mtt) REVERT: A 736 VAL cc_start: 0.9004 (p) cc_final: 0.8742 (m) REVERT: A 737 ASP cc_start: 0.7764 (t0) cc_final: 0.7186 (t0) REVERT: A 742 ILE cc_start: 0.8491 (mm) cc_final: 0.8105 (tp) REVERT: A 764 LYS cc_start: 0.8220 (ttpp) cc_final: 0.7981 (tppt) REVERT: A 765 ARG cc_start: 0.7997 (ttp-170) cc_final: 0.7582 (ttm170) REVERT: A 867 ASP cc_start: 0.8153 (p0) cc_final: 0.7852 (p0) REVERT: A 868 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7902 (mm-30) REVERT: A 902 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.8348 (tpp) REVERT: A 911 VAL cc_start: 0.9019 (t) cc_final: 0.8578 (m) REVERT: A 914 ASN cc_start: 0.8038 (p0) cc_final: 0.7331 (p0) REVERT: A 918 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7615 (mt-10) REVERT: A 960 ASN cc_start: 0.8452 (OUTLIER) cc_final: 0.8159 (t0) REVERT: A 964 LYS cc_start: 0.8861 (mmmt) cc_final: 0.8519 (mmmt) REVERT: A 977 LEU cc_start: 0.8372 (mp) cc_final: 0.7947 (pp) REVERT: A 994 ASP cc_start: 0.7406 (m-30) cc_final: 0.7118 (m-30) REVERT: A 998 THR cc_start: 0.8054 (m) cc_final: 0.7770 (p) REVERT: A 1031 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7220 (mt-10) REVERT: A 1073 LYS cc_start: 0.8347 (mmtt) cc_final: 0.7927 (mmtt) REVERT: A 1081 ILE cc_start: 0.8686 (pt) cc_final: 0.8381 (mm) REVERT: A 1103 PHE cc_start: 0.8357 (m-80) cc_final: 0.7953 (m-10) REVERT: A 1111 GLU cc_start: 0.7700 (tt0) cc_final: 0.7415 (tt0) REVERT: A 1118 ASP cc_start: 0.7768 (t70) cc_final: 0.7554 (t0) REVERT: A 1138 TYR cc_start: 0.7259 (t80) cc_final: 0.6991 (t80) REVERT: B 41 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8495 (mttp) REVERT: B 64 TRP cc_start: 0.7853 (t60) cc_final: 0.7615 (t-100) REVERT: B 104 TRP cc_start: 0.7797 (m-90) cc_final: 0.7423 (m-90) REVERT: B 106 PHE cc_start: 0.7739 (m-80) cc_final: 0.7458 (m-80) REVERT: B 129 LYS cc_start: 0.7937 (tppt) cc_final: 0.7602 (tmtt) REVERT: B 141 LEU cc_start: 0.8244 (mt) cc_final: 0.7899 (mt) REVERT: B 192 PHE cc_start: 0.8507 (m-80) cc_final: 0.8051 (m-10) REVERT: B 193 LYS cc_start: 0.8644 (ttmt) cc_final: 0.8354 (mtpt) REVERT: B 200 LYS cc_start: 0.8751 (mttt) cc_final: 0.8175 (mtmt) REVERT: B 204 LYS cc_start: 0.7805 (tppt) cc_final: 0.7499 (tptp) REVERT: B 205 HIS cc_start: 0.7782 (t70) cc_final: 0.7472 (t-90) REVERT: B 224 GLU cc_start: 0.7497 (mm-30) cc_final: 0.7014 (mm-30) REVERT: B 228 ASP cc_start: 0.7037 (t70) cc_final: 0.6211 (t0) REVERT: B 229 LEU cc_start: 0.8696 (mm) cc_final: 0.8404 (mm) REVERT: B 237 ARG cc_start: 0.8145 (mtp85) cc_final: 0.7914 (mtp85) REVERT: B 269 TYR cc_start: 0.7545 (m-80) cc_final: 0.6929 (m-80) REVERT: B 271 GLN cc_start: 0.7886 (mt0) cc_final: 0.7604 (mp-120) REVERT: B 275 PHE cc_start: 0.7938 (m-80) cc_final: 0.7444 (m-80) REVERT: B 278 LYS cc_start: 0.8871 (ttmp) cc_final: 0.8382 (ttmm) REVERT: B 298 GLU cc_start: 0.7403 (mt-10) cc_final: 0.6792 (mm-30) REVERT: B 324 GLU cc_start: 0.7778 (pm20) cc_final: 0.7309 (pm20) REVERT: B 353 TRP cc_start: 0.5789 (OUTLIER) cc_final: 0.5138 (p-90) REVERT: B 547 LYS cc_start: 0.8253 (mtmm) cc_final: 0.7913 (mtmm) REVERT: B 565 PHE cc_start: 0.6681 (m-10) cc_final: 0.6451 (m-10) REVERT: B 675 GLN cc_start: 0.7362 (tm-30) cc_final: 0.7156 (tm-30) REVERT: B 695 TYR cc_start: 0.8140 (p90) cc_final: 0.7514 (p90) REVERT: B 725 GLU cc_start: 0.8050 (tt0) cc_final: 0.7779 (tp30) REVERT: B 726 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8250 (mm) REVERT: B 737 ASP cc_start: 0.7919 (t0) cc_final: 0.7464 (p0) REVERT: B 740 MET cc_start: 0.7730 (OUTLIER) cc_final: 0.7020 (tmm) REVERT: B 764 LYS cc_start: 0.8511 (tppt) cc_final: 0.8284 (tppt) REVERT: B 773 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.6929 (tp30) REVERT: B 780 GLU cc_start: 0.7914 (pt0) cc_final: 0.7647 (tp30) REVERT: B 796 TYR cc_start: 0.8434 (t80) cc_final: 0.8195 (t80) REVERT: B 819 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7537 (mt-10) REVERT: B 820 ASP cc_start: 0.7611 (m-30) cc_final: 0.7309 (m-30) REVERT: B 869 MET cc_start: 0.8566 (mtt) cc_final: 0.8269 (mtt) REVERT: B 895 GLN cc_start: 0.8324 (pm20) cc_final: 0.7966 (pm20) REVERT: B 900 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.7993 (mpp) REVERT: B 914 ASN cc_start: 0.8567 (p0) cc_final: 0.8187 (p0) REVERT: B 921 LYS cc_start: 0.8712 (mmmt) cc_final: 0.8316 (mmmm) REVERT: B 925 ASN cc_start: 0.8937 (m-40) cc_final: 0.8702 (m-40) REVERT: B 929 SER cc_start: 0.8770 (m) cc_final: 0.8434 (p) REVERT: B 933 LYS cc_start: 0.8622 (mtmt) cc_final: 0.8147 (mtpp) REVERT: B 949 GLN cc_start: 0.8681 (mm-40) cc_final: 0.8250 (mm-40) REVERT: B 950 ASP cc_start: 0.7857 (m-30) cc_final: 0.7209 (m-30) REVERT: B 965 GLN cc_start: 0.8413 (mm-40) cc_final: 0.7845 (mm-40) REVERT: B 1031 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7510 (mm-30) REVERT: B 1038 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8576 (mmmt) REVERT: B 1081 ILE cc_start: 0.8790 (pt) cc_final: 0.8417 (mm) REVERT: B 1111 GLU cc_start: 0.7995 (tt0) cc_final: 0.7670 (tt0) REVERT: B 1118 ASP cc_start: 0.7439 (t70) cc_final: 0.6982 (t0) REVERT: B 1144 GLU cc_start: 0.8130 (mp0) cc_final: 0.7708 (mp0) REVERT: C 101 ILE cc_start: 0.8635 (mt) cc_final: 0.8135 (tp) REVERT: C 195 ILE cc_start: 0.8420 (mm) cc_final: 0.8123 (tp) REVERT: C 198 TYR cc_start: 0.6401 (m-80) cc_final: 0.5837 (m-10) REVERT: C 224 GLU cc_start: 0.7312 (pm20) cc_final: 0.6578 (mp0) REVERT: C 228 ASP cc_start: 0.6911 (t70) cc_final: 0.5186 (t0) REVERT: C 269 TYR cc_start: 0.7310 (m-10) cc_final: 0.6747 (m-80) REVERT: C 271 GLN cc_start: 0.7800 (tm-30) cc_final: 0.7464 (tm-30) REVERT: C 297 SER cc_start: 0.8364 (m) cc_final: 0.7972 (p) REVERT: C 298 GLU cc_start: 0.8236 (tt0) cc_final: 0.7691 (tp30) REVERT: C 346 ARG cc_start: 0.7557 (mmm160) cc_final: 0.7178 (mmm160) REVERT: C 357 ARG cc_start: 0.7538 (ttt90) cc_final: 0.7206 (ttt-90) REVERT: C 375 PHE cc_start: 0.7463 (m-80) cc_final: 0.6937 (m-10) REVERT: C 400 PHE cc_start: 0.7717 (p90) cc_final: 0.7041 (p90) REVERT: C 406 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7349 (mt-10) REVERT: C 408 ARG cc_start: 0.9050 (tmm160) cc_final: 0.8717 (ttp80) REVERT: C 421 TYR cc_start: 0.7229 (m-10) cc_final: 0.6487 (m-80) REVERT: C 436 TRP cc_start: 0.7247 (p90) cc_final: 0.6686 (p-90) REVERT: C 454 ARG cc_start: 0.7593 (ttt180) cc_final: 0.7215 (ttm170) REVERT: C 455 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7567 (tm) REVERT: C 535 LYS cc_start: 0.8807 (mmmm) cc_final: 0.8537 (mmmm) REVERT: C 542 ASN cc_start: 0.8029 (t0) cc_final: 0.7600 (t0) REVERT: C 547 LYS cc_start: 0.8607 (mtmm) cc_final: 0.8345 (mtmm) REVERT: C 571 ASP cc_start: 0.6210 (t0) cc_final: 0.5945 (t0) REVERT: C 602 THR cc_start: 0.8705 (OUTLIER) cc_final: 0.8283 (p) REVERT: C 664 ILE cc_start: 0.8462 (mt) cc_final: 0.8228 (mm) REVERT: C 675 GLN cc_start: 0.7769 (mm110) cc_final: 0.7337 (mm110) REVERT: C 705 VAL cc_start: 0.8723 (t) cc_final: 0.8451 (m) REVERT: C 708 SER cc_start: 0.8953 (t) cc_final: 0.8413 (m) REVERT: C 726 ILE cc_start: 0.8954 (OUTLIER) cc_final: 0.8491 (pt) REVERT: C 773 GLU cc_start: 0.7324 (tm-30) cc_final: 0.6649 (tm-30) REVERT: C 820 ASP cc_start: 0.7733 (m-30) cc_final: 0.7140 (m-30) REVERT: C 823 PHE cc_start: 0.7604 (m-80) cc_final: 0.7295 (m-80) REVERT: C 853 GLN cc_start: 0.8169 (mt0) cc_final: 0.7856 (mt0) REVERT: C 867 ASP cc_start: 0.8108 (m-30) cc_final: 0.7754 (m-30) REVERT: C 868 GLU cc_start: 0.7887 (tp30) cc_final: 0.7408 (tp30) REVERT: C 872 GLN cc_start: 0.8336 (tp40) cc_final: 0.7948 (tp40) REVERT: C 901 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.8367 (tm-30) REVERT: C 914 ASN cc_start: 0.8447 (p0) cc_final: 0.8149 (p0) REVERT: C 918 GLU cc_start: 0.7537 (mp0) cc_final: 0.6992 (mp0) REVERT: C 933 LYS cc_start: 0.8185 (mtmm) cc_final: 0.7736 (mmmm) REVERT: C 949 GLN cc_start: 0.8542 (mm-40) cc_final: 0.7819 (mm-40) REVERT: C 950 ASP cc_start: 0.7580 (t70) cc_final: 0.7039 (t0) REVERT: C 953 ASN cc_start: 0.8474 (m-40) cc_final: 0.8083 (m110) REVERT: C 964 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8255 (mmmm) REVERT: C 966 LEU cc_start: 0.9129 (tt) cc_final: 0.8868 (tp) REVERT: C 1014 ARG cc_start: 0.7934 (tpp80) cc_final: 0.7726 (tpp80) REVERT: C 1017 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7672 (tm-30) REVERT: C 1031 GLU cc_start: 0.8350 (mm-30) cc_final: 0.8123 (mm-30) REVERT: C 1038 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7712 (mmmm) REVERT: C 1048 HIS cc_start: 0.8440 (t-90) cc_final: 0.7984 (t70) REVERT: C 1111 GLU cc_start: 0.7128 (tm-30) cc_final: 0.6867 (tm-30) REVERT: D 6 GLN cc_start: 0.0796 (OUTLIER) cc_final: 0.0336 (tp40) REVERT: D 83 GLU cc_start: 0.2211 (OUTLIER) cc_final: 0.1883 (pp20) REVERT: D 160 MET cc_start: 0.2751 (mmm) cc_final: 0.2372 (mmp) REVERT: E 144 LEU cc_start: 0.6277 (mm) cc_final: 0.5888 (pp) REVERT: E 156 HIS cc_start: 0.7384 (m-70) cc_final: 0.6990 (m90) REVERT: E 158 MET cc_start: 0.4841 (mmm) cc_final: 0.4493 (mmm) REVERT: F 39 GLN cc_start: 0.7761 (pp30) cc_final: 0.7512 (pp30) REVERT: F 146 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8053 (tp) REVERT: F 159 TYR cc_start: 0.7028 (m-80) cc_final: 0.5632 (m-80) REVERT: F 206 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8608 (mt) REVERT: F 234 MET cc_start: 0.7297 (tpt) cc_final: 0.5558 (pmm) REVERT: G 4 LEU cc_start: 0.8592 (mt) cc_final: 0.8328 (tp) REVERT: G 28 ASN cc_start: 0.8568 (p0) cc_final: 0.8295 (p0) REVERT: G 54 GLN cc_start: 0.7824 (mm-40) cc_final: 0.7376 (mm-40) REVERT: G 191 ARG cc_start: 0.6951 (ptt90) cc_final: 0.6504 (ptt90) outliers start: 172 outliers final: 132 residues processed: 789 average time/residue: 0.2010 time to fit residues: 255.0539 Evaluate side-chains 810 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 657 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 659 SER Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 960 ASN Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 98 ASN Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 153 PHE Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain G residue 197 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 300 optimal weight: 0.5980 chunk 318 optimal weight: 30.0000 chunk 103 optimal weight: 6.9990 chunk 193 optimal weight: 3.9990 chunk 350 optimal weight: 0.0570 chunk 153 optimal weight: 0.7980 chunk 150 optimal weight: 4.9990 chunk 179 optimal weight: 0.8980 chunk 363 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 256 optimal weight: 7.9990 overall best weight: 1.0700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 ASN ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 GLN A 321 GLN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 960 ASN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 ASN E 206 GLN E 208 ASN ** G 28 ASN ** 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 = 0.4148 r_free = 0.4148 target = 0.163296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.119210 restraints weight = 67200.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.123437 restraints weight = 31275.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.126164 restraints weight = 18098.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.127801 restraints weight = 12158.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.129009 restraints weight = 9348.839| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.5074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32215 Z= 0.156 Angle : 0.705 17.012 43907 Z= 0.350 Chirality : 0.047 0.324 4962 Planarity : 0.005 0.052 5654 Dihedral : 6.147 81.186 4455 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.32 % Favored : 90.65 % Rotamer: Outliers : 4.81 % Allowed : 21.04 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.13), residues: 3970 helix: 1.04 (0.21), residues: 681 sheet: -1.04 (0.18), residues: 807 loop : -2.55 (0.12), residues: 2482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 328 TYR 0.041 0.001 TYR D 185 PHE 0.054 0.002 PHE C 643 TRP 0.062 0.002 TRP G 36 HIS 0.008 0.001 HIS E 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 (32147) covalent geometry : angle 0.69716 / 0.35 (43750) SS BOND : bond 0.00330 / 0.26 ( 47) SS BOND : angle 1.83150 / 1.26 ( 94) hydrogen bonds : bond 0.03269 / 2.16 ( 851) hydrogen bonds : angle 4.81240 / 3.35 ( 2274) link_NAG-ASN : bond 0.00287 / 0.19 ( 21) link_NAG-ASN : angle 1.95556 / 1.33 ( 63) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7940 Ramachandran restraints generated. 3970 Oldfield, 0 Emsley, 3970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7940 Ramachandran restraints generated. 3970 Oldfield, 0 Emsley, 3970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 834 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 669 time to evaluate : 1.167 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 36 VAL cc_start: 0.8486 (t) cc_final: 0.8191 (m) REVERT: A 117 LEU cc_start: 0.7185 (mt) cc_final: 0.6733 (mt) REVERT: A 121 ASN cc_start: 0.7302 (t0) cc_final: 0.6907 (t0) REVERT: A 224 GLU cc_start: 0.8376 (pm20) cc_final: 0.8022 (pm20) REVERT: A 235 ILE cc_start: 0.8793 (mt) cc_final: 0.8519 (mm) REVERT: A 238 PHE cc_start: 0.8772 (p90) cc_final: 0.8516 (p90) REVERT: A 271 GLN cc_start: 0.7577 (mt0) cc_final: 0.7233 (mt0) REVERT: A 278 LYS cc_start: 0.8623 (ttmt) cc_final: 0.8334 (tttt) REVERT: A 294 ASP cc_start: 0.7810 (t70) cc_final: 0.7524 (p0) REVERT: A 297 SER cc_start: 0.8513 (m) cc_final: 0.7938 (p) REVERT: A 498 ARG cc_start: 0.7091 (mmm160) cc_final: 0.6730 (mmm160) REVERT: A 532 ASN cc_start: 0.8675 (t0) cc_final: 0.8452 (t0) REVERT: A 577 ARG cc_start: 0.6685 (tpt-90) cc_final: 0.6182 (mmm-85) REVERT: A 587 ILE cc_start: 0.8848 (mt) cc_final: 0.8459 (tp) REVERT: A 602 THR cc_start: 0.8656 (OUTLIER) cc_final: 0.8281 (p) REVERT: A 655 TYR cc_start: 0.8279 (t80) cc_final: 0.7938 (t80) REVERT: A 664 ILE cc_start: 0.9005 (mt) cc_final: 0.8740 (mm) REVERT: A 697 MET cc_start: 0.8098 (mtm) cc_final: 0.7808 (mtt) REVERT: A 736 VAL cc_start: 0.8989 (p) cc_final: 0.8723 (m) REVERT: A 737 ASP cc_start: 0.7750 (t0) cc_final: 0.7236 (t0) REVERT: A 742 ILE cc_start: 0.8485 (mm) cc_final: 0.8100 (tp) REVERT: A 764 LYS cc_start: 0.8228 (ttpp) cc_final: 0.7997 (tppt) REVERT: A 765 ARG cc_start: 0.8008 (ttp-170) cc_final: 0.7599 (ttm170) REVERT: A 790 LYS cc_start: 0.8128 (mttp) cc_final: 0.7817 (mmtm) REVERT: A 867 ASP cc_start: 0.8139 (p0) cc_final: 0.7838 (p0) REVERT: A 868 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7884 (mm-30) REVERT: A 902 MET cc_start: 0.8630 (mmt) cc_final: 0.8358 (tpp) REVERT: A 911 VAL cc_start: 0.9070 (t) cc_final: 0.8721 (m) REVERT: A 914 ASN cc_start: 0.8060 (p0) cc_final: 0.7361 (p0) REVERT: A 918 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7605 (mt-10) REVERT: A 960 ASN cc_start: 0.8414 (OUTLIER) cc_final: 0.8137 (t0) REVERT: A 964 LYS cc_start: 0.8791 (mmmt) cc_final: 0.8411 (mmmt) REVERT: A 994 ASP cc_start: 0.7405 (m-30) cc_final: 0.7126 (m-30) REVERT: A 998 THR cc_start: 0.8116 (m) cc_final: 0.7831 (p) REVERT: A 1002 GLN cc_start: 0.8633 (tp40) cc_final: 0.8406 (tp40) REVERT: A 1031 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7234 (mt-10) REVERT: A 1073 LYS cc_start: 0.8338 (mmtt) cc_final: 0.7912 (mmtt) REVERT: A 1081 ILE cc_start: 0.8673 (pt) cc_final: 0.8374 (mm) REVERT: A 1103 PHE cc_start: 0.8367 (m-80) cc_final: 0.7968 (m-10) REVERT: A 1111 GLU cc_start: 0.7716 (tt0) cc_final: 0.7425 (tt0) REVERT: A 1118 ASP cc_start: 0.7752 (t70) cc_final: 0.7530 (t0) REVERT: A 1138 TYR cc_start: 0.7240 (t80) cc_final: 0.6969 (t80) REVERT: B 41 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8505 (mttp) REVERT: B 44 ARG cc_start: 0.8482 (mtt90) cc_final: 0.7883 (mtt180) REVERT: B 64 TRP cc_start: 0.7710 (t60) cc_final: 0.7474 (t-100) REVERT: B 104 TRP cc_start: 0.7786 (m-90) cc_final: 0.7470 (m-90) REVERT: B 106 PHE cc_start: 0.7710 (m-80) cc_final: 0.7481 (m-80) REVERT: B 129 LYS cc_start: 0.7906 (tppt) cc_final: 0.7566 (tmtt) REVERT: B 141 LEU cc_start: 0.8238 (mt) cc_final: 0.7916 (mt) REVERT: B 192 PHE cc_start: 0.8539 (m-80) cc_final: 0.8180 (m-10) REVERT: B 193 LYS cc_start: 0.8652 (ttmt) cc_final: 0.8377 (mtpt) REVERT: B 200 LYS cc_start: 0.8734 (mttt) cc_final: 0.8181 (mtmt) REVERT: B 204 LYS cc_start: 0.7818 (tppt) cc_final: 0.7514 (tptp) REVERT: B 205 HIS cc_start: 0.7773 (t70) cc_final: 0.7470 (t-90) REVERT: B 224 GLU cc_start: 0.7500 (mm-30) cc_final: 0.7010 (mm-30) REVERT: B 228 ASP cc_start: 0.7090 (t70) cc_final: 0.6202 (t0) REVERT: B 229 LEU cc_start: 0.8699 (mm) cc_final: 0.8436 (mm) REVERT: B 237 ARG cc_start: 0.8147 (mtp85) cc_final: 0.7913 (mtp85) REVERT: B 271 GLN cc_start: 0.7884 (mt0) cc_final: 0.7563 (mm110) REVERT: B 275 PHE cc_start: 0.8060 (m-80) cc_final: 0.7695 (m-80) REVERT: B 278 LYS cc_start: 0.8868 (ttmp) cc_final: 0.8396 (ttmm) REVERT: B 324 GLU cc_start: 0.7854 (pm20) cc_final: 0.7345 (pm20) REVERT: B 353 TRP cc_start: 0.5856 (OUTLIER) cc_final: 0.5241 (p-90) REVERT: B 547 LYS cc_start: 0.8290 (mtmm) cc_final: 0.7887 (mtmm) REVERT: B 565 PHE cc_start: 0.6686 (m-10) cc_final: 0.6441 (m-10) REVERT: B 655 TYR cc_start: 0.8319 (t80) cc_final: 0.8042 (t80) REVERT: B 695 TYR cc_start: 0.8143 (p90) cc_final: 0.7470 (p90) REVERT: B 725 GLU cc_start: 0.8040 (tt0) cc_final: 0.7767 (tp30) REVERT: B 726 ILE cc_start: 0.9155 (OUTLIER) cc_final: 0.8251 (mm) REVERT: B 737 ASP cc_start: 0.7935 (t0) cc_final: 0.7725 (t0) REVERT: B 740 MET cc_start: 0.7791 (OUTLIER) cc_final: 0.7505 (tmm) REVERT: B 764 LYS cc_start: 0.8500 (tppt) cc_final: 0.8264 (tppt) REVERT: B 780 GLU cc_start: 0.7935 (pt0) cc_final: 0.7623 (tp30) REVERT: B 819 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7538 (mt-10) REVERT: B 820 ASP cc_start: 0.7624 (m-30) cc_final: 0.7335 (m-30) REVERT: B 869 MET cc_start: 0.8562 (mtt) cc_final: 0.8264 (mtt) REVERT: B 895 GLN cc_start: 0.8348 (pm20) cc_final: 0.7979 (pm20) REVERT: B 900 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.7998 (mpp) REVERT: B 902 MET cc_start: 0.8705 (tpp) cc_final: 0.7815 (tpp) REVERT: B 914 ASN cc_start: 0.8633 (p0) cc_final: 0.8332 (p0) REVERT: B 921 LYS cc_start: 0.8719 (mmmt) cc_final: 0.8313 (mmmm) REVERT: B 925 ASN cc_start: 0.8929 (m-40) cc_final: 0.8723 (m-40) REVERT: B 929 SER cc_start: 0.8799 (m) cc_final: 0.8472 (p) REVERT: B 933 LYS cc_start: 0.8624 (mtmt) cc_final: 0.8114 (mtpp) REVERT: B 949 GLN cc_start: 0.8703 (mm-40) cc_final: 0.8419 (mm-40) REVERT: B 950 ASP cc_start: 0.7860 (m-30) cc_final: 0.7215 (m-30) REVERT: B 965 GLN cc_start: 0.8386 (mm-40) cc_final: 0.7812 (mm-40) REVERT: B 1031 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7529 (mm-30) REVERT: B 1038 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8553 (mmmm) REVERT: B 1081 ILE cc_start: 0.8786 (pt) cc_final: 0.8410 (mm) REVERT: B 1107 ARG cc_start: 0.7512 (mtt90) cc_final: 0.7076 (mtm-85) REVERT: B 1111 GLU cc_start: 0.8002 (tt0) cc_final: 0.7648 (tt0) REVERT: B 1118 ASP cc_start: 0.7431 (t70) cc_final: 0.6962 (t0) REVERT: B 1144 GLU cc_start: 0.8117 (mp0) cc_final: 0.7595 (mp0) REVERT: C 101 ILE cc_start: 0.8480 (mt) cc_final: 0.8122 (tp) REVERT: C 195 ILE cc_start: 0.8436 (mm) cc_final: 0.8129 (tp) REVERT: C 198 TYR cc_start: 0.6402 (m-80) cc_final: 0.5839 (m-10) REVERT: C 224 GLU cc_start: 0.7315 (pm20) cc_final: 0.6590 (mp0) REVERT: C 228 ASP cc_start: 0.6924 (t70) cc_final: 0.5218 (t0) REVERT: C 269 TYR cc_start: 0.7315 (m-10) cc_final: 0.6730 (m-80) REVERT: C 271 GLN cc_start: 0.7791 (tm-30) cc_final: 0.7469 (tm-30) REVERT: C 297 SER cc_start: 0.8358 (m) cc_final: 0.7931 (p) REVERT: C 298 GLU cc_start: 0.8242 (tt0) cc_final: 0.7690 (tp30) REVERT: C 346 ARG cc_start: 0.7591 (mmm160) cc_final: 0.7200 (mmm160) REVERT: C 357 ARG cc_start: 0.7545 (ttt90) cc_final: 0.7242 (ttt-90) REVERT: C 375 PHE cc_start: 0.7421 (m-80) cc_final: 0.6903 (m-10) REVERT: C 394 ASN cc_start: 0.8204 (t0) cc_final: 0.7075 (t0) REVERT: C 395 VAL cc_start: 0.8981 (m) cc_final: 0.8760 (p) REVERT: C 400 PHE cc_start: 0.7779 (p90) cc_final: 0.7150 (p90) REVERT: C 406 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7360 (mt-10) REVERT: C 408 ARG cc_start: 0.9052 (tmm160) cc_final: 0.8734 (ttp80) REVERT: C 436 TRP cc_start: 0.7251 (p90) cc_final: 0.6705 (p-90) REVERT: C 454 ARG cc_start: 0.7554 (ttt180) cc_final: 0.7109 (ttm170) REVERT: C 535 LYS cc_start: 0.8835 (mmmm) cc_final: 0.8555 (mmmm) REVERT: C 542 ASN cc_start: 0.7974 (t0) cc_final: 0.7567 (t0) REVERT: C 547 LYS cc_start: 0.8612 (mtmm) cc_final: 0.8348 (mtmm) REVERT: C 571 ASP cc_start: 0.6192 (t0) cc_final: 0.5949 (t0) REVERT: C 602 THR cc_start: 0.8702 (OUTLIER) cc_final: 0.8441 (p) REVERT: C 664 ILE cc_start: 0.8389 (mt) cc_final: 0.8171 (mm) REVERT: C 675 GLN cc_start: 0.7764 (mm110) cc_final: 0.7332 (mm110) REVERT: C 705 VAL cc_start: 0.8737 (t) cc_final: 0.8468 (m) REVERT: C 708 SER cc_start: 0.8959 (t) cc_final: 0.8433 (m) REVERT: C 718 PHE cc_start: 0.7819 (p90) cc_final: 0.7299 (p90) REVERT: C 725 GLU cc_start: 0.7700 (tp30) cc_final: 0.7426 (tp30) REVERT: C 726 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8514 (mm) REVERT: C 731 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8144 (pmm) REVERT: C 773 GLU cc_start: 0.7406 (tm-30) cc_final: 0.6565 (tm-30) REVERT: C 774 GLN cc_start: 0.7657 (mm-40) cc_final: 0.7170 (mm-40) REVERT: C 823 PHE cc_start: 0.7586 (m-80) cc_final: 0.7320 (m-80) REVERT: C 853 GLN cc_start: 0.8231 (mt0) cc_final: 0.7958 (mt0) REVERT: C 867 ASP cc_start: 0.8122 (m-30) cc_final: 0.7772 (m-30) REVERT: C 868 GLU cc_start: 0.7886 (tp30) cc_final: 0.7301 (tp30) REVERT: C 872 GLN cc_start: 0.8343 (tp40) cc_final: 0.7967 (tp40) REVERT: C 901 GLN cc_start: 0.8968 (OUTLIER) cc_final: 0.8363 (tm-30) REVERT: C 914 ASN cc_start: 0.8457 (p0) cc_final: 0.8155 (p0) REVERT: C 918 GLU cc_start: 0.7548 (mp0) cc_final: 0.7050 (mp0) REVERT: C 933 LYS cc_start: 0.8171 (mtmm) cc_final: 0.7732 (mmmm) REVERT: C 949 GLN cc_start: 0.8550 (mm-40) cc_final: 0.7869 (mm-40) REVERT: C 950 ASP cc_start: 0.7593 (t70) cc_final: 0.7044 (t0) REVERT: C 953 ASN cc_start: 0.8478 (m-40) cc_final: 0.8065 (m110) REVERT: C 964 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8271 (mmmm) REVERT: C 966 LEU cc_start: 0.9132 (tt) cc_final: 0.8836 (tp) REVERT: C 1017 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7710 (tm-30) REVERT: C 1038 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7711 (mmmm) REVERT: C 1048 HIS cc_start: 0.8413 (t-90) cc_final: 0.7929 (t70) REVERT: C 1111 GLU cc_start: 0.7167 (tm-30) cc_final: 0.6834 (tm-30) REVERT: D 83 GLU cc_start: 0.2213 (OUTLIER) cc_final: 0.1883 (pp20) REVERT: D 160 MET cc_start: 0.2851 (mmm) cc_final: 0.2634 (mmp) REVERT: E 144 LEU cc_start: 0.6233 (mm) cc_final: 0.5871 (pp) REVERT: E 156 HIS cc_start: 0.7372 (m-70) cc_final: 0.6956 (m90) REVERT: E 158 MET cc_start: 0.4796 (mmm) cc_final: 0.4445 (mmm) REVERT: F 39 GLN cc_start: 0.7692 (pp30) cc_final: 0.7402 (pp30) REVERT: F 146 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8308 (tp) REVERT: F 206 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8693 (mt) REVERT: F 234 MET cc_start: 0.7120 (tpt) cc_final: 0.5386 (pmm) REVERT: G 4 LEU cc_start: 0.8616 (mt) cc_final: 0.8364 (tp) REVERT: G 28 ASN cc_start: 0.8560 (p0) cc_final: 0.8282 (p0) REVERT: G 54 GLN cc_start: 0.7786 (mm-40) cc_final: 0.7341 (mm-40) REVERT: G 191 ARG cc_start: 0.6957 (ptt90) cc_final: 0.6506 (ptt90) outliers start: 165 outliers final: 130 residues processed: 780 average time/residue: 0.2076 time to fit residues: 257.3813 Evaluate side-chains 801 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 653 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 659 SER Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 960 ASN Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 98 ASN Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 153 PHE Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain G residue 197 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 19 optimal weight: 10.0000 chunk 360 optimal weight: 20.0000 chunk 143 optimal weight: 8.9990 chunk 353 optimal weight: 7.9990 chunk 185 optimal weight: 0.9990 chunk 183 optimal weight: 0.6980 chunk 125 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 chunk 170 optimal weight: 0.6980 chunk 255 optimal weight: 2.9990 chunk 310 optimal weight: 0.4980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 960 ASN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS B 360 ASN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.163408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.119360 restraints weight = 67481.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.123588 restraints weight = 31401.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.126275 restraints weight = 18154.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.127969 restraints weight = 12260.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.129122 restraints weight = 9372.306| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.5237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 32215 Z= 0.164 Angle : 0.712 15.891 43907 Z= 0.355 Chirality : 0.047 0.315 4962 Planarity : 0.005 0.052 5654 Dihedral : 6.155 81.031 4450 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.55 % Favored : 90.43 % Rotamer: Outliers : 4.63 % Allowed : 21.39 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.13), residues: 3970 helix: 1.02 (0.21), residues: 681 sheet: -1.05 (0.18), residues: 829 loop : -2.54 (0.12), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 328 TYR 0.041 0.001 TYR C 91 PHE 0.036 0.002 PHE C 643 TRP 0.060 0.002 TRP G 36 HIS 0.008 0.001 HIS E 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (32147) covalent geometry : angle 0.70467 / 0.35 (43750) SS BOND : bond 0.00335 / 0.25 ( 47) SS BOND : angle 1.79372 / 1.23 ( 94) hydrogen bonds : bond 0.03279 / 2.17 ( 851) hydrogen bonds : angle 4.84636 / 3.37 ( 2274) link_NAG-ASN : bond 0.00287 / 0.19 ( 21) link_NAG-ASN : angle 1.94914 / 1.33 ( 63) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7940 Ramachandran restraints generated. 3970 Oldfield, 0 Emsley, 3970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7940 Ramachandran restraints generated. 3970 Oldfield, 0 Emsley, 3970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 842 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 683 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 VAL cc_start: 0.8486 (t) cc_final: 0.8208 (m) REVERT: A 117 LEU cc_start: 0.7197 (mt) cc_final: 0.6625 (mt) REVERT: A 121 ASN cc_start: 0.7293 (t0) cc_final: 0.6908 (t0) REVERT: A 130 VAL cc_start: 0.7460 (p) cc_final: 0.7176 (p) REVERT: A 199 PHE cc_start: 0.7724 (OUTLIER) cc_final: 0.7243 (t80) REVERT: A 224 GLU cc_start: 0.8392 (pm20) cc_final: 0.8044 (pm20) REVERT: A 235 ILE cc_start: 0.8770 (mt) cc_final: 0.8431 (mm) REVERT: A 238 PHE cc_start: 0.8694 (p90) cc_final: 0.8449 (p90) REVERT: A 271 GLN cc_start: 0.7567 (mt0) cc_final: 0.7222 (mt0) REVERT: A 278 LYS cc_start: 0.8652 (ttmt) cc_final: 0.8355 (tttt) REVERT: A 293 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8214 (mp) REVERT: A 294 ASP cc_start: 0.7814 (t70) cc_final: 0.7515 (p0) REVERT: A 297 SER cc_start: 0.8495 (m) cc_final: 0.7940 (p) REVERT: A 498 ARG cc_start: 0.7062 (mmm160) cc_final: 0.6705 (mmm160) REVERT: A 532 ASN cc_start: 0.8700 (t0) cc_final: 0.8488 (t0) REVERT: A 577 ARG cc_start: 0.6780 (tpt-90) cc_final: 0.6213 (tpt170) REVERT: A 587 ILE cc_start: 0.8822 (mt) cc_final: 0.8430 (tp) REVERT: A 602 THR cc_start: 0.8664 (OUTLIER) cc_final: 0.8290 (p) REVERT: A 655 TYR cc_start: 0.8289 (t80) cc_final: 0.7950 (t80) REVERT: A 664 ILE cc_start: 0.9049 (mt) cc_final: 0.8799 (mm) REVERT: A 697 MET cc_start: 0.8069 (mtm) cc_final: 0.7812 (mtt) REVERT: A 736 VAL cc_start: 0.8983 (p) cc_final: 0.8761 (m) REVERT: A 737 ASP cc_start: 0.7761 (t0) cc_final: 0.7284 (t0) REVERT: A 742 ILE cc_start: 0.8457 (mm) cc_final: 0.8089 (tp) REVERT: A 764 LYS cc_start: 0.8218 (ttpp) cc_final: 0.7956 (tppt) REVERT: A 765 ARG cc_start: 0.8006 (ttp-170) cc_final: 0.7385 (ttm170) REVERT: A 768 THR cc_start: 0.8659 (m) cc_final: 0.8230 (p) REVERT: A 902 MET cc_start: 0.8629 (mmt) cc_final: 0.8355 (tpp) REVERT: A 911 VAL cc_start: 0.9069 (t) cc_final: 0.8713 (m) REVERT: A 914 ASN cc_start: 0.8089 (p0) cc_final: 0.7369 (p0) REVERT: A 918 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7594 (mt-10) REVERT: A 960 ASN cc_start: 0.8420 (OUTLIER) cc_final: 0.8162 (t0) REVERT: A 964 LYS cc_start: 0.8753 (mmmt) cc_final: 0.8332 (mmmt) REVERT: A 1002 GLN cc_start: 0.8559 (tp40) cc_final: 0.8358 (tp40) REVERT: A 1031 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7229 (mt-10) REVERT: A 1073 LYS cc_start: 0.8349 (mmtt) cc_final: 0.7926 (mmtt) REVERT: A 1081 ILE cc_start: 0.8677 (pt) cc_final: 0.8385 (mm) REVERT: A 1103 PHE cc_start: 0.8371 (m-80) cc_final: 0.7979 (m-10) REVERT: A 1111 GLU cc_start: 0.7722 (tt0) cc_final: 0.7428 (tt0) REVERT: A 1118 ASP cc_start: 0.7844 (t70) cc_final: 0.7573 (t0) REVERT: A 1138 TYR cc_start: 0.7257 (t80) cc_final: 0.6961 (t80) REVERT: B 41 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8513 (mttp) REVERT: B 44 ARG cc_start: 0.8505 (mtt90) cc_final: 0.8104 (mtt180) REVERT: B 64 TRP cc_start: 0.7657 (t60) cc_final: 0.7406 (t-100) REVERT: B 104 TRP cc_start: 0.7762 (m-90) cc_final: 0.7462 (m-90) REVERT: B 129 LYS cc_start: 0.7892 (tppt) cc_final: 0.7466 (tmmt) REVERT: B 141 LEU cc_start: 0.8277 (mt) cc_final: 0.7965 (mt) REVERT: B 192 PHE cc_start: 0.8533 (m-80) cc_final: 0.8158 (m-10) REVERT: B 193 LYS cc_start: 0.8623 (ttmt) cc_final: 0.8389 (ttmt) REVERT: B 200 LYS cc_start: 0.8766 (mttt) cc_final: 0.8334 (mtmt) REVERT: B 204 LYS cc_start: 0.7798 (tppt) cc_final: 0.7506 (tptp) REVERT: B 205 HIS cc_start: 0.7814 (t70) cc_final: 0.7516 (t-90) REVERT: B 224 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7034 (mm-30) REVERT: B 228 ASP cc_start: 0.7077 (t70) cc_final: 0.6194 (t0) REVERT: B 229 LEU cc_start: 0.8692 (mm) cc_final: 0.8431 (mm) REVERT: B 237 ARG cc_start: 0.8139 (mtp85) cc_final: 0.7897 (mtp85) REVERT: B 271 GLN cc_start: 0.7898 (mt0) cc_final: 0.7564 (mm110) REVERT: B 275 PHE cc_start: 0.8125 (m-80) cc_final: 0.7771 (m-80) REVERT: B 278 LYS cc_start: 0.8866 (ttmp) cc_final: 0.8392 (ttmm) REVERT: B 323 THR cc_start: 0.8368 (p) cc_final: 0.8106 (p) REVERT: B 353 TRP cc_start: 0.5918 (OUTLIER) cc_final: 0.5267 (p-90) REVERT: B 392 PHE cc_start: 0.7763 (m-80) cc_final: 0.7540 (t80) REVERT: B 547 LYS cc_start: 0.8309 (mtmm) cc_final: 0.7901 (mtmm) REVERT: B 574 ASP cc_start: 0.7273 (p0) cc_final: 0.6944 (p0) REVERT: B 655 TYR cc_start: 0.8324 (t80) cc_final: 0.8081 (t80) REVERT: B 695 TYR cc_start: 0.8165 (p90) cc_final: 0.7418 (p90) REVERT: B 725 GLU cc_start: 0.8047 (tt0) cc_final: 0.7768 (tp30) REVERT: B 726 ILE cc_start: 0.9167 (OUTLIER) cc_final: 0.8246 (mm) REVERT: B 737 ASP cc_start: 0.7937 (t0) cc_final: 0.7731 (t0) REVERT: B 780 GLU cc_start: 0.7914 (pt0) cc_final: 0.7619 (tp30) REVERT: B 819 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7594 (mt-10) REVERT: B 820 ASP cc_start: 0.7587 (m-30) cc_final: 0.7280 (m-30) REVERT: B 869 MET cc_start: 0.8554 (mtt) cc_final: 0.8282 (mtt) REVERT: B 895 GLN cc_start: 0.8372 (pm20) cc_final: 0.7996 (pm20) REVERT: B 902 MET cc_start: 0.8753 (tpp) cc_final: 0.7884 (tpp) REVERT: B 914 ASN cc_start: 0.8591 (p0) cc_final: 0.8259 (p0) REVERT: B 921 LYS cc_start: 0.8711 (mmmt) cc_final: 0.8316 (mmmm) REVERT: B 925 ASN cc_start: 0.8940 (m-40) cc_final: 0.8723 (m-40) REVERT: B 929 SER cc_start: 0.8822 (m) cc_final: 0.8442 (p) REVERT: B 933 LYS cc_start: 0.8587 (mtmt) cc_final: 0.8119 (mtpp) REVERT: B 949 GLN cc_start: 0.8696 (mm-40) cc_final: 0.8413 (mm-40) REVERT: B 950 ASP cc_start: 0.7867 (m-30) cc_final: 0.7230 (m-30) REVERT: B 957 GLN cc_start: 0.8448 (mt0) cc_final: 0.8075 (mt0) REVERT: B 965 GLN cc_start: 0.8399 (mm-40) cc_final: 0.7784 (mm-40) REVERT: B 1031 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7525 (mm-30) REVERT: B 1038 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8550 (mmmm) REVERT: B 1081 ILE cc_start: 0.8784 (pt) cc_final: 0.8405 (mm) REVERT: B 1111 GLU cc_start: 0.8021 (tt0) cc_final: 0.7660 (tt0) REVERT: B 1118 ASP cc_start: 0.7465 (t70) cc_final: 0.6973 (t0) REVERT: B 1144 GLU cc_start: 0.8149 (mp0) cc_final: 0.7769 (mp0) REVERT: C 34 ARG cc_start: 0.6978 (ttm110) cc_final: 0.6751 (ttm110) REVERT: C 91 TYR cc_start: 0.6367 (t80) cc_final: 0.6067 (t80) REVERT: C 195 ILE cc_start: 0.8444 (mm) cc_final: 0.8130 (tp) REVERT: C 198 TYR cc_start: 0.6397 (m-80) cc_final: 0.5830 (m-10) REVERT: C 224 GLU cc_start: 0.7347 (pm20) cc_final: 0.6613 (mp0) REVERT: C 228 ASP cc_start: 0.7028 (t70) cc_final: 0.5331 (t0) REVERT: C 269 TYR cc_start: 0.7354 (m-10) cc_final: 0.6800 (m-80) REVERT: C 297 SER cc_start: 0.8347 (m) cc_final: 0.7926 (p) REVERT: C 298 GLU cc_start: 0.8238 (tt0) cc_final: 0.7688 (tp30) REVERT: C 346 ARG cc_start: 0.7616 (mmm160) cc_final: 0.7223 (mmm160) REVERT: C 357 ARG cc_start: 0.7539 (ttt90) cc_final: 0.7213 (ttt-90) REVERT: C 375 PHE cc_start: 0.7419 (m-80) cc_final: 0.6893 (m-10) REVERT: C 394 ASN cc_start: 0.8126 (t0) cc_final: 0.6986 (t0) REVERT: C 395 VAL cc_start: 0.8991 (m) cc_final: 0.8770 (p) REVERT: C 400 PHE cc_start: 0.7787 (p90) cc_final: 0.7124 (p90) REVERT: C 406 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7329 (mt-10) REVERT: C 408 ARG cc_start: 0.9064 (tmm160) cc_final: 0.8751 (ttp80) REVERT: C 436 TRP cc_start: 0.7278 (p90) cc_final: 0.6907 (p90) REVERT: C 535 LYS cc_start: 0.8849 (mmmm) cc_final: 0.8611 (mmmt) REVERT: C 542 ASN cc_start: 0.7978 (t0) cc_final: 0.7538 (t0) REVERT: C 547 LYS cc_start: 0.8602 (mtmm) cc_final: 0.8334 (mtmm) REVERT: C 602 THR cc_start: 0.8707 (OUTLIER) cc_final: 0.8295 (p) REVERT: C 655 TYR cc_start: 0.7868 (t80) cc_final: 0.7644 (t80) REVERT: C 675 GLN cc_start: 0.7776 (mm110) cc_final: 0.7348 (mm110) REVERT: C 705 VAL cc_start: 0.8741 (t) cc_final: 0.8467 (m) REVERT: C 708 SER cc_start: 0.8962 (t) cc_final: 0.8447 (m) REVERT: C 718 PHE cc_start: 0.7870 (p90) cc_final: 0.7375 (p90) REVERT: C 725 GLU cc_start: 0.7674 (tp30) cc_final: 0.7402 (tp30) REVERT: C 726 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8482 (mm) REVERT: C 731 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8108 (pmm) REVERT: C 773 GLU cc_start: 0.7405 (tm-30) cc_final: 0.6558 (tm-30) REVERT: C 774 GLN cc_start: 0.7645 (mm-40) cc_final: 0.7132 (mm-40) REVERT: C 823 PHE cc_start: 0.7605 (m-80) cc_final: 0.7315 (m-80) REVERT: C 853 GLN cc_start: 0.8234 (mt0) cc_final: 0.7935 (mt0) REVERT: C 867 ASP cc_start: 0.8140 (m-30) cc_final: 0.7780 (m-30) REVERT: C 868 GLU cc_start: 0.7897 (tp30) cc_final: 0.7505 (tm-30) REVERT: C 872 GLN cc_start: 0.8355 (tp40) cc_final: 0.7942 (tp40) REVERT: C 901 GLN cc_start: 0.8965 (OUTLIER) cc_final: 0.8353 (tm-30) REVERT: C 918 GLU cc_start: 0.7575 (mp0) cc_final: 0.7133 (mp0) REVERT: C 933 LYS cc_start: 0.8130 (mtmm) cc_final: 0.7707 (mmmm) REVERT: C 949 GLN cc_start: 0.8513 (mm-40) cc_final: 0.7859 (mm-40) REVERT: C 950 ASP cc_start: 0.7604 (t70) cc_final: 0.7056 (t0) REVERT: C 953 ASN cc_start: 0.8437 (m-40) cc_final: 0.8033 (m110) REVERT: C 964 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8275 (mmmm) REVERT: C 966 LEU cc_start: 0.9141 (tt) cc_final: 0.8819 (tp) REVERT: C 1017 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7785 (tm-30) REVERT: C 1038 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7708 (mmmm) REVERT: C 1048 HIS cc_start: 0.8408 (t-90) cc_final: 0.7963 (t70) REVERT: C 1066 THR cc_start: 0.8949 (OUTLIER) cc_final: 0.8551 (p) REVERT: C 1111 GLU cc_start: 0.7147 (tm-30) cc_final: 0.6775 (tm-30) REVERT: D 83 GLU cc_start: 0.2231 (OUTLIER) cc_final: 0.1894 (pp20) REVERT: E 144 LEU cc_start: 0.6192 (mm) cc_final: 0.5843 (pp) REVERT: E 156 HIS cc_start: 0.7376 (m-70) cc_final: 0.6967 (m90) REVERT: E 158 MET cc_start: 0.4848 (mmm) cc_final: 0.4524 (mmm) REVERT: E 234 TYR cc_start: 0.6841 (t80) cc_final: 0.6635 (t80) REVERT: F 39 GLN cc_start: 0.7706 (pp30) cc_final: 0.7408 (pp30) REVERT: F 146 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8340 (tp) REVERT: F 206 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8744 (mt) REVERT: F 234 MET cc_start: 0.6947 (tpt) cc_final: 0.5239 (pmm) REVERT: G 4 LEU cc_start: 0.8655 (mt) cc_final: 0.8363 (tp) REVERT: G 28 ASN cc_start: 0.8541 (p0) cc_final: 0.8284 (p0) REVERT: G 191 ARG cc_start: 0.6965 (ptt90) cc_final: 0.6512 (ptt90) outliers start: 159 outliers final: 129 residues processed: 792 average time/residue: 0.2054 time to fit residues: 260.1049 Evaluate side-chains 823 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 675 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 659 SER Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 960 ASN Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 98 ASN Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 153 PHE Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain G residue 197 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 375 optimal weight: 7.9990 chunk 254 optimal weight: 0.9990 chunk 294 optimal weight: 0.8980 chunk 184 optimal weight: 4.9990 chunk 315 optimal weight: 20.0000 chunk 136 optimal weight: 10.0000 chunk 221 optimal weight: 4.9990 chunk 300 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 ASN A 66 HIS ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 960 ASN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 ASN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 71 ASN ** G 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.163279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.119282 restraints weight = 67798.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.123463 restraints weight = 31384.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.126162 restraints weight = 18175.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.127878 restraints weight = 12241.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.128682 restraints weight = 9349.627| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.5339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 32215 Z= 0.150 Angle : 0.720 13.179 43907 Z= 0.358 Chirality : 0.047 0.472 4962 Planarity : 0.005 0.052 5654 Dihedral : 6.182 80.930 4450 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.57 % Favored : 90.40 % Rotamer: Outliers : 4.55 % Allowed : 21.97 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.13), residues: 3970 helix: 1.12 (0.21), residues: 671 sheet: -1.12 (0.17), residues: 857 loop : -2.51 (0.12), residues: 2442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 328 TYR 0.037 0.001 TYR E 204 PHE 0.041 0.002 PHE B 981 TRP 0.049 0.002 TRP G 36 HIS 0.008 0.001 HIS E 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (32147) covalent geometry : angle 0.71301 / 0.36 (43750) SS BOND : bond 0.00318 / 0.24 ( 47) SS BOND : angle 1.83275 / 1.23 ( 94) hydrogen bonds : bond 0.03182 / 2.11 ( 851) hydrogen bonds : angle 4.81260 / 3.35 ( 2274) link_NAG-ASN : bond 0.00284 / 0.19 ( 21) link_NAG-ASN : angle 1.93254 / 1.31 ( 63) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7249.28 seconds wall clock time: 125 minutes 39.21 seconds (7539.21 seconds total)