Starting phenix.real_space_refine on Thu May 29 03:32:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wos_32657/05_2025/7wos_32657.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wos_32657/05_2025/7wos_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7wos_32657/05_2025/7wos_32657.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wos_32657/05_2025/7wos_32657.map" model { file = "/net/cci-nas-00/data/ceres_data/7wos_32657/05_2025/7wos_32657.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wos_32657/05_2025/7wos_32657.cif" } resolution = 3.91 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.79s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, '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: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, '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: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, '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 dihedrals: 15 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 dihedrals: 27 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 dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 17.60, per 1000 atoms: 0.56 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: 7.49 Conformation dependent library (CDL) restraints added in 4.1 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: 3.73 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: 12.64 Time building geometry restraints manager: 8.75 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: 18408 16.70 - 33.41: 773 33.41 - 50.11: 133 50.11 - 66.82: 27 66.82 - 83.52: 4 Dihedral angle restraints: 19345 sinusoidal: 7697 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 19342 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 1147 o \ r resid 1301 through 1305)) selection = (chain 'B' and (resid 26 through 243 or resid 262 through 1147 or resid 1301 thr \ ough 1305)) selection = (chain 'C' and (resid 26 through 1147 or resid 1301 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: 2.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.250 Check model and map are aligned: 0.260 Set scattering table: 0.320 Process input model: 66.450 Find NCS groups from input model: 1.610 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 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 : 9.083 83.522 11754 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.97 (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 TRP 0.007 0.001 TRP E 98 HIS 0.001 0.000 HIS A1064 PHE 0.010 0.001 PHE A 375 TYR 0.010 0.001 TYR A1067 ARG 0.002 0.000 ARG B1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00822 ( 21) link_NAG-ASN : angle 2.97903 ( 63) hydrogen bonds : bond 0.14003 ( 851) hydrogen bonds : angle 6.33162 ( 2274) SS BOND : bond 0.00342 ( 47) SS BOND : angle 0.68829 ( 94) covalent geometry : bond 0.00311 (32147) covalent geometry : angle 0.51846 (43750) *********************** 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 : 3.516 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: A 42 VAL cc_start: 0.8886 (t) cc_final: 0.8673 (t) REVERT: A 61 ASN cc_start: 0.7321 (m-40) cc_final: 0.6835 (p0) REVERT: A 92 PHE cc_start: 0.8210 (t80) cc_final: 0.7849 (t80) REVERT: A 104 TRP cc_start: 0.6816 (m-90) cc_final: 0.6495 (m-10) REVERT: A 117 LEU cc_start: 0.7729 (mt) cc_final: 0.7476 (mt) REVERT: A 128 ILE cc_start: 0.8680 (mp) cc_final: 0.7915 (mm) REVERT: A 130 VAL cc_start: 0.7856 (OUTLIER) cc_final: 0.7469 (t) REVERT: A 135 PHE cc_start: 0.6728 (OUTLIER) cc_final: 0.6519 (p90) REVERT: A 168 PHE cc_start: 0.7526 (t80) cc_final: 0.6863 (t80) REVERT: A 192 PHE cc_start: 0.7551 (m-10) cc_final: 0.7216 (m-10) REVERT: A 193 LYS cc_start: 0.7328 (mtmt) cc_final: 0.6991 (ptpt) REVERT: A 235 ILE cc_start: 0.8885 (mt) cc_final: 0.8251 (tp) REVERT: A 265 TYR cc_start: 0.7736 (p90) cc_final: 0.7501 (p90) REVERT: A 276 LEU cc_start: 0.8655 (tp) cc_final: 0.8373 (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: 0.8641 (mp) REVERT: A 300 LYS cc_start: 0.7961 (mtmt) cc_final: 0.7601 (mtmm) REVERT: A 326 ILE cc_start: 0.7922 (mt) cc_final: 0.7306 (mm) REVERT: A 557 LYS cc_start: 0.7986 (mmtm) cc_final: 0.7670 (mmtm) REVERT: A 559 PHE cc_start: 0.7176 (m-80) cc_final: 0.6911 (m-80) REVERT: A 587 ILE cc_start: 0.8508 (mt) cc_final: 0.8286 (tp) REVERT: A 591 SER cc_start: 0.7315 (p) cc_final: 0.6855 (m) REVERT: A 602 THR cc_start: 0.8172 (m) cc_final: 0.7781 (p) REVERT: A 619 GLU cc_start: 0.7035 (mt-10) cc_final: 0.6737 (mt-10) REVERT: A 644 GLN cc_start: 0.7720 (tp40) cc_final: 0.7442 (tp40) REVERT: A 664 ILE cc_start: 0.8769 (mt) cc_final: 0.8561 (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: 0.7195 (t80) REVERT: A 710 ASN cc_start: 0.7662 (p0) cc_final: 0.7457 (p0) REVERT: A 725 GLU cc_start: 0.7790 (tt0) cc_final: 0.6951 (tt0) REVERT: A 732 THR cc_start: 0.9171 (OUTLIER) cc_final: 0.8942 (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: 0.7988 (mm) cc_final: 0.7639 (tp) REVERT: A 765 ARG cc_start: 0.7566 (ttp-170) cc_final: 0.7277 (ptm160) REVERT: A 768 THR cc_start: 0.8418 (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: 0.8324 (mp) REVERT: A 905 ARG cc_start: 0.8254 (mtt-85) cc_final: 0.6986 (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: 0.7525 (t80) REVERT: A 949 GLN cc_start: 0.8195 (mm110) cc_final: 0.7301 (mm-40) REVERT: A 953 ASN cc_start: 0.7601 (m-40) cc_final: 0.7249 (m-40) REVERT: A 964 LYS cc_start: 0.8521 (tmtm) cc_final: 0.7994 (tmtm) REVERT: A 977 LEU cc_start: 0.8812 (mp) cc_final: 0.7393 (mm) REVERT: A 993 ILE cc_start: 0.7799 (tp) cc_final: 0.7530 (tp) REVERT: A 1002 GLN cc_start: 0.7846 (tp-100) cc_final: 0.7581 (tp40) REVERT: A 1028 LYS cc_start: 0.8541 (ttmm) cc_final: 0.7795 (tttt) REVERT: A 1103 PHE cc_start: 0.7897 (m-80) cc_final: 0.7683 (m-80) REVERT: A 1118 ASP cc_start: 0.7398 (t70) cc_final: 0.7041 (t0) REVERT: B 41 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8333 (mttt) REVERT: B 43 PHE cc_start: 0.8420 (t80) cc_final: 0.8104 (t80) REVERT: B 44 ARG cc_start: 0.8184 (mtt90) cc_final: 0.7661 (mtt180) REVERT: B 92 PHE cc_start: 0.8310 (t80) cc_final: 0.8021 (t80) REVERT: B 104 TRP cc_start: 0.7156 (m-90) cc_final: 0.6874 (m-90) REVERT: B 168 PHE cc_start: 0.8029 (t80) cc_final: 0.7113 (t80) REVERT: B 187 LEU cc_start: 0.8649 (tp) cc_final: 0.8433 (tp) REVERT: B 190 PHE cc_start: 0.8255 (m-80) cc_final: 0.7749 (m-10) REVERT: B 200 LYS cc_start: 0.8734 (mttt) cc_final: 0.8244 (mtmt) REVERT: B 228 ASP cc_start: 0.6643 (t70) cc_final: 0.6027 (t0) REVERT: B 237 ARG cc_start: 0.7894 (ttm110) cc_final: 0.7682 (mtp85) REVERT: B 241 LEU cc_start: 0.6070 (pt) cc_final: 0.5400 (pp) REVERT: B 271 GLN cc_start: 0.7789 (mt0) cc_final: 0.7476 (mp-120) REVERT: B 275 PHE cc_start: 0.7439 (m-80) cc_final: 0.7195 (m-80) REVERT: B 278 LYS cc_start: 0.8752 (ttmp) cc_final: 0.8310 (ttmm) REVERT: B 281 GLU cc_start: 0.7266 (pp20) cc_final: 0.7036 (pp20) REVERT: B 297 SER cc_start: 0.7730 (m) cc_final: 0.7224 (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: 0.7645 (p) REVERT: B 342 PHE cc_start: 0.8021 (m-80) cc_final: 0.7753 (m-10) REVERT: B 433 VAL cc_start: 0.8793 (p) cc_final: 0.8531 (p) REVERT: B 584 ILE cc_start: 0.8030 (OUTLIER) cc_final: 0.7659 (tt) REVERT: B 585 LEU cc_start: 0.8274 (mt) cc_final: 0.8053 (mp) REVERT: B 610 VAL cc_start: 0.8375 (t) cc_final: 0.8123 (m) REVERT: B 619 GLU cc_start: 0.7707 (tt0) cc_final: 0.7321 (tt0) REVERT: B 641 ASN cc_start: 0.6771 (m-40) cc_final: 0.6129 (t0) REVERT: B 731 MET cc_start: 0.8155 (ttt) cc_final: 0.7895 (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: 0.8380 (m110) REVERT: B 868 GLU cc_start: 0.7676 (tp30) cc_final: 0.7458 (tp30) REVERT: B 869 MET cc_start: 0.8399 (mtt) cc_final: 0.8171 (mtm) REVERT: B 894 LEU cc_start: 0.8314 (mt) cc_final: 0.7713 (mt) REVERT: B 895 GLN cc_start: 0.7235 (pt0) cc_final: 0.7034 (pm20) REVERT: B 900 MET cc_start: 0.8027 (mtp) cc_final: 0.7778 (mtm) REVERT: B 905 ARG cc_start: 0.7860 (mtt-85) cc_final: 0.7519 (mtt-85) REVERT: B 914 ASN cc_start: 0.8498 (p0) cc_final: 0.8255 (p0) REVERT: B 921 LYS cc_start: 0.8402 (mmmt) cc_final: 0.8135 (mmmm) REVERT: B 922 LEU cc_start: 0.8736 (tp) cc_final: 0.8448 (tp) REVERT: B 929 SER cc_start: 0.8624 (m) cc_final: 0.8286 (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: 0.7207 (mp) REVERT: B 1081 ILE cc_start: 0.8811 (pt) cc_final: 0.8491 (mm) REVERT: B 1086 LYS cc_start: 0.7425 (mmmm) cc_final: 0.7115 (mppt) REVERT: B 1111 GLU cc_start: 0.7626 (tt0) cc_final: 0.7141 (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: 0.6615 (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: 0.6514 (t70) REVERT: C 117 LEU cc_start: 0.7397 (tp) cc_final: 0.6997 (mt) REVERT: C 127 VAL cc_start: 0.7221 (OUTLIER) cc_final: 0.6873 (m) REVERT: C 170 TYR cc_start: 0.7641 (t80) cc_final: 0.7434 (t80) REVERT: C 223 LEU cc_start: 0.7454 (mt) cc_final: 0.7020 (mt) REVERT: C 269 TYR cc_start: 0.6923 (m-10) cc_final: 0.6553 (m-80) REVERT: C 287 ASP cc_start: 0.7148 (p0) cc_final: 0.6886 (p0) REVERT: C 294 ASP cc_start: 0.8117 (p0) cc_final: 0.7763 (p0) REVERT: C 297 SER cc_start: 0.8216 (m) cc_final: 0.7745 (p) REVERT: C 298 GLU cc_start: 0.8078 (tt0) cc_final: 0.7408 (tp30) REVERT: C 300 LYS cc_start: 0.8968 (mttt) cc_final: 0.8722 (mtpt) REVERT: C 306 PHE cc_start: 0.7649 (m-80) cc_final: 0.7158 (m-80) REVERT: C 310 LYS cc_start: 0.8726 (ttpp) cc_final: 0.8445 (ttpp) REVERT: C 326 ILE cc_start: 0.8722 (mp) cc_final: 0.8241 (mp) REVERT: C 375 PHE cc_start: 0.7416 (m-10) cc_final: 0.7041 (m-10) REVERT: C 387 LEU cc_start: 0.8716 (tp) cc_final: 0.8259 (tp) REVERT: C 406 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7507 (mt-10) REVERT: C 425 LEU cc_start: 0.9041 (mp) cc_final: 0.8661 (tp) REVERT: C 433 VAL cc_start: 0.8488 (p) cc_final: 0.8055 (p) REVERT: C 539 VAL cc_start: 0.8567 (m) cc_final: 0.8091 (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: 0.8053 (mtmm) REVERT: C 553 THR cc_start: 0.8702 (p) cc_final: 0.8451 (p) REVERT: C 587 ILE cc_start: 0.8637 (mt) cc_final: 0.8186 (pt) REVERT: C 655 TYR cc_start: 0.7988 (t80) cc_final: 0.7533 (t80) REVERT: C 705 VAL cc_start: 0.8474 (t) cc_final: 0.8153 (m) REVERT: C 708 SER cc_start: 0.8866 (t) cc_final: 0.8516 (m) REVERT: C 764 LYS cc_start: 0.7888 (mtpp) cc_final: 0.7586 (mtpp) REVERT: C 765 ARG cc_start: 0.7470 (ttp-110) cc_final: 0.7221 (ttm110) REVERT: C 773 GLU cc_start: 0.6899 (tm-30) cc_final: 0.6042 (tm-30) REVERT: C 820 ASP cc_start: 0.7604 (m-30) cc_final: 0.7152 (m-30) REVERT: C 867 ASP cc_start: 0.7882 (m-30) cc_final: 0.7676 (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: 0.7343 (mm-40) REVERT: C 953 ASN cc_start: 0.8142 (m-40) cc_final: 0.7925 (m-40) REVERT: C 960 ASN cc_start: 0.7887 (m110) cc_final: 0.7383 (m110) REVERT: C 961 THR cc_start: 0.7799 (m) cc_final: 0.7589 (p) REVERT: C 973 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.8108 (pp) REVERT: C 1028 LYS cc_start: 0.8503 (mttt) cc_final: 0.7717 (mtpp) REVERT: C 1048 HIS cc_start: 0.8412 (t70) cc_final: 0.7722 (t70) REVERT: C 1049 LEU cc_start: 0.8289 (mt) cc_final: 0.7936 (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: -0.0330 (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: 0.4650 (mmm) REVERT: E 238 MET cc_start: 0.5484 (ttm) cc_final: 0.5016 (ttm) REVERT: F 128 VAL cc_start: 0.6680 (OUTLIER) cc_final: 0.6266 (p) REVERT: F 159 TYR cc_start: 0.6631 (m-80) cc_final: 0.6196 (m-80) REVERT: G 4 LEU cc_start: 0.8693 (mt) cc_final: 0.8193 (tp) REVERT: G 32 ASN cc_start: 0.7043 (m110) cc_final: 0.6794 (m-40) outliers start: 182 outliers final: 71 residues processed: 1073 average time/residue: 0.4407 time to fit residues: 740.2340 Evaluate side-chains 816 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 734 time to evaluate : 3.262 ------------------------------------------------------------------------------- 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 535 LYS 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 337 optimal weight: 30.0000 chunk 303 optimal weight: 4.9990 chunk 168 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 204 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 313 optimal weight: 40.0000 chunk 121 optimal weight: 7.9990 chunk 190 optimal weight: 5.9990 chunk 233 optimal weight: 3.9990 chunk 363 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 173 GLN A 321 GLN A 394 ASN A 409 GLN A 414 GLN A 422 ASN A 536 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A 675 GLN A 690 GLN A 777 ASN A 784 GLN A 853 GLN A 901 GLN A 957 GLN A1002 GLN A1011 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1125 ASN B 87 ASN B 173 GLN B 181 GLN B 234 ASN B 245 HIS B 370 ASN B 388 ASN B 409 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 ASN B 784 GLN B 853 GLN B 914 ASN B1002 GLN ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS B1119 ASN ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN C 409 GLN C 414 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN C 450 ASN C 487 ASN C 540 ASN C 580 GLN C 616 ASN C 755 GLN C 784 GLN C 853 GLN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN C 955 ASN C1011 GLN C1048 HIS ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1071 GLN C1083 HIS 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 98 ASN D 129 GLN D 165 GLN D 202 ASN E 35 ASN ** E 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 GLN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 129 GLN F 165 GLN F 202 ASN ** G 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 GLN G 137 GLN G 206 GLN ** G 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 75 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.165532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.120124 restraints weight = 66920.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.124297 restraints weight = 31573.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.126927 restraints weight = 18522.008| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.115 32215 Z= 0.287 Angle : 0.741 14.102 43907 Z= 0.376 Chirality : 0.048 0.289 4962 Planarity : 0.005 0.050 5654 Dihedral : 7.406 79.964 4966 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.03 % Favored : 89.95 % Rotamer: Outliers : 5.16 % Allowed : 14.13 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.28 (0.12), residues: 3970 helix: 0.34 (0.21), residues: 667 sheet: -1.88 (0.17), residues: 805 loop : -3.21 (0.11), residues: 2498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP G 36 HIS 0.011 0.002 HIS B1083 PHE 0.027 0.002 PHE A 190 TYR 0.033 0.002 TYR A1067 ARG 0.007 0.001 ARG C 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00295 ( 21) link_NAG-ASN : angle 2.55663 ( 63) hydrogen bonds : bond 0.04203 ( 851) hydrogen bonds : angle 5.10364 ( 2274) SS BOND : bond 0.00807 ( 47) SS BOND : angle 2.12228 ( 94) covalent geometry : bond 0.00588 (32147) covalent geometry : angle 0.72956 (43750) *********************** 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 939 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 762 time to evaluate : 3.568 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: 0.8400 (t) cc_final: 0.8091 (m) REVERT: A 61 ASN cc_start: 0.7668 (m-40) cc_final: 0.7187 (p0) REVERT: A 86 PHE cc_start: 0.7266 (t80) cc_final: 0.7000 (t80) REVERT: A 92 PHE cc_start: 0.8230 (t80) cc_final: 0.7687 (t80) REVERT: A 135 PHE cc_start: 0.6692 (OUTLIER) cc_final: 0.6449 (p90) REVERT: A 177 MET cc_start: 0.6497 (ppp) cc_final: 0.6149 (ppp) REVERT: A 189 GLU cc_start: 0.6335 (pm20) cc_final: 0.5864 (pm20) REVERT: A 193 LYS cc_start: 0.8364 (mtmt) cc_final: 0.8154 (mtpt) REVERT: A 224 GLU cc_start: 0.8470 (pm20) cc_final: 0.8264 (pm20) REVERT: A 235 ILE cc_start: 0.8977 (mt) cc_final: 0.8476 (tp) REVERT: A 276 LEU cc_start: 0.8603 (tp) cc_final: 0.8390 (tt) REVERT: A 278 LYS cc_start: 0.8849 (ttmt) cc_final: 0.8464 (tttt) REVERT: A 294 ASP cc_start: 0.7732 (p0) cc_final: 0.7108 (p0) REVERT: A 297 SER cc_start: 0.8509 (m) cc_final: 0.8097 (p) REVERT: A 533 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8203 (pp) REVERT: A 587 ILE cc_start: 0.8743 (mt) cc_final: 0.8339 (tp) REVERT: A 602 THR cc_start: 0.8628 (m) cc_final: 0.8179 (p) REVERT: A 618 THR cc_start: 0.8348 (p) cc_final: 0.7397 (p) REVERT: A 644 GLN cc_start: 0.7602 (tp40) cc_final: 0.7227 (tp40) REVERT: A 664 ILE cc_start: 0.8788 (mt) cc_final: 0.8538 (mm) REVERT: A 697 MET cc_start: 0.7759 (ptm) cc_final: 0.7420 (ptm) REVERT: A 709 ASN cc_start: 0.7657 (OUTLIER) cc_final: 0.7310 (p0) REVERT: A 737 ASP cc_start: 0.7705 (t0) cc_final: 0.5575 (p0) REVERT: A 742 ILE cc_start: 0.8485 (mm) cc_final: 0.7903 (tp) REVERT: A 764 LYS cc_start: 0.8365 (ttpp) cc_final: 0.7993 (tppt) REVERT: A 765 ARG cc_start: 0.8005 (ttp-170) cc_final: 0.7506 (ttm170) REVERT: A 768 THR cc_start: 0.8709 (m) cc_final: 0.8421 (p) REVERT: A 776 LYS cc_start: 0.8798 (tmmt) cc_final: 0.8539 (ttmm) REVERT: A 886 TRP cc_start: 0.8662 (p90) cc_final: 0.7626 (p90) REVERT: A 911 VAL cc_start: 0.8996 (t) cc_final: 0.8667 (m) REVERT: A 914 ASN cc_start: 0.7980 (p0) cc_final: 0.7730 (p0) REVERT: A 957 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7838 (tt0) REVERT: A 977 LEU cc_start: 0.8512 (mp) cc_final: 0.7568 (mm) REVERT: A 981 PHE cc_start: 0.6231 (m-80) cc_final: 0.5841 (m-80) REVERT: A 995 ARG cc_start: 0.7807 (ptm160) cc_final: 0.7597 (ptm160) REVERT: A 1072 GLU cc_start: 0.8709 (pm20) cc_final: 0.7901 (pm20) REVERT: A 1073 LYS cc_start: 0.8579 (tttm) cc_final: 0.7921 (ttmm) REVERT: A 1081 ILE cc_start: 0.8683 (pt) cc_final: 0.8397 (mm) REVERT: A 1103 PHE cc_start: 0.8349 (m-80) cc_final: 0.8106 (m-80) REVERT: A 1118 ASP cc_start: 0.7855 (t70) cc_final: 0.7634 (t0) REVERT: A 1138 TYR cc_start: 0.7356 (t80) cc_final: 0.7133 (t80) REVERT: A 1141 LEU cc_start: 0.9102 (mp) cc_final: 0.8740 (mm) REVERT: B 37 TYR cc_start: 0.7670 (p90) cc_final: 0.6743 (p90) REVERT: B 41 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8542 (mttp) REVERT: B 43 PHE cc_start: 0.8774 (t80) cc_final: 0.8211 (t80) REVERT: B 65 PHE cc_start: 0.7488 (m-80) cc_final: 0.7278 (m-10) REVERT: B 95 ILE cc_start: 0.7104 (OUTLIER) cc_final: 0.6604 (pt) REVERT: B 104 TRP cc_start: 0.7834 (m-90) cc_final: 0.7321 (m-90) REVERT: B 129 LYS cc_start: 0.7914 (tppt) cc_final: 0.7514 (tppt) REVERT: B 190 PHE cc_start: 0.8345 (m-80) cc_final: 0.8084 (m-10) REVERT: B 193 LYS cc_start: 0.8471 (ttpt) cc_final: 0.8003 (ttmm) REVERT: B 200 LYS cc_start: 0.8796 (mttt) cc_final: 0.8295 (mtmt) REVERT: B 224 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7220 (mm-30) REVERT: B 228 ASP cc_start: 0.7187 (t70) cc_final: 0.6237 (t0) REVERT: B 229 LEU cc_start: 0.8749 (mm) cc_final: 0.8547 (mm) REVERT: B 237 ARG cc_start: 0.7920 (ttm110) cc_final: 0.7707 (mmm-85) REVERT: B 271 GLN cc_start: 0.7869 (mt0) cc_final: 0.7451 (mm-40) REVERT: B 275 PHE cc_start: 0.7856 (m-80) cc_final: 0.7409 (m-80) REVERT: B 278 LYS cc_start: 0.8876 (ttmp) cc_final: 0.8384 (ttmm) REVERT: B 297 SER cc_start: 0.8375 (m) cc_final: 0.7951 (p) REVERT: B 307 THR cc_start: 0.8276 (m) cc_final: 0.7934 (p) REVERT: B 378 LYS cc_start: 0.8912 (tptt) cc_final: 0.8575 (tptt) REVERT: B 581 THR cc_start: 0.8016 (t) cc_final: 0.7803 (t) REVERT: B 587 ILE cc_start: 0.8899 (mp) cc_final: 0.8696 (mp) REVERT: B 663 ASP cc_start: 0.7683 (t70) cc_final: 0.7435 (t70) REVERT: B 695 TYR cc_start: 0.8136 (p90) cc_final: 0.7398 (p90) REVERT: B 730 SER cc_start: 0.8843 (t) cc_final: 0.8406 (p) REVERT: B 737 ASP cc_start: 0.8023 (t0) cc_final: 0.7148 (p0) REVERT: B 740 MET cc_start: 0.7495 (ttp) cc_final: 0.6761 (ttp) REVERT: B 764 LYS cc_start: 0.8490 (tppt) cc_final: 0.8230 (tppt) REVERT: B 796 TYR cc_start: 0.8456 (t80) cc_final: 0.8072 (t80) REVERT: B 803 SER cc_start: 0.8419 (m) cc_final: 0.7910 (p) REVERT: B 804 GLN cc_start: 0.8351 (mp10) cc_final: 0.8107 (mp10) REVERT: B 820 ASP cc_start: 0.7717 (m-30) cc_final: 0.7314 (m-30) REVERT: B 824 ASN cc_start: 0.8778 (m-40) cc_final: 0.8541 (m-40) REVERT: B 865 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8217 (mt) REVERT: B 868 GLU cc_start: 0.8056 (tp30) cc_final: 0.7809 (mm-30) REVERT: B 869 MET cc_start: 0.8564 (mtt) cc_final: 0.8330 (mtt) REVERT: B 895 GLN cc_start: 0.7777 (pt0) cc_final: 0.7539 (pm20) REVERT: B 902 MET cc_start: 0.8613 (tpp) cc_final: 0.8212 (tpp) REVERT: B 914 ASN cc_start: 0.8683 (p0) cc_final: 0.8193 (p0) REVERT: B 918 GLU cc_start: 0.8251 (mt-10) cc_final: 0.8010 (mt-10) REVERT: B 921 LYS cc_start: 0.8719 (mmmt) cc_final: 0.8316 (mmmm) REVERT: B 925 ASN cc_start: 0.8940 (m-40) cc_final: 0.8681 (m-40) REVERT: B 929 SER cc_start: 0.8840 (m) cc_final: 0.8509 (p) REVERT: B 933 LYS cc_start: 0.8709 (mtmt) cc_final: 0.8249 (mtmm) REVERT: B 947 LYS cc_start: 0.9240 (OUTLIER) cc_final: 0.8971 (mtmt) REVERT: B 949 GLN cc_start: 0.8645 (mm110) cc_final: 0.8335 (mm110) REVERT: B 950 ASP cc_start: 0.7693 (m-30) cc_final: 0.7476 (m-30) REVERT: B 1000 ARG cc_start: 0.8512 (ttm170) cc_final: 0.8248 (mtt-85) REVERT: B 1031 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7664 (mt-10) REVERT: B 1038 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8574 (mmmm) REVERT: B 1072 GLU cc_start: 0.8633 (pm20) cc_final: 0.7587 (mp0) REVERT: B 1081 ILE cc_start: 0.8852 (pt) cc_final: 0.8528 (mm) REVERT: B 1091 ARG cc_start: 0.7263 (ttm170) cc_final: 0.7042 (ttm-80) REVERT: B 1111 GLU cc_start: 0.8020 (tt0) cc_final: 0.7120 (tt0) REVERT: B 1113 GLN cc_start: 0.8140 (mt0) cc_final: 0.7676 (mp-120) REVERT: B 1118 ASP cc_start: 0.7486 (t70) cc_final: 0.6665 (t0) REVERT: C 41 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8429 (mtmm) REVERT: C 101 ILE cc_start: 0.8656 (mt) cc_final: 0.8405 (mm) REVERT: C 170 TYR cc_start: 0.8059 (t80) cc_final: 0.7711 (t80) REVERT: C 190 PHE cc_start: 0.7820 (m-80) cc_final: 0.7358 (m-80) REVERT: C 192 PHE cc_start: 0.8530 (m-80) cc_final: 0.8313 (m-10) REVERT: C 218 GLN cc_start: 0.7897 (mt0) cc_final: 0.7593 (mm-40) REVERT: C 228 ASP cc_start: 0.7251 (t70) cc_final: 0.6329 (t0) REVERT: C 269 TYR cc_start: 0.7236 (m-10) cc_final: 0.6741 (m-10) REVERT: C 271 GLN cc_start: 0.7794 (tm-30) cc_final: 0.7264 (tm-30) REVERT: C 287 ASP cc_start: 0.7225 (p0) cc_final: 0.6818 (p0) REVERT: C 297 SER cc_start: 0.8474 (m) cc_final: 0.8124 (p) REVERT: C 306 PHE cc_start: 0.7875 (m-80) cc_final: 0.7262 (m-80) REVERT: C 328 ARG cc_start: 0.8246 (mtp180) cc_final: 0.7917 (mtp85) REVERT: C 377 PHE cc_start: 0.7486 (t80) cc_final: 0.7237 (t80) REVERT: C 387 LEU cc_start: 0.8903 (tp) cc_final: 0.8535 (tp) REVERT: C 390 LEU cc_start: 0.8904 (tp) cc_final: 0.8110 (tt) REVERT: C 392 PHE cc_start: 0.7255 (m-80) cc_final: 0.6374 (m-80) REVERT: C 406 GLU cc_start: 0.8294 (mt-10) cc_final: 0.7837 (mt-10) REVERT: C 421 TYR cc_start: 0.7184 (m-10) cc_final: 0.6695 (m-80) REVERT: C 454 ARG cc_start: 0.7523 (ttt180) cc_final: 0.7298 (ttm170) REVERT: C 455 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7610 (tm) REVERT: C 540 ASN cc_start: 0.8039 (m-40) cc_final: 0.7822 (t0) REVERT: C 542 ASN cc_start: 0.8029 (t0) cc_final: 0.7650 (t0) REVERT: C 547 LYS cc_start: 0.8588 (mtmm) cc_final: 0.8368 (mtmm) REVERT: C 552 LEU cc_start: 0.8986 (mt) cc_final: 0.8272 (mt) REVERT: C 571 ASP cc_start: 0.6033 (t0) cc_final: 0.5788 (t0) REVERT: C 587 ILE cc_start: 0.8939 (mt) cc_final: 0.8512 (pt) REVERT: C 660 TYR cc_start: 0.8286 (m-80) cc_final: 0.8020 (m-80) REVERT: C 675 GLN cc_start: 0.7940 (mm110) cc_final: 0.7680 (mm110) REVERT: C 764 LYS cc_start: 0.8217 (mtpp) cc_final: 0.7880 (mtpp) REVERT: C 773 GLU cc_start: 0.7493 (tm-30) cc_final: 0.6673 (tm-30) REVERT: C 816 SER cc_start: 0.8628 (p) cc_final: 0.7344 (m) REVERT: C 820 ASP cc_start: 0.7842 (m-30) cc_final: 0.7469 (m-30) REVERT: C 856 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8455 (tptp) REVERT: C 868 GLU cc_start: 0.7774 (tp30) cc_final: 0.7397 (tp30) REVERT: C 901 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8126 (tm-30) REVERT: C 902 MET cc_start: 0.8827 (tpp) cc_final: 0.8582 (tpp) REVERT: C 933 LYS cc_start: 0.8272 (mtmm) cc_final: 0.7925 (mmmm) REVERT: C 949 GLN cc_start: 0.8402 (mm-40) cc_final: 0.7562 (mm-40) REVERT: C 950 ASP cc_start: 0.7455 (t70) cc_final: 0.7007 (t0) REVERT: C 953 ASN cc_start: 0.8472 (m-40) cc_final: 0.8112 (m-40) REVERT: C 964 LYS cc_start: 0.8706 (mtmp) cc_final: 0.8328 (mmmm) REVERT: C 984 LEU cc_start: 0.7249 (tp) cc_final: 0.6862 (tp) REVERT: C 990 GLU cc_start: 0.6804 (OUTLIER) cc_final: 0.6508 (mp0) REVERT: C 1017 GLU cc_start: 0.8106 (tm-30) cc_final: 0.7608 (tm-30) REVERT: C 1028 LYS cc_start: 0.8438 (mttt) cc_final: 0.8160 (ttmm) REVERT: C 1038 LYS cc_start: 0.8165 (mtmp) cc_final: 0.7854 (mmmm) REVERT: C 1111 GLU cc_start: 0.7437 (tt0) cc_final: 0.7179 (tt0) REVERT: D 6 GLN cc_start: 0.1223 (OUTLIER) cc_final: 0.0242 (tp40) REVERT: D 83 GLU cc_start: 0.2430 (OUTLIER) cc_final: 0.2132 (pp20) REVERT: E 156 HIS cc_start: 0.7255 (m-70) cc_final: 0.7030 (m90) REVERT: E 158 MET cc_start: 0.5361 (mmm) cc_final: 0.4938 (mmm) REVERT: E 238 MET cc_start: 0.5318 (ttm) cc_final: 0.4769 (ttm) REVERT: F 146 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8071 (tp) REVERT: F 159 TYR cc_start: 0.7289 (m-80) cc_final: 0.6108 (m-80) REVERT: F 178 TYR cc_start: 0.6712 (m-80) cc_final: 0.6365 (m-80) REVERT: F 206 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8724 (mp) REVERT: F 230 TYR cc_start: 0.6944 (t80) cc_final: 0.6706 (t80) REVERT: G 4 LEU cc_start: 0.8667 (mt) cc_final: 0.8202 (tp) REVERT: G 32 ASN cc_start: 0.6791 (m110) cc_final: 0.6585 (m-40) REVERT: G 52 ASN cc_start: 0.8938 (p0) cc_final: 0.8738 (p0) REVERT: G 238 MET cc_start: 0.6586 (mmt) cc_final: 0.6282 (mmt) outliers start: 177 outliers final: 104 residues processed: 897 average time/residue: 0.4207 time to fit residues: 598.5232 Evaluate side-chains 799 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 677 time to evaluate : 3.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 PHE 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 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 533 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 895 GLN 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 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 203 SER 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 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 549 THR Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 865 LEU 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 41 LYS 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 312 ILE Chi-restraints excluded: chain C residue 362 VAL 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 659 SER Chi-restraints excluded: chain C residue 666 ILE 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 975 SER 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 1089 PHE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1130 ILE 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 205 TYR 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 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 159 HIS 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 22 CYS 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 146 LEU Chi-restraints excluded: chain F residue 153 PHE Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 205 TYR 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 G residue 19 THR Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 175 ILE 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 171 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 333 optimal weight: 0.0170 chunk 3 optimal weight: 1.9990 chunk 371 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 133 optimal weight: 0.9990 chunk 283 optimal weight: 0.7980 chunk 310 optimal weight: 6.9990 chunk 298 optimal weight: 1.9990 chunk 197 optimal weight: 0.0970 overall best weight: 0.7820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 GLN ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN A 563 GLN ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A 957 GLN A 960 ASN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS ** A1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN B 564 GLN B 690 GLN B1023 ASN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS C 314 GLN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN C 580 GLN C 641 ASN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 920 GLN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN C1088 HIS ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 GLN ** G 52 ASN ** 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 = 0.4197 r_free = 0.4197 target = 0.166740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.121808 restraints weight = 67154.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.126057 restraints weight = 31366.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.128724 restraints weight = 18207.002| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 32215 Z= 0.132 Angle : 0.642 12.469 43907 Z= 0.316 Chirality : 0.045 0.281 4962 Planarity : 0.004 0.048 5654 Dihedral : 6.874 80.911 4919 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.81 % Favored : 92.17 % Rotamer: Outliers : 5.24 % Allowed : 16.67 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.12), residues: 3970 helix: 0.78 (0.21), residues: 674 sheet: -1.60 (0.17), residues: 823 loop : -3.01 (0.11), residues: 2473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 64 HIS 0.011 0.001 HIS E 159 PHE 0.038 0.001 PHE B 981 TYR 0.030 0.001 TYR C 369 ARG 0.006 0.000 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00298 ( 21) link_NAG-ASN : angle 2.18420 ( 63) hydrogen bonds : bond 0.03329 ( 851) hydrogen bonds : angle 4.83145 ( 2274) SS BOND : bond 0.00537 ( 47) SS BOND : angle 2.26144 ( 94) covalent geometry : bond 0.00293 (32147) covalent geometry : angle 0.62954 (43750) *********************** 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 889 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 709 time to evaluate : 3.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.8472 (m-80) cc_final: 0.8068 (m-10) REVERT: A 36 VAL cc_start: 0.8358 (t) cc_final: 0.8105 (m) REVERT: A 92 PHE cc_start: 0.8206 (t80) cc_final: 0.7699 (t80) REVERT: A 135 PHE cc_start: 0.6874 (OUTLIER) cc_final: 0.6567 (p90) REVERT: A 224 GLU cc_start: 0.8487 (pm20) cc_final: 0.8233 (pm20) REVERT: A 235 ILE cc_start: 0.8923 (mt) cc_final: 0.8414 (tp) REVERT: A 276 LEU cc_start: 0.8587 (tp) cc_final: 0.8381 (tt) REVERT: A 278 LYS cc_start: 0.8765 (ttmt) cc_final: 0.8432 (tttt) REVERT: A 294 ASP cc_start: 0.7806 (p0) cc_final: 0.6903 (p0) REVERT: A 297 SER cc_start: 0.8524 (m) cc_final: 0.7844 (p) REVERT: A 498 ARG cc_start: 0.6771 (mmm160) cc_final: 0.6450 (mmm160) REVERT: A 562 PHE cc_start: 0.6655 (p90) cc_final: 0.6378 (p90) REVERT: A 587 ILE cc_start: 0.8772 (mt) cc_final: 0.8359 (tp) REVERT: A 602 THR cc_start: 0.8527 (m) cc_final: 0.8113 (p) REVERT: A 664 ILE cc_start: 0.8832 (mt) cc_final: 0.8528 (mm) REVERT: A 736 VAL cc_start: 0.8832 (m) cc_final: 0.8464 (p) REVERT: A 737 ASP cc_start: 0.7594 (t0) cc_final: 0.6429 (p0) REVERT: A 741 TYR cc_start: 0.8145 (t80) cc_final: 0.7849 (t80) REVERT: A 742 ILE cc_start: 0.8190 (mm) cc_final: 0.7514 (tp) REVERT: A 764 LYS cc_start: 0.8220 (ttpp) cc_final: 0.7925 (tppt) REVERT: A 765 ARG cc_start: 0.7965 (ttp-170) cc_final: 0.7435 (ttm170) REVERT: A 768 THR cc_start: 0.8657 (m) cc_final: 0.8355 (p) REVERT: A 776 LYS cc_start: 0.8735 (tmmt) cc_final: 0.8510 (ttmm) REVERT: A 869 MET cc_start: 0.8700 (mtt) cc_final: 0.8301 (mpp) REVERT: A 904 TYR cc_start: 0.8564 (m-10) cc_final: 0.8041 (m-10) REVERT: A 911 VAL cc_start: 0.8964 (t) cc_final: 0.8620 (m) REVERT: A 914 ASN cc_start: 0.7877 (p0) cc_final: 0.7534 (p0) REVERT: A 962 LEU cc_start: 0.9062 (tp) cc_final: 0.8742 (tp) REVERT: A 964 LYS cc_start: 0.8621 (mmmt) cc_final: 0.8247 (mmmt) REVERT: A 965 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7935 (tt0) REVERT: A 977 LEU cc_start: 0.8440 (mp) cc_final: 0.7320 (mm) REVERT: A 981 PHE cc_start: 0.6216 (m-10) cc_final: 0.5913 (m-80) REVERT: A 995 ARG cc_start: 0.7815 (ptm160) cc_final: 0.7601 (ptm160) REVERT: A 1031 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7334 (mt-10) REVERT: A 1081 ILE cc_start: 0.8686 (pt) cc_final: 0.8358 (mm) REVERT: A 1107 ARG cc_start: 0.7467 (mtt180) cc_final: 0.7246 (mtt180) REVERT: A 1118 ASP cc_start: 0.7813 (t70) cc_final: 0.7580 (t0) REVERT: A 1138 TYR cc_start: 0.7336 (t80) cc_final: 0.7130 (t80) REVERT: A 1141 LEU cc_start: 0.8785 (mp) cc_final: 0.8043 (mm) REVERT: B 41 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8347 (mttp) REVERT: B 64 TRP cc_start: 0.7854 (t60) cc_final: 0.7589 (t-100) REVERT: B 104 TRP cc_start: 0.7414 (m-90) cc_final: 0.6975 (m-90) REVERT: B 106 PHE cc_start: 0.7870 (m-80) cc_final: 0.7492 (m-80) REVERT: B 129 LYS cc_start: 0.7824 (tppt) cc_final: 0.7443 (tppt) REVERT: B 192 PHE cc_start: 0.8418 (m-80) cc_final: 0.7985 (m-10) REVERT: B 194 ASN cc_start: 0.8528 (t0) cc_final: 0.8320 (t0) REVERT: B 200 LYS cc_start: 0.8732 (mttt) cc_final: 0.8251 (mtmt) REVERT: B 204 LYS cc_start: 0.7929 (tptp) cc_final: 0.7704 (tptp) REVERT: B 224 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7246 (mm-30) REVERT: B 228 ASP cc_start: 0.7110 (t70) cc_final: 0.6170 (t0) REVERT: B 229 LEU cc_start: 0.8758 (mm) cc_final: 0.8467 (mm) REVERT: B 269 TYR cc_start: 0.7587 (m-10) cc_final: 0.7295 (m-80) REVERT: B 271 GLN cc_start: 0.7841 (mt0) cc_final: 0.7417 (mm110) REVERT: B 278 LYS cc_start: 0.8888 (ttmp) cc_final: 0.8446 (ttmm) REVERT: B 298 GLU cc_start: 0.7284 (mt-10) cc_final: 0.7003 (mt-10) REVERT: B 307 THR cc_start: 0.8212 (m) cc_final: 0.7865 (p) REVERT: B 324 GLU cc_start: 0.7519 (pm20) cc_final: 0.7211 (pm20) REVERT: B 378 LYS cc_start: 0.8578 (tptt) cc_final: 0.8130 (tptp) REVERT: B 606 ASN cc_start: 0.8448 (m-40) cc_final: 0.8202 (m-40) REVERT: B 695 TYR cc_start: 0.8087 (p90) cc_final: 0.7426 (p90) REVERT: B 712 ILE cc_start: 0.8684 (tp) cc_final: 0.8409 (tp) REVERT: B 725 GLU cc_start: 0.8172 (tt0) cc_final: 0.7932 (tt0) REVERT: B 730 SER cc_start: 0.8828 (t) cc_final: 0.8277 (p) REVERT: B 737 ASP cc_start: 0.7801 (t0) cc_final: 0.7427 (p0) REVERT: B 740 MET cc_start: 0.7317 (OUTLIER) cc_final: 0.6741 (ttp) REVERT: B 762 GLN cc_start: 0.8205 (mp10) cc_final: 0.7950 (mp10) REVERT: B 780 GLU cc_start: 0.7821 (pt0) cc_final: 0.7520 (tp30) REVERT: B 796 TYR cc_start: 0.8383 (t80) cc_final: 0.8030 (t80) REVERT: B 803 SER cc_start: 0.8313 (m) cc_final: 0.8072 (p) REVERT: B 824 ASN cc_start: 0.8709 (m-40) cc_final: 0.8467 (m-40) REVERT: B 865 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8157 (mp) REVERT: B 868 GLU cc_start: 0.8008 (tp30) cc_final: 0.7768 (mm-30) REVERT: B 869 MET cc_start: 0.8557 (mtt) cc_final: 0.8271 (mtt) REVERT: B 895 GLN cc_start: 0.7656 (pt0) cc_final: 0.7359 (pm20) REVERT: B 902 MET cc_start: 0.8507 (tpp) cc_final: 0.8031 (tpp) REVERT: B 916 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8520 (tp) REVERT: B 921 LYS cc_start: 0.8651 (mmmt) cc_final: 0.8269 (mmmm) REVERT: B 925 ASN cc_start: 0.8899 (m-40) cc_final: 0.8628 (m-40) REVERT: B 929 SER cc_start: 0.8788 (m) cc_final: 0.8413 (p) REVERT: B 933 LYS cc_start: 0.8620 (mtmt) cc_final: 0.8134 (mtpp) REVERT: B 949 GLN cc_start: 0.8593 (mm110) cc_final: 0.8226 (mm-40) REVERT: B 950 ASP cc_start: 0.7650 (m-30) cc_final: 0.7029 (m-30) REVERT: B 990 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7750 (tm-30) REVERT: B 1002 GLN cc_start: 0.8114 (tp40) cc_final: 0.7573 (tp40) REVERT: B 1031 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7480 (mm-30) REVERT: B 1038 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8578 (mmmm) REVERT: B 1081 ILE cc_start: 0.8814 (pt) cc_final: 0.8484 (mm) REVERT: B 1091 ARG cc_start: 0.7178 (ttm170) cc_final: 0.6937 (ttm-80) REVERT: B 1107 ARG cc_start: 0.7382 (mtt90) cc_final: 0.7061 (mtt90) REVERT: B 1111 GLU cc_start: 0.7961 (tt0) cc_final: 0.7182 (tt0) REVERT: B 1113 GLN cc_start: 0.8156 (mt0) cc_final: 0.7691 (mp-120) REVERT: B 1118 ASP cc_start: 0.7377 (t70) cc_final: 0.6882 (t0) REVERT: C 127 VAL cc_start: 0.7305 (OUTLIER) cc_final: 0.6997 (m) REVERT: C 170 TYR cc_start: 0.7894 (t80) cc_final: 0.7643 (t80) REVERT: C 189 GLU cc_start: 0.7855 (tp30) cc_final: 0.6823 (tm-30) REVERT: C 223 LEU cc_start: 0.7774 (mt) cc_final: 0.7330 (mt) REVERT: C 224 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6849 (mp0) REVERT: C 228 ASP cc_start: 0.7192 (t70) cc_final: 0.6662 (t0) REVERT: C 269 TYR cc_start: 0.7079 (m-10) cc_final: 0.6754 (m-10) REVERT: C 271 GLN cc_start: 0.7824 (tm-30) cc_final: 0.7387 (tm-30) REVERT: C 280 ASN cc_start: 0.8808 (t0) cc_final: 0.8497 (t0) REVERT: C 287 ASP cc_start: 0.6880 (p0) cc_final: 0.6500 (p0) REVERT: C 297 SER cc_start: 0.8428 (m) cc_final: 0.8001 (p) REVERT: C 298 GLU cc_start: 0.8158 (tt0) cc_final: 0.7628 (tp30) REVERT: C 306 PHE cc_start: 0.7854 (m-80) cc_final: 0.7269 (m-80) REVERT: C 328 ARG cc_start: 0.8145 (mtp180) cc_final: 0.7412 (mtp85) REVERT: C 357 ARG cc_start: 0.7153 (ptp-110) cc_final: 0.6879 (ptm-80) REVERT: C 365 TYR cc_start: 0.6952 (m-10) cc_final: 0.6665 (m-10) REVERT: C 375 PHE cc_start: 0.7401 (m-80) cc_final: 0.6655 (m-10) REVERT: C 377 PHE cc_start: 0.7317 (t80) cc_final: 0.7076 (t80) REVERT: C 392 PHE cc_start: 0.7264 (m-80) cc_final: 0.6765 (m-80) REVERT: C 406 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7565 (mt-10) REVERT: C 421 TYR cc_start: 0.7085 (m-10) cc_final: 0.6720 (m-80) REVERT: C 436 TRP cc_start: 0.7306 (p90) cc_final: 0.6906 (p90) REVERT: C 454 ARG cc_start: 0.7550 (ttt180) cc_final: 0.7263 (ttm170) REVERT: C 455 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7552 (tm) REVERT: C 537 LYS cc_start: 0.8594 (tptt) cc_final: 0.8115 (tptt) REVERT: C 540 ASN cc_start: 0.8141 (m-40) cc_final: 0.7900 (t0) REVERT: C 542 ASN cc_start: 0.7848 (t0) cc_final: 0.7450 (t0) REVERT: C 547 LYS cc_start: 0.8567 (mtmm) cc_final: 0.8327 (mtmm) REVERT: C 571 ASP cc_start: 0.6006 (t0) cc_final: 0.5672 (t0) REVERT: C 587 ILE cc_start: 0.8902 (mt) cc_final: 0.8522 (pt) REVERT: C 598 ILE cc_start: 0.8825 (mp) cc_final: 0.8482 (tt) REVERT: C 602 THR cc_start: 0.8844 (OUTLIER) cc_final: 0.8448 (p) REVERT: C 664 ILE cc_start: 0.8333 (mt) cc_final: 0.8109 (mm) REVERT: C 675 GLN cc_start: 0.8017 (mm110) cc_final: 0.7583 (mm110) REVERT: C 708 SER cc_start: 0.8935 (t) cc_final: 0.8444 (m) REVERT: C 726 ILE cc_start: 0.9289 (OUTLIER) cc_final: 0.8324 (mm) REVERT: C 764 LYS cc_start: 0.7945 (mtpp) cc_final: 0.7666 (mtpp) REVERT: C 773 GLU cc_start: 0.7353 (tm-30) cc_final: 0.6514 (tm-30) REVERT: C 816 SER cc_start: 0.8570 (p) cc_final: 0.7293 (m) REVERT: C 820 ASP cc_start: 0.7804 (m-30) cc_final: 0.7396 (m-30) REVERT: C 853 GLN cc_start: 0.8205 (mt0) cc_final: 0.7970 (mt0) REVERT: C 856 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8512 (tptp) REVERT: C 901 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.8110 (tm-30) REVERT: C 918 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7344 (mp0) REVERT: C 933 LYS cc_start: 0.8199 (mtmm) cc_final: 0.7816 (mmmm) REVERT: C 949 GLN cc_start: 0.8392 (mm-40) cc_final: 0.7462 (mm-40) REVERT: C 950 ASP cc_start: 0.7430 (t70) cc_final: 0.7014 (t70) REVERT: C 953 ASN cc_start: 0.8500 (m-40) cc_final: 0.7994 (m-40) REVERT: C 957 GLN cc_start: 0.8433 (mt0) cc_final: 0.8164 (tt0) REVERT: C 964 LYS cc_start: 0.8651 (mtmp) cc_final: 0.8202 (mmmm) REVERT: C 966 LEU cc_start: 0.9283 (mt) cc_final: 0.9061 (tp) REVERT: C 990 GLU cc_start: 0.6873 (OUTLIER) cc_final: 0.6543 (mp0) REVERT: C 1017 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7607 (tm-30) REVERT: C 1038 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7778 (mmmm) REVERT: C 1048 HIS cc_start: 0.8476 (t-90) cc_final: 0.7959 (t70) REVERT: C 1071 GLN cc_start: 0.8343 (mm-40) cc_final: 0.7993 (mm-40) REVERT: C 1086 LYS cc_start: 0.7957 (mmmt) cc_final: 0.7576 (mmmt) REVERT: C 1111 GLU cc_start: 0.7478 (tt0) cc_final: 0.7166 (tt0) REVERT: D 6 GLN cc_start: 0.1106 (OUTLIER) cc_final: 0.0222 (tp40) REVERT: D 83 GLU cc_start: 0.2446 (OUTLIER) cc_final: 0.2130 (pp20) REVERT: D 219 TYR cc_start: 0.1636 (m-80) cc_final: 0.1150 (m-80) REVERT: E 158 MET cc_start: 0.4442 (mmm) cc_final: 0.3939 (mmm) REVERT: E 159 HIS cc_start: 0.7646 (m170) cc_final: 0.7427 (m170) REVERT: E 238 MET cc_start: 0.5280 (ttm) cc_final: 0.4754 (ttm) REVERT: F 146 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.7912 (tp) REVERT: F 159 TYR cc_start: 0.7160 (m-80) cc_final: 0.6133 (m-80) REVERT: F 206 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8536 (mp) REVERT: G 4 LEU cc_start: 0.8699 (mt) cc_final: 0.8143 (tp) REVERT: G 32 ASN cc_start: 0.6670 (m110) cc_final: 0.6351 (m-40) REVERT: G 52 ASN cc_start: 0.8832 (p0) cc_final: 0.8487 (p0) REVERT: G 67 LYS cc_start: 0.7887 (ttmm) cc_final: 0.7492 (ttmm) REVERT: G 238 MET cc_start: 0.6555 (mmt) cc_final: 0.6296 (mmt) REVERT: G 249 VAL cc_start: 0.2668 (OUTLIER) cc_final: 0.2452 (t) outliers start: 180 outliers final: 102 residues processed: 840 average time/residue: 0.4162 time to fit residues: 554.0265 Evaluate side-chains 787 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 664 time to evaluate : 3.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 135 PHE 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 321 GLN 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 533 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 649 CYS 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 856 LYS Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 965 GLN 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 83 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 241 LEU 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 582 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 916 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 1073 LYS 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 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 224 GLU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 396 TYR 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 649 CYS 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 765 ARG Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 869 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 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 81 GLN Chi-restraints excluded: chain D residue 83 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 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 181 SER Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 22 CYS 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 111 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 G residue 19 THR Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 106 LEU 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 163 optimal weight: 5.9990 chunk 185 optimal weight: 3.9990 chunk 302 optimal weight: 1.9990 chunk 377 optimal weight: 20.0000 chunk 181 optimal weight: 1.9990 chunk 298 optimal weight: 0.8980 chunk 30 optimal weight: 7.9990 chunk 191 optimal weight: 0.6980 chunk 26 optimal weight: 10.0000 chunk 56 optimal weight: 0.7980 chunk 19 optimal weight: 20.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A 957 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS A1119 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 978 ASN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN C 913 GLN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN C1088 HIS ** 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 159 HIS ** E 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.165524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.120833 restraints weight = 67279.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.125004 restraints weight = 31466.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.127616 restraints weight = 18302.450| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 32215 Z= 0.168 Angle : 0.652 12.635 43907 Z= 0.322 Chirality : 0.045 0.266 4962 Planarity : 0.004 0.048 5654 Dihedral : 6.795 81.264 4904 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.04 % Favored : 90.91 % Rotamer: Outliers : 5.27 % Allowed : 17.80 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.13), residues: 3970 helix: 0.96 (0.21), residues: 676 sheet: -1.42 (0.17), residues: 832 loop : -2.89 (0.11), residues: 2462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP G 36 HIS 0.006 0.001 HIS B1083 PHE 0.041 0.002 PHE B 981 TYR 0.027 0.001 TYR F 51 ARG 0.007 0.000 ARG B 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00396 ( 21) link_NAG-ASN : angle 2.95161 ( 63) hydrogen bonds : bond 0.03332 ( 851) hydrogen bonds : angle 4.79626 ( 2274) SS BOND : bond 0.00652 ( 47) SS BOND : angle 2.01159 ( 94) covalent geometry : bond 0.00358 (32147) covalent geometry : angle 0.63656 (43750) *********************** 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 867 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 686 time to evaluate : 3.498 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 28 TYR cc_start: 0.8449 (m-80) cc_final: 0.8183 (m-80) REVERT: A 36 VAL cc_start: 0.8406 (t) cc_final: 0.8115 (m) REVERT: A 92 PHE cc_start: 0.8229 (t80) cc_final: 0.7818 (t80) REVERT: A 121 ASN cc_start: 0.7261 (t0) cc_final: 0.6778 (t0) REVERT: A 135 PHE cc_start: 0.7064 (OUTLIER) cc_final: 0.6811 (p90) REVERT: A 204 LYS cc_start: 0.7827 (tptm) cc_final: 0.7537 (tptm) REVERT: A 224 GLU cc_start: 0.8485 (pm20) cc_final: 0.8220 (pm20) REVERT: A 235 ILE cc_start: 0.8869 (mt) cc_final: 0.8356 (tp) REVERT: A 278 LYS cc_start: 0.8776 (ttmt) cc_final: 0.8417 (tttt) REVERT: A 293 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8133 (mp) REVERT: A 294 ASP cc_start: 0.7890 (p0) cc_final: 0.6977 (p0) REVERT: A 297 SER cc_start: 0.8510 (m) cc_final: 0.7810 (p) REVERT: A 298 GLU cc_start: 0.8058 (tp30) cc_final: 0.7796 (tp30) REVERT: A 587 ILE cc_start: 0.8827 (mt) cc_final: 0.8433 (tp) REVERT: A 602 THR cc_start: 0.8601 (OUTLIER) cc_final: 0.8197 (p) REVERT: A 642 VAL cc_start: 0.9195 (t) cc_final: 0.8898 (m) REVERT: A 644 GLN cc_start: 0.7745 (tp40) cc_final: 0.7476 (tp40) REVERT: A 664 ILE cc_start: 0.8897 (mt) cc_final: 0.8595 (mm) REVERT: A 736 VAL cc_start: 0.8811 (m) cc_final: 0.8591 (p) REVERT: A 742 ILE cc_start: 0.8377 (mm) cc_final: 0.7729 (tp) REVERT: A 764 LYS cc_start: 0.8230 (ttpp) cc_final: 0.7969 (tppt) REVERT: A 765 ARG cc_start: 0.7990 (ttp-170) cc_final: 0.7432 (ttm170) REVERT: A 768 THR cc_start: 0.8683 (m) cc_final: 0.8376 (p) REVERT: A 776 LYS cc_start: 0.8757 (tmmt) cc_final: 0.8527 (ttmm) REVERT: A 858 LEU cc_start: 0.8761 (mp) cc_final: 0.8546 (mm) REVERT: A 869 MET cc_start: 0.8740 (mtt) cc_final: 0.8337 (mpp) REVERT: A 911 VAL cc_start: 0.9031 (t) cc_final: 0.8652 (m) REVERT: A 914 ASN cc_start: 0.7978 (p0) cc_final: 0.7619 (p0) REVERT: A 960 ASN cc_start: 0.8496 (t0) cc_final: 0.8056 (t0) REVERT: A 964 LYS cc_start: 0.8669 (mmmt) cc_final: 0.8203 (mmmt) REVERT: A 977 LEU cc_start: 0.8457 (mp) cc_final: 0.7322 (mm) REVERT: A 981 PHE cc_start: 0.6233 (m-10) cc_final: 0.5920 (m-80) REVERT: A 1031 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7368 (mt-10) REVERT: A 1073 LYS cc_start: 0.8192 (mmtt) cc_final: 0.7905 (mmtt) REVERT: A 1081 ILE cc_start: 0.8719 (pt) cc_final: 0.8430 (mm) REVERT: A 1118 ASP cc_start: 0.7848 (t70) cc_final: 0.7645 (t0) REVERT: B 41 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8432 (mttp) REVERT: B 43 PHE cc_start: 0.8818 (t80) cc_final: 0.8574 (t80) REVERT: B 81 ASN cc_start: 0.7654 (p0) cc_final: 0.7403 (p0) REVERT: B 104 TRP cc_start: 0.7570 (m-90) cc_final: 0.7142 (m-90) REVERT: B 106 PHE cc_start: 0.7819 (m-80) cc_final: 0.7389 (m-80) REVERT: B 129 LYS cc_start: 0.7846 (tppt) cc_final: 0.7391 (tppt) REVERT: B 141 LEU cc_start: 0.8282 (mt) cc_final: 0.7904 (mm) REVERT: B 192 PHE cc_start: 0.8444 (m-80) cc_final: 0.8002 (m-10) REVERT: B 200 LYS cc_start: 0.8729 (mttt) cc_final: 0.8284 (mtmt) REVERT: B 204 LYS cc_start: 0.8168 (tptp) cc_final: 0.7764 (tptp) REVERT: B 224 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7116 (mm-30) REVERT: B 228 ASP cc_start: 0.7110 (t70) cc_final: 0.6144 (t0) REVERT: B 229 LEU cc_start: 0.8743 (mm) cc_final: 0.8465 (mm) REVERT: B 237 ARG cc_start: 0.8176 (mtp85) cc_final: 0.7929 (mtp85) REVERT: B 269 TYR cc_start: 0.7606 (m-10) cc_final: 0.6999 (m-80) REVERT: B 271 GLN cc_start: 0.7847 (mt0) cc_final: 0.7535 (mp-120) REVERT: B 275 PHE cc_start: 0.7879 (m-80) cc_final: 0.7410 (m-80) REVERT: B 278 LYS cc_start: 0.8906 (ttmp) cc_final: 0.8416 (ttmm) REVERT: B 307 THR cc_start: 0.8247 (m) cc_final: 0.7950 (p) REVERT: B 324 GLU cc_start: 0.7471 (pm20) cc_final: 0.7147 (pm20) REVERT: B 378 LYS cc_start: 0.8303 (tptt) cc_final: 0.7969 (tptt) REVERT: B 606 ASN cc_start: 0.8452 (m-40) cc_final: 0.8209 (m-40) REVERT: B 695 TYR cc_start: 0.8119 (p90) cc_final: 0.7466 (p90) REVERT: B 702 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7740 (mm-30) REVERT: B 703 ASN cc_start: 0.7378 (t0) cc_final: 0.7053 (t0) REVERT: B 712 ILE cc_start: 0.8732 (tp) cc_final: 0.8513 (tp) REVERT: B 730 SER cc_start: 0.8924 (t) cc_final: 0.8383 (p) REVERT: B 731 MET cc_start: 0.8243 (ttt) cc_final: 0.7954 (ttt) REVERT: B 740 MET cc_start: 0.7333 (ttp) cc_final: 0.6845 (ttp) REVERT: B 796 TYR cc_start: 0.8432 (t80) cc_final: 0.8079 (t80) REVERT: B 803 SER cc_start: 0.8463 (m) cc_final: 0.8047 (p) REVERT: B 804 GLN cc_start: 0.8370 (mp10) cc_final: 0.8163 (mt0) REVERT: B 820 ASP cc_start: 0.7660 (m-30) cc_final: 0.7272 (m-30) REVERT: B 824 ASN cc_start: 0.8707 (m-40) cc_final: 0.8468 (m-40) REVERT: B 868 GLU cc_start: 0.8028 (tp30) cc_final: 0.7790 (mm-30) REVERT: B 869 MET cc_start: 0.8588 (mtt) cc_final: 0.8295 (mtt) REVERT: B 895 GLN cc_start: 0.7673 (pt0) cc_final: 0.7383 (pm20) REVERT: B 902 MET cc_start: 0.8506 (tpp) cc_final: 0.8125 (tpp) REVERT: B 916 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8551 (tp) REVERT: B 921 LYS cc_start: 0.8651 (mmmt) cc_final: 0.8230 (mmmm) REVERT: B 925 ASN cc_start: 0.8929 (m-40) cc_final: 0.8684 (m-40) REVERT: B 929 SER cc_start: 0.8808 (m) cc_final: 0.8465 (p) REVERT: B 933 LYS cc_start: 0.8621 (mtmt) cc_final: 0.8152 (mtpp) REVERT: B 949 GLN cc_start: 0.8625 (mm110) cc_final: 0.8213 (mm110) REVERT: B 950 ASP cc_start: 0.7774 (m-30) cc_final: 0.7100 (m-30) REVERT: B 990 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7886 (tm-30) REVERT: B 1002 GLN cc_start: 0.8128 (tp40) cc_final: 0.7675 (tp40) REVERT: B 1038 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8601 (mmmm) REVERT: B 1072 GLU cc_start: 0.8607 (pm20) cc_final: 0.8139 (pm20) REVERT: B 1081 ILE cc_start: 0.8775 (pt) cc_final: 0.8445 (mm) REVERT: B 1107 ARG cc_start: 0.7471 (mtt90) cc_final: 0.7223 (mtt90) REVERT: B 1113 GLN cc_start: 0.8154 (mt0) cc_final: 0.7951 (mm-40) REVERT: B 1118 ASP cc_start: 0.7411 (t70) cc_final: 0.6930 (t0) REVERT: C 67 VAL cc_start: 0.7184 (OUTLIER) cc_final: 0.6946 (t) REVERT: C 91 TYR cc_start: 0.7253 (t80) cc_final: 0.6795 (t80) REVERT: C 102 ARG cc_start: 0.6646 (tpp80) cc_final: 0.6086 (mtt90) REVERT: C 117 LEU cc_start: 0.7839 (mp) cc_final: 0.7608 (mm) REVERT: C 127 VAL cc_start: 0.7320 (OUTLIER) cc_final: 0.7030 (m) REVERT: C 135 PHE cc_start: 0.6451 (OUTLIER) cc_final: 0.6054 (m-80) REVERT: C 170 TYR cc_start: 0.7894 (t80) cc_final: 0.7663 (t80) REVERT: C 189 GLU cc_start: 0.7958 (tp30) cc_final: 0.7727 (tp30) REVERT: C 223 LEU cc_start: 0.7792 (mt) cc_final: 0.7583 (mt) REVERT: C 228 ASP cc_start: 0.7275 (t0) cc_final: 0.6658 (t0) REVERT: C 269 TYR cc_start: 0.7169 (m-10) cc_final: 0.6837 (m-10) REVERT: C 271 GLN cc_start: 0.7867 (tm-30) cc_final: 0.7559 (tm-30) REVERT: C 280 ASN cc_start: 0.8753 (t0) cc_final: 0.8544 (t0) REVERT: C 281 GLU cc_start: 0.8340 (pp20) cc_final: 0.8106 (pp20) REVERT: C 297 SER cc_start: 0.8431 (m) cc_final: 0.8067 (p) REVERT: C 357 ARG cc_start: 0.7380 (ptp-110) cc_final: 0.7117 (ptm-80) REVERT: C 375 PHE cc_start: 0.7446 (m-80) cc_final: 0.6790 (m-10) REVERT: C 377 PHE cc_start: 0.7400 (t80) cc_final: 0.7186 (t80) REVERT: C 406 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7666 (mt-10) REVERT: C 421 TYR cc_start: 0.7074 (m-10) cc_final: 0.6299 (m-80) REVERT: C 436 TRP cc_start: 0.7386 (p90) cc_final: 0.6840 (p90) REVERT: C 454 ARG cc_start: 0.7500 (ttt180) cc_final: 0.7134 (ttm170) REVERT: C 455 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7605 (tm) REVERT: C 537 LYS cc_start: 0.8571 (tptt) cc_final: 0.8060 (tptt) REVERT: C 542 ASN cc_start: 0.7953 (t0) cc_final: 0.6842 (t0) REVERT: C 547 LYS cc_start: 0.8569 (mtmm) cc_final: 0.8307 (mmtt) REVERT: C 571 ASP cc_start: 0.6131 (t0) cc_final: 0.5808 (t0) REVERT: C 586 ASP cc_start: 0.8271 (t0) cc_final: 0.8059 (t0) REVERT: C 587 ILE cc_start: 0.8964 (mt) cc_final: 0.8424 (pt) REVERT: C 598 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8498 (tt) REVERT: C 602 THR cc_start: 0.8815 (OUTLIER) cc_final: 0.8432 (p) REVERT: C 675 GLN cc_start: 0.8054 (mm110) cc_final: 0.7625 (mm110) REVERT: C 708 SER cc_start: 0.8939 (t) cc_final: 0.8456 (m) REVERT: C 725 GLU cc_start: 0.7665 (tm-30) cc_final: 0.7367 (tm-30) REVERT: C 726 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8381 (mm) REVERT: C 764 LYS cc_start: 0.8085 (mtpp) cc_final: 0.7866 (mtpp) REVERT: C 773 GLU cc_start: 0.7282 (tm-30) cc_final: 0.6496 (tm-30) REVERT: C 816 SER cc_start: 0.8611 (p) cc_final: 0.7321 (m) REVERT: C 820 ASP cc_start: 0.7827 (m-30) cc_final: 0.7442 (m-30) REVERT: C 853 GLN cc_start: 0.8167 (mt0) cc_final: 0.7925 (mt0) REVERT: C 901 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.8215 (tm-30) REVERT: C 921 LYS cc_start: 0.8812 (mmmm) cc_final: 0.8203 (mmmm) REVERT: C 933 LYS cc_start: 0.8233 (mtmm) cc_final: 0.7849 (mmmm) REVERT: C 949 GLN cc_start: 0.8508 (mm-40) cc_final: 0.7567 (mm-40) REVERT: C 950 ASP cc_start: 0.7542 (t70) cc_final: 0.6923 (t0) REVERT: C 953 ASN cc_start: 0.8536 (m-40) cc_final: 0.8048 (m-40) REVERT: C 964 LYS cc_start: 0.8662 (mtmp) cc_final: 0.8221 (mmmm) REVERT: C 966 LEU cc_start: 0.9272 (mt) cc_final: 0.8854 (tp) REVERT: C 990 GLU cc_start: 0.6904 (OUTLIER) cc_final: 0.6578 (mp0) REVERT: C 1017 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7546 (tm-30) REVERT: C 1038 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7786 (mmmm) REVERT: C 1048 HIS cc_start: 0.8478 (t-90) cc_final: 0.7931 (t70) REVERT: C 1111 GLU cc_start: 0.7517 (tt0) cc_final: 0.7191 (tt0) REVERT: D 6 GLN cc_start: 0.1120 (OUTLIER) cc_final: 0.0255 (tp40) REVERT: D 83 GLU cc_start: 0.2505 (OUTLIER) cc_final: 0.2197 (pp20) REVERT: E 158 MET cc_start: 0.4918 (mmm) cc_final: 0.4549 (mmm) REVERT: E 238 MET cc_start: 0.5109 (ttm) cc_final: 0.4595 (ttm) REVERT: F 146 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8027 (tp) REVERT: F 159 TYR cc_start: 0.7221 (m-80) cc_final: 0.5606 (m-80) REVERT: F 178 TYR cc_start: 0.6713 (m-80) cc_final: 0.6184 (m-80) REVERT: F 206 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8610 (mp) REVERT: G 4 LEU cc_start: 0.8788 (mt) cc_final: 0.8170 (tp) REVERT: G 32 ASN cc_start: 0.6694 (m110) cc_final: 0.6453 (m-40) REVERT: G 52 ASN cc_start: 0.8820 (p0) cc_final: 0.8598 (p0) REVERT: G 128 LEU cc_start: 0.7240 (mm) cc_final: 0.6915 (mm) REVERT: G 191 ARG cc_start: 0.7080 (ptt90) cc_final: 0.6659 (ptt90) outliers start: 181 outliers final: 124 residues processed: 818 average time/residue: 0.4174 time to fit residues: 545.6340 Evaluate side-chains 800 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 656 time to evaluate : 3.176 ------------------------------------------------------------------------------- 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 135 PHE Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 293 LEU 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 533 LEU 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 602 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 743 CYS Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 856 LYS Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 957 GLN 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 36 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 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 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 587 ILE 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 29 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 56 LEU 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 203 SER Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 396 TYR 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 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 856 LYS Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 960 ASN Chi-restraints excluded: chain C residue 990 GLU 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 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 175 ILE Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 22 CYS 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 111 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 216 THR Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain G residue 19 THR 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 197 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 213 optimal weight: 8.9990 chunk 277 optimal weight: 3.9990 chunk 395 optimal weight: 10.0000 chunk 272 optimal weight: 0.6980 chunk 45 optimal weight: 8.9990 chunk 330 optimal weight: 8.9990 chunk 370 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 243 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 66 HIS ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN A1058 HIS ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN B1023 ASN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN ** 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** D 207 GLN D 209 ASN E 156 HIS ** G 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.164442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.119753 restraints weight = 67345.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.123861 restraints weight = 31729.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.126356 restraints weight = 18503.234| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 32215 Z= 0.147 Angle : 0.651 17.246 43907 Z= 0.319 Chirality : 0.045 0.267 4962 Planarity : 0.004 0.052 5654 Dihedral : 6.701 81.422 4903 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.77 % Favored : 91.18 % Rotamer: Outliers : 5.33 % Allowed : 18.53 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.13), residues: 3970 helix: 1.12 (0.21), residues: 675 sheet: -1.29 (0.17), residues: 823 loop : -2.74 (0.11), residues: 2472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP B 64 HIS 0.007 0.001 HIS A 66 PHE 0.042 0.001 PHE B 981 TYR 0.034 0.001 TYR E 204 ARG 0.010 0.001 ARG C 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00277 ( 21) link_NAG-ASN : angle 2.97105 ( 63) hydrogen bonds : bond 0.03228 ( 851) hydrogen bonds : angle 4.74068 ( 2274) SS BOND : bond 0.00398 ( 47) SS BOND : angle 1.88740 ( 94) covalent geometry : bond 0.00318 (32147) covalent geometry : angle 0.63685 (43750) *********************** 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 859 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 676 time to evaluate : 3.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.8440 (m-80) cc_final: 0.8223 (m-80) REVERT: A 36 VAL cc_start: 0.8407 (t) cc_final: 0.8097 (m) REVERT: A 92 PHE cc_start: 0.8234 (t80) cc_final: 0.7814 (t80) REVERT: A 121 ASN cc_start: 0.7210 (t0) cc_final: 0.6688 (t0) REVERT: A 135 PHE cc_start: 0.7052 (OUTLIER) cc_final: 0.6678 (p90) REVERT: A 170 TYR cc_start: 0.7848 (t80) cc_final: 0.7497 (t80) REVERT: A 204 LYS cc_start: 0.7845 (tptm) cc_final: 0.7567 (tptm) REVERT: A 224 GLU cc_start: 0.8467 (pm20) cc_final: 0.8175 (pm20) REVERT: A 235 ILE cc_start: 0.8840 (mt) cc_final: 0.8588 (mm) REVERT: A 271 GLN cc_start: 0.7670 (mt0) cc_final: 0.7430 (mt0) REVERT: A 278 LYS cc_start: 0.8726 (ttmt) cc_final: 0.8436 (tttt) REVERT: A 294 ASP cc_start: 0.7873 (p0) cc_final: 0.7056 (p0) REVERT: A 297 SER cc_start: 0.8517 (m) cc_final: 0.8062 (p) REVERT: A 562 PHE cc_start: 0.7210 (p90) cc_final: 0.6806 (p90) REVERT: A 587 ILE cc_start: 0.8844 (mt) cc_final: 0.8455 (tp) REVERT: A 602 THR cc_start: 0.8552 (OUTLIER) cc_final: 0.8134 (p) REVERT: A 642 VAL cc_start: 0.9224 (t) cc_final: 0.8957 (m) REVERT: A 644 GLN cc_start: 0.7737 (tp40) cc_final: 0.7428 (tp40) REVERT: A 664 ILE cc_start: 0.8936 (mt) cc_final: 0.8613 (mm) REVERT: A 736 VAL cc_start: 0.8807 (m) cc_final: 0.8534 (p) REVERT: A 737 ASP cc_start: 0.7519 (t0) cc_final: 0.6821 (p0) REVERT: A 742 ILE cc_start: 0.8347 (mm) cc_final: 0.7686 (tp) REVERT: A 764 LYS cc_start: 0.8219 (ttpp) cc_final: 0.7961 (tppt) REVERT: A 765 ARG cc_start: 0.8009 (ttp-170) cc_final: 0.7453 (ttm170) REVERT: A 768 THR cc_start: 0.8672 (m) cc_final: 0.8344 (p) REVERT: A 869 MET cc_start: 0.8748 (mtt) cc_final: 0.8525 (mtm) REVERT: A 911 VAL cc_start: 0.9019 (t) cc_final: 0.8639 (m) REVERT: A 914 ASN cc_start: 0.7989 (p0) cc_final: 0.7618 (p0) REVERT: A 964 LYS cc_start: 0.8736 (mmmt) cc_final: 0.8277 (mmmt) REVERT: A 977 LEU cc_start: 0.8461 (mp) cc_final: 0.7231 (mm) REVERT: A 981 PHE cc_start: 0.6268 (m-10) cc_final: 0.5988 (m-80) REVERT: A 995 ARG cc_start: 0.8001 (ptp-110) cc_final: 0.7275 (ttp80) REVERT: A 998 THR cc_start: 0.8006 (m) cc_final: 0.7726 (p) REVERT: A 1031 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7326 (mt-10) REVERT: A 1073 LYS cc_start: 0.8251 (mmtt) cc_final: 0.7896 (mmtt) REVERT: A 1081 ILE cc_start: 0.8501 (pt) cc_final: 0.8248 (mm) REVERT: A 1103 PHE cc_start: 0.8371 (m-80) cc_final: 0.8034 (m-10) REVERT: A 1107 ARG cc_start: 0.7514 (mtt180) cc_final: 0.7207 (mtt180) REVERT: A 1111 GLU cc_start: 0.7803 (tt0) cc_final: 0.7505 (tt0) REVERT: A 1118 ASP cc_start: 0.7859 (t70) cc_final: 0.7601 (t0) REVERT: B 41 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8384 (mttp) REVERT: B 81 ASN cc_start: 0.7703 (p0) cc_final: 0.7350 (p0) REVERT: B 104 TRP cc_start: 0.7634 (m-90) cc_final: 0.7200 (m-90) REVERT: B 106 PHE cc_start: 0.7750 (m-80) cc_final: 0.7473 (m-80) REVERT: B 129 LYS cc_start: 0.7878 (tppt) cc_final: 0.7394 (tppt) REVERT: B 192 PHE cc_start: 0.8480 (m-80) cc_final: 0.8091 (m-10) REVERT: B 200 LYS cc_start: 0.8726 (mttt) cc_final: 0.8274 (mtmt) REVERT: B 204 LYS cc_start: 0.8123 (tptp) cc_final: 0.7835 (tptp) REVERT: B 205 HIS cc_start: 0.7639 (t-170) cc_final: 0.7361 (t70) REVERT: B 224 GLU cc_start: 0.7448 (mm-30) cc_final: 0.7121 (mm-30) REVERT: B 228 ASP cc_start: 0.7090 (t70) cc_final: 0.6120 (t0) REVERT: B 229 LEU cc_start: 0.8754 (mm) cc_final: 0.8497 (mm) REVERT: B 271 GLN cc_start: 0.7847 (mt0) cc_final: 0.7452 (mm110) REVERT: B 275 PHE cc_start: 0.7869 (m-80) cc_final: 0.7319 (m-80) REVERT: B 278 LYS cc_start: 0.8904 (ttmp) cc_final: 0.8434 (ttmm) REVERT: B 298 GLU cc_start: 0.7241 (mt-10) cc_final: 0.6664 (mp0) REVERT: B 307 THR cc_start: 0.8258 (m) cc_final: 0.7980 (p) REVERT: B 321 GLN cc_start: 0.7593 (tp-100) cc_final: 0.7229 (tp40) REVERT: B 324 GLU cc_start: 0.7548 (pm20) cc_final: 0.7184 (pm20) REVERT: B 606 ASN cc_start: 0.8450 (m-40) cc_final: 0.8204 (m-40) REVERT: B 695 TYR cc_start: 0.8123 (p90) cc_final: 0.7433 (p90) REVERT: B 703 ASN cc_start: 0.7333 (t0) cc_final: 0.7042 (t0) REVERT: B 712 ILE cc_start: 0.8737 (tp) cc_final: 0.8482 (tp) REVERT: B 725 GLU cc_start: 0.8170 (tt0) cc_final: 0.7912 (tp30) REVERT: B 726 ILE cc_start: 0.9198 (OUTLIER) cc_final: 0.8347 (mm) REVERT: B 730 SER cc_start: 0.8939 (t) cc_final: 0.8331 (p) REVERT: B 731 MET cc_start: 0.8260 (ttt) cc_final: 0.7994 (ttt) REVERT: B 778 THR cc_start: 0.8783 (m) cc_final: 0.8561 (t) REVERT: B 780 GLU cc_start: 0.7895 (pt0) cc_final: 0.7583 (tp30) REVERT: B 796 TYR cc_start: 0.8445 (t80) cc_final: 0.8112 (t80) REVERT: B 803 SER cc_start: 0.8449 (m) cc_final: 0.8232 (p) REVERT: B 804 GLN cc_start: 0.8342 (mp10) cc_final: 0.8132 (mp10) REVERT: B 820 ASP cc_start: 0.7665 (m-30) cc_final: 0.7309 (m-30) REVERT: B 824 ASN cc_start: 0.8682 (m-40) cc_final: 0.8454 (m-40) REVERT: B 868 GLU cc_start: 0.8013 (tp30) cc_final: 0.7809 (mm-30) REVERT: B 869 MET cc_start: 0.8601 (mtt) cc_final: 0.8303 (mtt) REVERT: B 895 GLN cc_start: 0.7701 (pt0) cc_final: 0.7361 (pm20) REVERT: B 902 MET cc_start: 0.8479 (tpp) cc_final: 0.8001 (tpp) REVERT: B 921 LYS cc_start: 0.8625 (mmmt) cc_final: 0.8208 (mmmm) REVERT: B 925 ASN cc_start: 0.8930 (m-40) cc_final: 0.8647 (m-40) REVERT: B 929 SER cc_start: 0.8799 (m) cc_final: 0.8444 (p) REVERT: B 933 LYS cc_start: 0.8594 (mtmt) cc_final: 0.8134 (mtpp) REVERT: B 949 GLN cc_start: 0.8635 (mm110) cc_final: 0.8352 (mm-40) REVERT: B 950 ASP cc_start: 0.7787 (m-30) cc_final: 0.7159 (m-30) REVERT: B 990 GLU cc_start: 0.8332 (tm-30) cc_final: 0.7979 (tm-30) REVERT: B 996 LEU cc_start: 0.8563 (mt) cc_final: 0.8347 (mm) REVERT: B 1002 GLN cc_start: 0.8140 (tp40) cc_final: 0.7678 (tp40) REVERT: B 1031 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7821 (mm-30) REVERT: B 1081 ILE cc_start: 0.8789 (pt) cc_final: 0.8422 (mm) REVERT: B 1107 ARG cc_start: 0.7497 (mtt90) cc_final: 0.7259 (mtt90) REVERT: B 1111 GLU cc_start: 0.8103 (tt0) cc_final: 0.7563 (tt0) REVERT: B 1118 ASP cc_start: 0.7444 (t70) cc_final: 0.7016 (t0) REVERT: C 67 VAL cc_start: 0.7184 (OUTLIER) cc_final: 0.6911 (t) REVERT: C 91 TYR cc_start: 0.7193 (t80) cc_final: 0.6852 (t80) REVERT: C 127 VAL cc_start: 0.7350 (OUTLIER) cc_final: 0.7048 (m) REVERT: C 135 PHE cc_start: 0.6510 (OUTLIER) cc_final: 0.6146 (m-80) REVERT: C 160 TYR cc_start: 0.7886 (OUTLIER) cc_final: 0.7636 (m-10) REVERT: C 170 TYR cc_start: 0.7822 (t80) cc_final: 0.7580 (t80) REVERT: C 189 GLU cc_start: 0.7915 (tp30) cc_final: 0.7565 (tp30) REVERT: C 223 LEU cc_start: 0.7771 (mt) cc_final: 0.7454 (mt) REVERT: C 228 ASP cc_start: 0.7511 (t0) cc_final: 0.6752 (t0) REVERT: C 269 TYR cc_start: 0.7190 (m-10) cc_final: 0.6900 (m-10) REVERT: C 271 GLN cc_start: 0.7901 (tm-30) cc_final: 0.7580 (tm-30) REVERT: C 280 ASN cc_start: 0.8750 (t0) cc_final: 0.8414 (t0) REVERT: C 297 SER cc_start: 0.8482 (m) cc_final: 0.8094 (p) REVERT: C 298 GLU cc_start: 0.8209 (tt0) cc_final: 0.7678 (tp30) REVERT: C 354 ASN cc_start: 0.8445 (t0) cc_final: 0.8158 (t0) REVERT: C 375 PHE cc_start: 0.7503 (m-80) cc_final: 0.7000 (m-10) REVERT: C 377 PHE cc_start: 0.7475 (t80) cc_final: 0.7197 (t80) REVERT: C 406 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7574 (mt-10) REVERT: C 421 TYR cc_start: 0.7079 (m-10) cc_final: 0.6765 (m-80) REVERT: C 436 TRP cc_start: 0.7403 (p90) cc_final: 0.6876 (p90) REVERT: C 454 ARG cc_start: 0.7488 (ttt180) cc_final: 0.7120 (ttm170) REVERT: C 455 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7587 (tm) REVERT: C 465 GLU cc_start: 0.8083 (tp30) cc_final: 0.7726 (tp30) REVERT: C 533 LEU cc_start: 0.8963 (tp) cc_final: 0.8677 (tt) REVERT: C 535 LYS cc_start: 0.8523 (tppp) cc_final: 0.8244 (tppp) REVERT: C 537 LYS cc_start: 0.8548 (tptt) cc_final: 0.8147 (tptt) REVERT: C 542 ASN cc_start: 0.7916 (t0) cc_final: 0.7564 (t0) REVERT: C 547 LYS cc_start: 0.8586 (mtmm) cc_final: 0.8370 (mtmm) REVERT: C 571 ASP cc_start: 0.6189 (t0) cc_final: 0.5875 (t0) REVERT: C 587 ILE cc_start: 0.8991 (mt) cc_final: 0.8531 (pt) REVERT: C 602 THR cc_start: 0.8776 (OUTLIER) cc_final: 0.8501 (p) REVERT: C 643 PHE cc_start: 0.7453 (t80) cc_final: 0.7201 (t80) REVERT: C 664 ILE cc_start: 0.8479 (mt) cc_final: 0.8201 (mm) REVERT: C 675 GLN cc_start: 0.8032 (mm110) cc_final: 0.7598 (mm110) REVERT: C 708 SER cc_start: 0.8920 (t) cc_final: 0.8457 (m) REVERT: C 725 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7326 (tm-30) REVERT: C 726 ILE cc_start: 0.8819 (OUTLIER) cc_final: 0.8350 (mm) REVERT: C 764 LYS cc_start: 0.8125 (mtpp) cc_final: 0.7801 (mtpp) REVERT: C 773 GLU cc_start: 0.7239 (tm-30) cc_final: 0.6548 (tm-30) REVERT: C 816 SER cc_start: 0.8578 (p) cc_final: 0.8038 (m) REVERT: C 853 GLN cc_start: 0.8142 (mt0) cc_final: 0.7907 (mt0) REVERT: C 901 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.8213 (tm-30) REVERT: C 918 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7338 (mp0) REVERT: C 921 LYS cc_start: 0.8814 (mmmm) cc_final: 0.8198 (mmmm) REVERT: C 933 LYS cc_start: 0.8194 (mtmm) cc_final: 0.7790 (mmmm) REVERT: C 949 GLN cc_start: 0.8492 (mm-40) cc_final: 0.7533 (mm-40) REVERT: C 950 ASP cc_start: 0.7508 (t70) cc_final: 0.6909 (t0) REVERT: C 953 ASN cc_start: 0.8544 (m-40) cc_final: 0.8017 (m-40) REVERT: C 964 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8205 (mmmm) REVERT: C 966 LEU cc_start: 0.9186 (mt) cc_final: 0.8817 (tp) REVERT: C 979 ASP cc_start: 0.8257 (m-30) cc_final: 0.8056 (m-30) REVERT: C 983 ARG cc_start: 0.7913 (mmp80) cc_final: 0.7684 (mmp80) REVERT: C 1017 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7703 (tm-30) REVERT: C 1038 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7712 (mmmm) REVERT: C 1048 HIS cc_start: 0.8483 (t-90) cc_final: 0.7906 (t70) REVERT: C 1050 MET cc_start: 0.7254 (OUTLIER) cc_final: 0.6811 (mtm) REVERT: C 1086 LYS cc_start: 0.8184 (mmmt) cc_final: 0.7947 (mmmt) REVERT: C 1111 GLU cc_start: 0.7464 (tt0) cc_final: 0.7063 (tt0) REVERT: D 6 GLN cc_start: 0.1260 (OUTLIER) cc_final: 0.0371 (tp40) REVERT: D 83 GLU cc_start: 0.2506 (OUTLIER) cc_final: 0.2204 (pp20) REVERT: D 160 MET cc_start: 0.2842 (mmm) cc_final: 0.2551 (mmp) REVERT: D 219 TYR cc_start: 0.1790 (m-80) cc_final: 0.1497 (m-80) REVERT: E 158 MET cc_start: 0.4712 (mmm) cc_final: 0.4271 (mmm) REVERT: E 238 MET cc_start: 0.5173 (ttm) cc_final: 0.4670 (ttm) REVERT: F 39 GLN cc_start: 0.8119 (pp30) cc_final: 0.7750 (pm20) REVERT: F 146 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8176 (tp) REVERT: F 159 TYR cc_start: 0.7080 (m-80) cc_final: 0.6039 (m-80) REVERT: F 206 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8670 (mp) REVERT: F 229 TYR cc_start: 0.6445 (t80) cc_final: 0.5845 (t80) REVERT: G 4 LEU cc_start: 0.8736 (mt) cc_final: 0.8266 (tp) REVERT: G 28 ASN cc_start: 0.8384 (OUTLIER) cc_final: 0.8070 (p0) REVERT: G 32 ASN cc_start: 0.6623 (m110) cc_final: 0.6419 (m-40) REVERT: G 52 ASN cc_start: 0.8836 (p0) cc_final: 0.8557 (p0) REVERT: G 128 LEU cc_start: 0.7290 (mm) cc_final: 0.6964 (mm) REVERT: G 191 ARG cc_start: 0.7049 (ptt90) cc_final: 0.6634 (ptt90) outliers start: 183 outliers final: 134 residues processed: 806 average time/residue: 0.4175 time to fit residues: 537.5302 Evaluate side-chains 810 residues out of total 3482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 656 time to evaluate : 3.252 ------------------------------------------------------------------------------- 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 135 PHE Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 171 VAL 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 358 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 528 LYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 533 LEU 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 649 CYS Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 856 LYS Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 949 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 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 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 582 LEU Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1001 LEU 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 56 LEU 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 157 PHE 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 203 SER Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 312 ILE 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 396 TYR 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 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 856 LYS Chi-restraints excluded: chain C residue 866 THR 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 929 SER 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 1029 MET Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 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 130 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 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 175 ILE Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 22 CYS 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 111 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 216 THR 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 G residue 19 THR Chi-restraints excluded: chain G residue 28 ASN 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 197 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 65.4077 > 50: distance: 16 - 23: 3.132 distance: 48 - 54: 21.773 distance: 54 - 55: 18.777 distance: 54 - 200: 22.101 distance: 55 - 56: 13.715 distance: 55 - 58: 12.670 distance: 56 - 57: 31.952 distance: 56 - 66: 20.754 distance: 57 - 197: 12.833 distance: 58 - 59: 24.120 distance: 59 - 60: 11.271 distance: 59 - 61: 6.042 distance: 60 - 62: 13.897 distance: 61 - 63: 6.188 distance: 62 - 64: 7.702 distance: 63 - 64: 9.751 distance: 64 - 65: 14.474 distance: 66 - 67: 7.548 distance: 67 - 68: 17.691 distance: 67 - 70: 21.935 distance: 68 - 69: 25.660 distance: 68 - 75: 23.321 distance: 70 - 71: 18.814 distance: 71 - 72: 19.830 distance: 72 - 73: 12.300 distance: 72 - 74: 7.791 distance: 75 - 76: 40.656 distance: 75 - 187: 21.826 distance: 76 - 77: 24.948 distance: 76 - 79: 26.480 distance: 77 - 78: 24.452 distance: 77 - 82: 13.777 distance: 79 - 80: 33.690 distance: 79 - 81: 22.545 distance: 82 - 83: 24.959 distance: 83 - 84: 40.004 distance: 83 - 86: 24.629 distance: 84 - 85: 13.614 distance: 84 - 88: 31.089 distance: 86 - 87: 46.072 distance: 88 - 89: 34.354 distance: 89 - 90: 11.607 distance: 89 - 92: 20.466 distance: 90 - 91: 22.671 distance: 90 - 96: 13.376 distance: 92 - 93: 33.674 distance: 93 - 94: 18.306 distance: 93 - 95: 22.132 distance: 96 - 97: 24.422 distance: 97 - 98: 10.959 distance: 97 - 100: 10.345 distance: 98 - 99: 24.572 distance: 98 - 107: 20.576 distance: 100 - 101: 16.998 distance: 101 - 102: 22.525 distance: 101 - 103: 21.176 distance: 102 - 104: 31.149 distance: 103 - 105: 15.052 distance: 104 - 106: 22.237 distance: 105 - 106: 24.812 distance: 107 - 108: 20.883 distance: 108 - 109: 23.431 distance: 108 - 111: 36.667 distance: 109 - 110: 20.179 distance: 109 - 118: 36.139 distance: 111 - 112: 38.452 distance: 112 - 113: 4.354 distance: 113 - 114: 17.051 distance: 114 - 115: 22.610 distance: 115 - 117: 4.418 distance: 118 - 119: 29.439 distance: 119 - 120: 31.555 distance: 119 - 122: 51.612 distance: 120 - 121: 58.525 distance: 120 - 125: 25.678 distance: 122 - 123: 9.205 distance: 122 - 124: 12.495 distance: 125 - 126: 24.724 distance: 126 - 127: 19.361 distance: 126 - 129: 26.199 distance: 127 - 128: 27.214 distance: 127 - 134: 24.712 distance: 129 - 130: 28.576 distance: 130 - 131: 32.433 distance: 131 - 132: 19.486 distance: 131 - 133: 18.186 distance: 134 - 135: 19.390 distance: 134 - 140: 34.739 distance: 135 - 136: 23.442 distance: 135 - 138: 33.273 distance: 136 - 137: 10.246 distance: 136 - 141: 24.014 distance: 138 - 139: 41.894 distance: 139 - 140: 33.588