Starting phenix.real_space_refine on Fri Jun 27 06:29:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wou_32659/06_2025/7wou_32659.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wou_32659/06_2025/7wou_32659.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wou_32659/06_2025/7wou_32659.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wou_32659/06_2025/7wou_32659.map" model { file = "/net/cci-nas-00/data/ceres_data/7wou_32659/06_2025/7wou_32659.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wou_32659/06_2025/7wou_32659.cif" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 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 19974 2.51 5 N 5206 2.21 5 O 6076 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.69s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 31397 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 8005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 8005 Classifications: {'peptide': 1028} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 57, 'TRANS': 970} Chain breaks: 8 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: "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: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" 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 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 17.97, per 1000 atoms: 0.57 Number of scatterers: 31397 At special positions: 0 Unit cell: (142.576, 163.856, 207.48, 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 6076 8.00 N 5206 7.00 C 19974 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=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 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 282 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 709 " " NAG A1304 " - " ASN A 717 " " NAG A1305 " - " ASN A 801 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A1098 " " NAG A1308 " - " ASN A1134 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 709 " " NAG B1304 " - " ASN B 717 " " NAG B1305 " - " ASN B 801 " " NAG B1306 " - " ASN B1098 " " NAG B1307 " - " ASN B1134 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 709 " " NAG C1304 " - " ASN C 717 " " NAG C1305 " - " ASN C 801 " " NAG C1306 " - " ASN C1074 " " NAG C1307 " - " ASN C1098 " " NAG C1308 " - " ASN C1134 " Time building additional restraints: 7.09 Conformation dependent library (CDL) restraints added in 4.0 seconds 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7440 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 67 sheets defined 17.4% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.25 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.847A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 364 through 372 removed outlier: 4.098A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 removed outlier: 3.503A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 423 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.712A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 783 removed outlier: 3.535A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) removed outlier: 3.871A 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: 4.069A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 removed outlier: 3.798A pdb=" N GLY A 908 " --> pdb=" O TYR A 904 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) removed outlier: 3.577A 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: 3.536A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.644A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) removed outlier: 3.740A 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: 4.205A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 3.936A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 removed outlier: 3.901A pdb=" N THR B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 341 removed outlier: 4.200A 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: 3.872A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.603A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) 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: 3.516A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 3.883A 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 855 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 907 removed outlier: 3.901A pdb=" N ASN B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 939 removed outlier: 4.364A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.532A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.837A 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 1032 removed outlier: 4.263A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU B1001 " --> pdb=" O ILE B 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 1143 through 1147 removed outlier: 3.729A pdb=" N ASP B1146 " --> pdb=" O PRO B1143 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N SER B1147 " --> pdb=" O GLU B1144 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1143 through 1147' Processing helix chain 'C' and resid 294 through 302 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: 3.818A pdb=" N ASN C 388 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.583A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.648A 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: 3.657A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 778 removed outlier: 3.853A 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 882 Processing helix chain 'C' and resid 897 through 907 removed outlier: 3.512A pdb=" N ALA C 903 " --> pdb=" O PRO C 899 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG C 905 " --> pdb=" O GLN C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 938 removed outlier: 3.599A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.557A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU C 959 " --> pdb=" O ASN C 955 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN C 965 " --> pdb=" O THR C 961 " (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 981 removed outlier: 4.378A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N PHE C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 976 through 981' Processing helix chain 'C' and resid 985 through 993 removed outlier: 4.211A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 1033 removed outlier: 3.590A pdb=" N GLY C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.037A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 84 Processing helix chain 'E' and resid 152 through 156 Processing helix chain 'G' and resid 80 through 84 Processing helix chain 'G' and resid 152 through 156 Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.496A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 63 through 66 removed outlier: 3.526A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.739A 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: 7.546A pdb=" N ILE A 201 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER A 203 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.849A 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: 3.983A 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 356 through 358 removed outlier: 6.231A pdb=" N PHE A 392 " --> pdb=" O THR A 523 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 356 through 358 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.551A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.443A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB6, first strand: chain 'A' and resid 712 through 722 removed outlier: 6.756A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 725 through 728 Processing sheet with id=AB8, first strand: chain 'A' and resid 734 through 735 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AC1, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC2, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.664A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.933A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AC6, first strand: chain 'B' and resid 89 through 92 removed outlier: 3.610A pdb=" N TYR B 198 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU B 229 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE B 201 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL B 227 " --> pdb=" O ILE B 201 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N SER B 203 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 120 through 122 removed outlier: 3.551A pdb=" N VAL B 127 " --> pdb=" O VAL B 120 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AC9, first strand: chain 'B' and resid 318 through 319 Processing sheet with id=AD1, first strand: chain 'B' and resid 325 through 326 Processing sheet with id=AD2, first strand: chain 'B' and resid 356 through 358 removed outlier: 4.479A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.641A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.938A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 712 through 718 removed outlier: 7.016A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 721 through 728 removed outlier: 7.181A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 734 through 735 Processing sheet with id=AD8, first strand: chain 'B' and resid 788 through 789 removed outlier: 5.543A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE1, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.645A 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=AE2, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AE3, first strand: chain 'C' and resid 93 through 96 removed outlier: 3.892A pdb=" N SER C 94 " --> pdb=" O ARG C 188 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU C 96 " --> pdb=" O ASN C 186 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN C 186 " --> pdb=" O GLU C 96 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 192 through 194 removed outlier: 7.359A pdb=" N ILE C 201 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.960A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 325 through 326 removed outlier: 3.690A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 356 through 358 removed outlier: 4.371A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.695A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 660 removed outlier: 5.791A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 712 through 713 Processing sheet with id=AF2, first strand: chain 'C' and resid 717 through 718 Processing sheet with id=AF3, first strand: chain 'C' and resid 721 through 728 removed outlier: 3.700A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.591A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 3.758A pdb=" N SER C1123 " --> pdb=" O ALA C1087 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF7, first strand: chain 'D' and resid 47 through 50 removed outlier: 6.826A pdb=" N TRP D 37 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR D 88 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N THR D 106 " --> pdb=" O TYR D 88 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 66 through 69 removed outlier: 3.704A pdb=" N SER D 67 " --> pdb=" O SER D 74 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 172 through 176 removed outlier: 5.981A pdb=" N TRP D 173 " --> pdb=" O ARG D 164 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ARG D 164 " --> pdb=" O TRP D 173 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 21 through 23 Processing sheet with id=AG2, first strand: chain 'E' and resid 46 through 49 removed outlier: 5.025A pdb=" N LEU E 47 " --> pdb=" O GLN E 38 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N GLN E 38 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN E 97 " --> pdb=" O ASP E 93 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 46 through 49 removed outlier: 5.025A pdb=" N LEU E 47 " --> pdb=" O GLN E 38 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N GLN E 38 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR E 87 " --> pdb=" O THR E 104 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 143 through 144 Processing sheet with id=AG5, first strand: chain 'E' and resid 182 through 184 removed outlier: 6.608A pdb=" N TRP E 160 " --> pdb=" O VAL E 172 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N VAL E 174 " --> pdb=" O MET E 158 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N MET E 158 " --> pdb=" O VAL E 174 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 47 through 50 removed outlier: 6.137A pdb=" N LEU F 48 " --> pdb=" O GLN F 39 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLN F 39 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE F 50 " --> pdb=" O TRP F 37 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 66 through 69 removed outlier: 3.697A pdb=" N SER F 67 " --> pdb=" O SER F 74 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 172 through 176 removed outlier: 5.979A pdb=" N TRP F 173 " --> pdb=" O ARG F 164 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ARG F 164 " --> pdb=" O TRP F 173 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 21 through 23 Processing sheet with id=AH1, first strand: chain 'G' and resid 46 through 49 removed outlier: 5.019A pdb=" N LEU G 47 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N GLN G 38 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASN G 97 " --> pdb=" O ASP G 93 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'G' and resid 46 through 49 removed outlier: 5.019A pdb=" N LEU G 47 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N GLN G 38 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR G 87 " --> pdb=" O THR G 104 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'G' and resid 130 through 131 removed outlier: 3.564A pdb=" N SER G 131 " --> pdb=" O SER G 145 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'G' and resid 182 through 184 removed outlier: 6.631A pdb=" N TRP G 160 " --> pdb=" O VAL G 172 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL G 174 " --> pdb=" O MET G 158 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N MET G 158 " --> pdb=" O VAL G 174 " (cutoff:3.500A) 867 hydrogen bonds defined for protein. 2271 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: 12.98 Time building geometry restraints manager: 8.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5791 1.33 - 1.45: 8620 1.45 - 1.57: 17537 1.57 - 1.69: 0 1.69 - 1.82: 182 Bond restraints: 32130 Sorted by residual: bond pdb=" CA TYR A 707 " pdb=" C TYR A 707 " ideal model delta sigma weight residual 1.526 1.435 0.091 1.20e-02 6.94e+03 5.74e+01 bond pdb=" CA ASN B1134 " pdb=" C ASN B1134 " ideal model delta sigma weight residual 1.523 1.449 0.074 1.21e-02 6.83e+03 3.75e+01 bond pdb=" N ASN B 616 " pdb=" CA ASN B 616 " ideal model delta sigma weight residual 1.457 1.385 0.072 1.29e-02 6.01e+03 3.12e+01 bond pdb=" CA ASN B 801 " pdb=" C ASN B 801 " ideal model delta sigma weight residual 1.523 1.458 0.065 1.21e-02 6.83e+03 2.91e+01 bond pdb=" CA ASN A 801 " pdb=" C ASN A 801 " ideal model delta sigma weight residual 1.523 1.457 0.066 1.23e-02 6.61e+03 2.86e+01 ... (remaining 32125 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 42439 1.45 - 2.90: 1043 2.90 - 4.35: 195 4.35 - 5.80: 33 5.80 - 7.25: 15 Bond angle restraints: 43725 Sorted by residual: angle pdb=" O ALA A 706 " pdb=" C ALA A 706 " pdb=" N TYR A 707 " ideal model delta sigma weight residual 122.89 115.64 7.25 1.22e+00 6.72e-01 3.53e+01 angle pdb=" O VAL B 615 " pdb=" C VAL B 615 " pdb=" N ASN B 616 " ideal model delta sigma weight residual 123.03 128.29 -5.26 1.05e+00 9.07e-01 2.51e+01 angle pdb=" CA ALA A 706 " pdb=" C ALA A 706 " pdb=" N TYR A 707 " ideal model delta sigma weight residual 115.88 122.23 -6.35 1.28e+00 6.10e-01 2.46e+01 angle pdb=" N PRO A 330 " pdb=" CA PRO A 330 " pdb=" C PRO A 330 " ideal model delta sigma weight residual 111.34 117.79 -6.45 1.55e+00 4.16e-01 1.73e+01 angle pdb=" CA VAL B 615 " pdb=" C VAL B 615 " pdb=" N ASN B 616 " ideal model delta sigma weight residual 115.61 109.92 5.69 1.38e+00 5.25e-01 1.70e+01 ... (remaining 43720 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 18438 17.89 - 35.78: 772 35.78 - 53.67: 116 53.67 - 71.55: 28 71.55 - 89.44: 4 Dihedral angle restraints: 19358 sinusoidal: 7726 harmonic: 11632 Sorted by residual: dihedral pdb=" CA ASN B 709 " pdb=" C ASN B 709 " pdb=" N ASN B 710 " pdb=" CA ASN B 710 " ideal model delta harmonic sigma weight residual 180.00 161.04 18.96 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" C ASN B1134 " pdb=" N ASN B1134 " pdb=" CA ASN B1134 " pdb=" CB ASN B1134 " ideal model delta harmonic sigma weight residual -122.60 -113.97 -8.63 0 2.50e+00 1.60e-01 1.19e+01 dihedral pdb=" CA ILE A 332 " pdb=" C ILE A 332 " pdb=" N THR A 333 " pdb=" CA THR A 333 " ideal model delta harmonic sigma weight residual 180.00 -162.91 -17.09 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 19355 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 4490 0.076 - 0.151: 463 0.151 - 0.227: 6 0.227 - 0.302: 3 0.302 - 0.378: 3 Chirality restraints: 4965 Sorted by residual: chirality pdb=" C1 NAG C1303 " pdb=" ND2 ASN C 709 " pdb=" C2 NAG C1303 " pdb=" O5 NAG C1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.57e+00 chirality pdb=" C1 NAG B1301 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG B1301 " pdb=" O5 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.11e+00 chirality pdb=" C1 NAG A1307 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG A1307 " pdb=" O5 NAG A1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.61e+00 ... (remaining 4962 not shown) Planarity restraints: 5671 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1302 " -0.349 2.00e-02 2.50e+03 3.01e-01 1.13e+03 pdb=" C7 NAG B1302 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG B1302 " -0.103 2.00e-02 2.50e+03 pdb=" N2 NAG B1302 " 0.536 2.00e-02 2.50e+03 pdb=" O7 NAG B1302 " -0.166 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1307 " 0.341 2.00e-02 2.50e+03 2.96e-01 1.10e+03 pdb=" C7 NAG C1307 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG C1307 " 0.094 2.00e-02 2.50e+03 pdb=" N2 NAG C1307 " -0.528 2.00e-02 2.50e+03 pdb=" O7 NAG C1307 " 0.170 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1301 " -0.343 2.00e-02 2.50e+03 2.95e-01 1.09e+03 pdb=" C7 NAG B1301 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG B1301 " -0.153 2.00e-02 2.50e+03 pdb=" N2 NAG B1301 " 0.523 2.00e-02 2.50e+03 pdb=" O7 NAG B1301 " -0.112 2.00e-02 2.50e+03 ... (remaining 5668 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2831 2.75 - 3.28: 31430 3.28 - 3.82: 51427 3.82 - 4.36: 59480 4.36 - 4.90: 103071 Nonbonded interactions: 248239 Sorted by model distance: nonbonded pdb=" OG SER D 91 " pdb=" OE1 GLN D 227 " model vdw 2.208 3.040 nonbonded pdb=" OG SER F 91 " pdb=" OE1 GLN F 227 " model vdw 2.217 3.040 nonbonded pdb=" OE1 GLN B 52 " pdb=" OG1 THR B 274 " model vdw 2.219 3.040 nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.231 3.040 nonbonded pdb=" OG SER C 735 " pdb=" OG1 THR C 859 " model vdw 2.231 3.040 ... (remaining 248234 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 1147 or resid 1301 thr \ ough 1307)) selection = (chain 'B' and (resid 26 through 243 or resid 262 through 516 or resid 522 throu \ gh 1147 or resid 1301 through 1307)) selection = (chain 'C' and (resid 26 through 516 or resid 522 through 1147 or resid 1301 thr \ ough 1307)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.170 Check model and map are aligned: 0.230 Set scattering table: 0.270 Process input model: 68.790 Find NCS groups from input model: 1.770 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6460 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 0.091 32200 Z= 0.198 Angle : 0.583 7.250 43888 Z= 0.336 Chirality : 0.043 0.378 4965 Planarity : 0.014 0.301 5648 Dihedral : 9.568 89.442 11777 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.97 % Favored : 92.00 % Rotamer: Outliers : 5.49 % Allowed : 8.37 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.25 (0.11), residues: 3963 helix: -0.88 (0.19), residues: 632 sheet: -2.70 (0.16), residues: 762 loop : -3.62 (0.10), residues: 2569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 98 HIS 0.002 0.000 HIS G 159 PHE 0.007 0.001 PHE B 92 TYR 0.016 0.001 TYR C 28 ARG 0.002 0.000 ARG C 847 Details of bonding type rmsd link_NAG-ASN : bond 0.00827 ( 23) link_NAG-ASN : angle 2.69424 ( 69) hydrogen bonds : bond 0.16232 ( 847) hydrogen bonds : angle 6.44720 ( 2271) SS BOND : bond 0.00130 ( 47) SS BOND : angle 0.50479 ( 94) covalent geometry : bond 0.00307 (32130) covalent geometry : angle 0.57355 (43725) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 913 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 725 time to evaluate : 3.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.8199 (t) cc_final: 0.7804 (p) REVERT: A 53 ASP cc_start: 0.6577 (t0) cc_final: 0.6367 (t0) REVERT: A 63 THR cc_start: 0.7714 (m) cc_final: 0.6559 (t) REVERT: A 102 ARG cc_start: 0.5330 (mtm110) cc_final: 0.5080 (mtm110) REVERT: A 117 LEU cc_start: 0.7888 (mt) cc_final: 0.7590 (mp) REVERT: A 201 ILE cc_start: 0.8187 (mt) cc_final: 0.7751 (tt) REVERT: A 541 PHE cc_start: 0.7934 (p90) cc_final: 0.7525 (p90) REVERT: A 549 THR cc_start: 0.8288 (p) cc_final: 0.8044 (m) REVERT: A 596 SER cc_start: 0.8379 (m) cc_final: 0.8094 (p) REVERT: A 644 GLN cc_start: 0.7864 (tp40) cc_final: 0.7435 (tp40) REVERT: A 714 ILE cc_start: 0.7974 (mm) cc_final: 0.7350 (mt) REVERT: A 733 LYS cc_start: 0.8268 (mtmt) cc_final: 0.7434 (mtpt) REVERT: A 743 CYS cc_start: 0.5736 (m) cc_final: 0.5341 (m) REVERT: A 746 SER cc_start: 0.8643 (OUTLIER) cc_final: 0.8246 (t) REVERT: A 776 LYS cc_start: 0.8103 (tmmt) cc_final: 0.7892 (tmmt) REVERT: A 854 LYS cc_start: 0.7444 (ttpp) cc_final: 0.7000 (ttpp) REVERT: A 950 ASP cc_start: 0.6531 (t70) cc_final: 0.6080 (t0) REVERT: A 953 ASN cc_start: 0.7552 (m-40) cc_final: 0.7290 (m-40) REVERT: A 981 PHE cc_start: 0.7512 (m-10) cc_final: 0.7262 (m-80) REVERT: A 1028 LYS cc_start: 0.8286 (ttmm) cc_final: 0.7843 (ttmm) REVERT: A 1081 ILE cc_start: 0.8151 (pt) cc_final: 0.7918 (mt) REVERT: A 1138 TYR cc_start: 0.6389 (t80) cc_final: 0.6160 (t80) REVERT: B 95 ILE cc_start: 0.7390 (mt) cc_final: 0.7110 (mt) REVERT: B 105 ILE cc_start: 0.7903 (mm) cc_final: 0.7684 (mm) REVERT: B 121 ASN cc_start: 0.7007 (t0) cc_final: 0.6196 (t0) REVERT: B 126 VAL cc_start: 0.7106 (t) cc_final: 0.6892 (m) REVERT: B 130 VAL cc_start: 0.7420 (OUTLIER) cc_final: 0.7126 (p) REVERT: B 193 LYS cc_start: 0.7795 (ttpt) cc_final: 0.7500 (ttpt) REVERT: B 203 SER cc_start: 0.8309 (p) cc_final: 0.8053 (t) REVERT: B 227 VAL cc_start: 0.7934 (m) cc_final: 0.7713 (m) REVERT: B 265 TYR cc_start: 0.7272 (p90) cc_final: 0.6774 (p90) REVERT: B 275 PHE cc_start: 0.8096 (m-80) cc_final: 0.7842 (m-80) REVERT: B 281 GLU cc_start: 0.6681 (pp20) cc_final: 0.6460 (pp20) REVERT: B 355 ARG cc_start: 0.4706 (OUTLIER) cc_final: 0.4247 (tmt90) REVERT: B 483 VAL cc_start: 0.5192 (OUTLIER) cc_final: 0.4897 (p) REVERT: B 542 ASN cc_start: 0.7580 (OUTLIER) cc_final: 0.7242 (t0) REVERT: B 547 LYS cc_start: 0.8026 (mtmt) cc_final: 0.7555 (mttm) REVERT: B 619 GLU cc_start: 0.6908 (tt0) cc_final: 0.6646 (tt0) REVERT: B 656 VAL cc_start: 0.8338 (p) cc_final: 0.8026 (m) REVERT: B 751 ASN cc_start: 0.8232 (m-40) cc_final: 0.7854 (m110) REVERT: B 765 ARG cc_start: 0.6857 (ttp-170) cc_final: 0.6532 (mtm110) REVERT: B 884 SER cc_start: 0.8601 (t) cc_final: 0.8289 (p) REVERT: B 918 GLU cc_start: 0.6921 (mt-10) cc_final: 0.6701 (mt-10) REVERT: B 933 LYS cc_start: 0.7740 (mtmt) cc_final: 0.7448 (mtpp) REVERT: B 957 GLN cc_start: 0.6500 (OUTLIER) cc_final: 0.6184 (tm130) REVERT: B 964 LYS cc_start: 0.7957 (ttpp) cc_final: 0.7724 (mtpp) REVERT: B 1014 ARG cc_start: 0.7367 (ttm170) cc_final: 0.7147 (mtm-85) REVERT: B 1073 LYS cc_start: 0.8094 (mtpm) cc_final: 0.7763 (ttmt) REVERT: B 1097 SER cc_start: 0.8797 (t) cc_final: 0.8436 (p) REVERT: B 1107 ARG cc_start: 0.6802 (mtt90) cc_final: 0.4936 (mtt180) REVERT: B 1111 GLU cc_start: 0.7262 (tt0) cc_final: 0.7014 (tt0) REVERT: B 1113 GLN cc_start: 0.7784 (mt0) cc_final: 0.7571 (mt0) REVERT: B 1138 TYR cc_start: 0.6693 (t80) cc_final: 0.6366 (t80) REVERT: B 1144 GLU cc_start: 0.7028 (mm-30) cc_final: 0.6789 (mm-30) REVERT: C 51 THR cc_start: 0.8422 (t) cc_final: 0.8170 (p) REVERT: C 83 VAL cc_start: 0.7869 (t) cc_final: 0.7635 (p) REVERT: C 105 ILE cc_start: 0.7342 (mt) cc_final: 0.7098 (mt) REVERT: C 187 LEU cc_start: 0.7017 (tp) cc_final: 0.6269 (mt) REVERT: C 269 TYR cc_start: 0.7396 (m-10) cc_final: 0.7141 (m-10) REVERT: C 302 THR cc_start: 0.8129 (t) cc_final: 0.7734 (p) REVERT: C 537 LYS cc_start: 0.7906 (ttmm) cc_final: 0.7668 (ttmm) REVERT: C 542 ASN cc_start: 0.7783 (t0) cc_final: 0.7405 (t0) REVERT: C 546 LEU cc_start: 0.7251 (tt) cc_final: 0.6903 (tp) REVERT: C 564 GLN cc_start: 0.7054 (mm-40) cc_final: 0.6722 (mm110) REVERT: C 578 ASP cc_start: 0.7619 (t0) cc_final: 0.7368 (t0) REVERT: C 586 ASP cc_start: 0.7149 (t0) cc_final: 0.6934 (t0) REVERT: C 603 ASN cc_start: 0.7673 (t0) cc_final: 0.7297 (t0) REVERT: C 619 GLU cc_start: 0.7023 (tt0) cc_final: 0.6763 (tt0) REVERT: C 778 THR cc_start: 0.7990 (p) cc_final: 0.7658 (p) REVERT: C 821 LEU cc_start: 0.7890 (tp) cc_final: 0.7510 (tt) REVERT: C 867 ASP cc_start: 0.7781 (m-30) cc_final: 0.7511 (m-30) REVERT: C 868 GLU cc_start: 0.7006 (tp30) cc_final: 0.6780 (tp30) REVERT: C 914 ASN cc_start: 0.7933 (p0) cc_final: 0.7566 (p0) REVERT: C 933 LYS cc_start: 0.7849 (mtmm) cc_final: 0.7486 (mtmm) REVERT: C 953 ASN cc_start: 0.8139 (m-40) cc_final: 0.7863 (m-40) REVERT: C 979 ASP cc_start: 0.6589 (m-30) cc_final: 0.6015 (m-30) REVERT: C 994 ASP cc_start: 0.7188 (m-30) cc_final: 0.6766 (t70) REVERT: C 1014 ARG cc_start: 0.7498 (tpp80) cc_final: 0.7276 (mtm-85) REVERT: C 1038 LYS cc_start: 0.8080 (mtmp) cc_final: 0.7783 (mtmm) REVERT: C 1097 SER cc_start: 0.8746 (t) cc_final: 0.8416 (p) REVERT: C 1111 GLU cc_start: 0.7322 (tt0) cc_final: 0.7016 (tt0) REVERT: C 1123 SER cc_start: 0.6962 (t) cc_final: 0.6617 (p) REVERT: C 1129 VAL cc_start: 0.8086 (OUTLIER) cc_final: 0.7879 (p) REVERT: C 1136 THR cc_start: 0.7652 (OUTLIER) cc_final: 0.7418 (p) REVERT: C 1141 LEU cc_start: 0.8241 (tp) cc_final: 0.7988 (tp) REVERT: D 111 LEU cc_start: -0.1551 (OUTLIER) cc_final: -0.2478 (tm) REVERT: E 207 MET cc_start: 0.6149 (mtp) cc_final: 0.5492 (mtp) REVERT: F 144 LEU cc_start: 0.1831 (OUTLIER) cc_final: 0.1614 (tm) REVERT: F 148 CYS cc_start: 0.3721 (OUTLIER) cc_final: 0.3034 (p) REVERT: G 67 LYS cc_start: 0.4831 (OUTLIER) cc_final: 0.4330 (tmmm) outliers start: 188 outliers final: 73 residues processed: 881 average time/residue: 0.5636 time to fit residues: 790.4252 Evaluate side-chains 636 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 551 time to evaluate : 4.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 29 THR 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 130 VAL Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE 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 993 ILE Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1129 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 90 CYS Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 193 PHE Chi-restraints excluded: chain F residue 205 TYR Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain G residue 125 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 336 optimal weight: 30.0000 chunk 302 optimal weight: 0.5980 chunk 167 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 203 optimal weight: 2.9990 chunk 161 optimal weight: 0.0020 chunk 312 optimal weight: 0.1980 chunk 121 optimal weight: 7.9990 chunk 190 optimal weight: 0.5980 chunk 232 optimal weight: 10.0000 chunk 362 optimal weight: 10.0000 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 121 ASN A 173 GLN A 186 ASN A 271 GLN A 370 ASN A 388 ASN A 409 GLN A 448 ASN A 487 ASN A 506 GLN A 540 ASN A 762 GLN A 784 GLN A 787 GLN A 804 GLN A 872 GLN A 901 GLN A1002 GLN A1010 GLN A1011 GLN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN B 181 GLN B 186 ASN B 205 HIS B 245 HIS B 354 ASN B 370 ASN B 388 ASN B 409 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN B 477 ASN B 540 ASN B 544 ASN B 563 GLN B 606 ASN B 613 GLN B 853 GLN B 935 GLN B1048 HIS B1119 ASN C 49 HIS C 81 ASN C 87 ASN C 164 ASN C 321 GLN C 354 ASN C 370 ASN C 388 ASN C 409 GLN C 422 ASN C 448 ASN C 477 ASN C 487 ASN C 540 ASN C 580 GLN C 755 GLN C 901 GLN C 914 ASN C 955 ASN C1005 GLN C1011 GLN C1048 HIS ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS C1119 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN D 39 GLN D 40 GLN D 129 GLN D 165 GLN D 202 ASN E 52 ASN E 80 GLN E 97 ASN E 127 GLN E 137 GLN E 201 ASN E 206 GLN E 233 ASN F 33 ASN F 39 GLN F 40 GLN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 165 GLN F 202 ASN G 52 ASN G 80 GLN G 97 ASN G 127 GLN G 137 GLN G 159 HIS G 201 ASN G 206 GLN Total number of N/Q/H flips: 92 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.223708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.165977 restraints weight = 51585.434| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 2.81 r_work: 0.3598 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 32200 Z= 0.121 Angle : 0.582 11.996 43888 Z= 0.287 Chirality : 0.045 0.406 4965 Planarity : 0.005 0.149 5648 Dihedral : 7.408 80.607 5011 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 4.61 % Allowed : 12.99 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.48 (0.12), residues: 3963 helix: 0.15 (0.21), residues: 669 sheet: -2.19 (0.16), residues: 811 loop : -3.27 (0.10), residues: 2483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 37 HIS 0.006 0.001 HIS A1048 PHE 0.026 0.001 PHE C 541 TYR 0.022 0.001 TYR A 674 ARG 0.008 0.000 ARG B 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00452 ( 23) link_NAG-ASN : angle 2.52759 ( 69) hydrogen bonds : bond 0.03611 ( 847) hydrogen bonds : angle 4.93743 ( 2271) SS BOND : bond 0.00343 ( 47) SS BOND : angle 1.64678 ( 94) covalent geometry : bond 0.00271 (32130) covalent geometry : angle 0.56907 (43725) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 558 time to evaluate : 2.990 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: A 51 THR cc_start: 0.8397 (t) cc_final: 0.7927 (p) REVERT: A 63 THR cc_start: 0.8059 (m) cc_final: 0.6793 (t) REVERT: A 281 GLU cc_start: 0.7331 (pp20) cc_final: 0.7028 (pp20) REVERT: A 320 VAL cc_start: 0.7883 (OUTLIER) cc_final: 0.7372 (m) REVERT: A 541 PHE cc_start: 0.7945 (p90) cc_final: 0.7681 (p90) REVERT: A 563 GLN cc_start: 0.7569 (mt0) cc_final: 0.7326 (mt0) REVERT: A 596 SER cc_start: 0.8612 (m) cc_final: 0.8335 (p) REVERT: A 658 ASN cc_start: 0.7653 (m-40) cc_final: 0.7428 (m-40) REVERT: A 708 SER cc_start: 0.8440 (t) cc_final: 0.8062 (p) REVERT: A 714 ILE cc_start: 0.8038 (mm) cc_final: 0.7306 (mt) REVERT: A 746 SER cc_start: 0.8411 (OUTLIER) cc_final: 0.8138 (t) REVERT: A 765 ARG cc_start: 0.7567 (ttp-110) cc_final: 0.6775 (ttp80) REVERT: A 854 LYS cc_start: 0.7582 (ttpp) cc_final: 0.7158 (tptp) REVERT: A 914 ASN cc_start: 0.7665 (p0) cc_final: 0.7411 (p0) REVERT: A 950 ASP cc_start: 0.7191 (t70) cc_final: 0.6748 (t70) REVERT: A 953 ASN cc_start: 0.7899 (m-40) cc_final: 0.7691 (m-40) REVERT: A 964 LYS cc_start: 0.8425 (tmtm) cc_final: 0.8141 (ttmm) REVERT: A 1072 GLU cc_start: 0.7894 (pm20) cc_final: 0.7655 (pm20) REVERT: A 1091 ARG cc_start: 0.7769 (ttm170) cc_final: 0.7446 (ttp-170) REVERT: A 1138 TYR cc_start: 0.7050 (t80) cc_final: 0.6588 (t80) REVERT: B 126 VAL cc_start: 0.7308 (t) cc_final: 0.7004 (m) REVERT: B 130 VAL cc_start: 0.7757 (OUTLIER) cc_final: 0.7365 (p) REVERT: B 193 LYS cc_start: 0.8277 (ttpt) cc_final: 0.7924 (ttpt) REVERT: B 203 SER cc_start: 0.8622 (p) cc_final: 0.8386 (t) REVERT: B 281 GLU cc_start: 0.7320 (pp20) cc_final: 0.6988 (pp20) REVERT: B 355 ARG cc_start: 0.4720 (OUTLIER) cc_final: 0.4233 (tmt90) REVERT: B 542 ASN cc_start: 0.7689 (OUTLIER) cc_final: 0.7411 (t0) REVERT: B 574 ASP cc_start: 0.7447 (t70) cc_final: 0.7160 (t0) REVERT: B 578 ASP cc_start: 0.7583 (t0) cc_final: 0.7292 (t0) REVERT: B 591 SER cc_start: 0.8061 (t) cc_final: 0.7651 (m) REVERT: B 603 ASN cc_start: 0.8102 (t0) cc_final: 0.7870 (t0) REVERT: B 619 GLU cc_start: 0.7456 (tt0) cc_final: 0.7256 (tt0) REVERT: B 751 ASN cc_start: 0.8437 (m-40) cc_final: 0.8057 (m110) REVERT: B 774 GLN cc_start: 0.7743 (mm-40) cc_final: 0.7470 (mm-40) REVERT: B 884 SER cc_start: 0.8782 (t) cc_final: 0.8372 (p) REVERT: B 902 MET cc_start: 0.7857 (tpp) cc_final: 0.7611 (tpp) REVERT: B 933 LYS cc_start: 0.7853 (mtmt) cc_final: 0.7524 (mtpp) REVERT: B 957 GLN cc_start: 0.7078 (OUTLIER) cc_final: 0.6633 (tm130) REVERT: B 964 LYS cc_start: 0.8451 (ttpp) cc_final: 0.8066 (mtpp) REVERT: B 1055 SER cc_start: 0.8500 (t) cc_final: 0.8136 (m) REVERT: B 1097 SER cc_start: 0.8778 (t) cc_final: 0.8364 (p) REVERT: B 1118 ASP cc_start: 0.7221 (t70) cc_final: 0.6875 (t0) REVERT: B 1138 TYR cc_start: 0.7378 (t80) cc_final: 0.6995 (t80) REVERT: B 1144 GLU cc_start: 0.7485 (mm-30) cc_final: 0.6997 (mm-30) REVERT: C 51 THR cc_start: 0.8522 (t) cc_final: 0.8293 (p) REVERT: C 59 PHE cc_start: 0.8073 (m-10) cc_final: 0.7727 (m-80) REVERT: C 85 PRO cc_start: 0.7439 (Cg_endo) cc_final: 0.7150 (Cg_exo) REVERT: C 91 TYR cc_start: 0.6366 (t80) cc_final: 0.5637 (t80) REVERT: C 95 ILE cc_start: 0.8351 (mt) cc_final: 0.7928 (mt) REVERT: C 105 ILE cc_start: 0.7801 (mt) cc_final: 0.7529 (mt) REVERT: C 106 PHE cc_start: 0.8089 (m-10) cc_final: 0.7783 (m-10) REVERT: C 190 PHE cc_start: 0.7385 (m-80) cc_final: 0.7093 (m-80) REVERT: C 298 GLU cc_start: 0.7913 (tp30) cc_final: 0.7626 (tp30) REVERT: C 327 VAL cc_start: 0.8403 (t) cc_final: 0.8102 (m) REVERT: C 541 PHE cc_start: 0.7594 (p90) cc_final: 0.7169 (p90) REVERT: C 542 ASN cc_start: 0.8001 (t0) cc_final: 0.7714 (t0) REVERT: C 564 GLN cc_start: 0.7429 (mm-40) cc_final: 0.7154 (mm110) REVERT: C 578 ASP cc_start: 0.8048 (t0) cc_final: 0.7574 (t0) REVERT: C 586 ASP cc_start: 0.7429 (t0) cc_final: 0.7180 (t0) REVERT: C 603 ASN cc_start: 0.7981 (t0) cc_final: 0.7604 (t0) REVERT: C 619 GLU cc_start: 0.7870 (tt0) cc_final: 0.7540 (tt0) REVERT: C 821 LEU cc_start: 0.7942 (tp) cc_final: 0.7732 (tt) REVERT: C 914 ASN cc_start: 0.8306 (p0) cc_final: 0.8004 (p0) REVERT: C 935 GLN cc_start: 0.7699 (tt0) cc_final: 0.7421 (mt0) REVERT: C 979 ASP cc_start: 0.6775 (OUTLIER) cc_final: 0.6531 (m-30) REVERT: C 994 ASP cc_start: 0.7580 (m-30) cc_final: 0.7046 (t0) REVERT: C 1014 ARG cc_start: 0.7916 (tpp80) cc_final: 0.7683 (mtm-85) REVERT: C 1073 LYS cc_start: 0.7898 (ttpp) cc_final: 0.7674 (ttmm) REVERT: C 1081 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8358 (pt) REVERT: C 1097 SER cc_start: 0.8888 (t) cc_final: 0.8519 (p) REVERT: C 1111 GLU cc_start: 0.8108 (tt0) cc_final: 0.7827 (tt0) REVERT: C 1125 ASN cc_start: 0.7709 (p0) cc_final: 0.7302 (p0) REVERT: C 1129 VAL cc_start: 0.8263 (OUTLIER) cc_final: 0.8001 (p) REVERT: C 1136 THR cc_start: 0.7838 (OUTLIER) cc_final: 0.7615 (p) REVERT: D 111 LEU cc_start: -0.1370 (OUTLIER) cc_final: -0.2017 (tm) REVERT: E 207 MET cc_start: 0.6187 (mtp) cc_final: 0.5964 (mtp) outliers start: 158 outliers final: 80 residues processed: 682 average time/residue: 0.4443 time to fit residues: 478.6207 Evaluate side-chains 597 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 506 time to evaluate : 3.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 29 THR 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 130 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1129 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 111 LEU Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 221 CYS Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 193 PHE Chi-restraints excluded: chain F residue 205 TYR Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 125 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 353 optimal weight: 0.5980 chunk 185 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 323 optimal weight: 20.0000 chunk 73 optimal weight: 0.6980 chunk 138 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 354 optimal weight: 0.0470 chunk 335 optimal weight: 9.9990 chunk 324 optimal weight: 9.9990 overall best weight: 0.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1002 GLN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN B 66 HIS B 121 ASN B 317 ASN B 422 ASN B 613 GLN B 690 GLN B 901 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 87 ASN C 205 HIS C 218 GLN C 895 GLN C 901 GLN C 955 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 GLN E 159 HIS E 201 ASN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.221379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.162777 restraints weight = 51334.974| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.76 r_work: 0.3538 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 32200 Z= 0.142 Angle : 0.584 13.181 43888 Z= 0.289 Chirality : 0.045 0.277 4965 Planarity : 0.005 0.161 5648 Dihedral : 7.142 81.057 4974 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 4.93 % Allowed : 14.53 % Favored : 80.54 % 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: -3.05 (0.12), residues: 3963 helix: 0.65 (0.21), residues: 663 sheet: -1.97 (0.17), residues: 820 loop : -2.99 (0.11), residues: 2480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 37 HIS 0.008 0.001 HIS A1048 PHE 0.021 0.002 PHE B 168 TYR 0.028 0.001 TYR A 674 ARG 0.005 0.000 ARG A 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00297 ( 23) link_NAG-ASN : angle 1.87719 ( 69) hydrogen bonds : bond 0.03583 ( 847) hydrogen bonds : angle 4.81078 ( 2271) SS BOND : bond 0.00355 ( 47) SS BOND : angle 1.82054 ( 94) covalent geometry : bond 0.00321 (32130) covalent geometry : angle 0.57371 (43725) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 534 time to evaluate : 3.307 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: A 43 PHE cc_start: 0.8706 (t80) cc_final: 0.8495 (t80) REVERT: A 51 THR cc_start: 0.8383 (t) cc_final: 0.7930 (p) REVERT: A 63 THR cc_start: 0.8214 (m) cc_final: 0.7379 (m) REVERT: A 102 ARG cc_start: 0.7217 (mtm110) cc_final: 0.6800 (mtm110) REVERT: A 186 ASN cc_start: 0.6823 (OUTLIER) cc_final: 0.6111 (p0) REVERT: A 188 ARG cc_start: 0.8465 (ptp-170) cc_final: 0.7928 (ptp-170) REVERT: A 541 PHE cc_start: 0.7953 (p90) cc_final: 0.7658 (p90) REVERT: A 563 GLN cc_start: 0.7598 (mm-40) cc_final: 0.7368 (mt0) REVERT: A 596 SER cc_start: 0.8658 (m) cc_final: 0.8390 (p) REVERT: A 658 ASN cc_start: 0.7673 (m-40) cc_final: 0.7452 (m-40) REVERT: A 708 SER cc_start: 0.8473 (t) cc_final: 0.8068 (p) REVERT: A 714 ILE cc_start: 0.8188 (mm) cc_final: 0.7566 (mt) REVERT: A 746 SER cc_start: 0.8371 (OUTLIER) cc_final: 0.8088 (t) REVERT: A 765 ARG cc_start: 0.7764 (ttp-110) cc_final: 0.7420 (ttp80) REVERT: A 854 LYS cc_start: 0.7791 (ttpp) cc_final: 0.7560 (tttp) REVERT: A 914 ASN cc_start: 0.7962 (p0) cc_final: 0.7730 (p0) REVERT: A 950 ASP cc_start: 0.7548 (t70) cc_final: 0.7039 (t0) REVERT: A 964 LYS cc_start: 0.8521 (tmtm) cc_final: 0.8258 (ttmm) REVERT: A 1002 GLN cc_start: 0.7764 (tp-100) cc_final: 0.7489 (tp-100) REVERT: A 1072 GLU cc_start: 0.7931 (pm20) cc_final: 0.7728 (pm20) REVERT: A 1097 SER cc_start: 0.8685 (t) cc_final: 0.8406 (p) REVERT: B 54 LEU cc_start: 0.8506 (mt) cc_final: 0.8277 (mt) REVERT: B 126 VAL cc_start: 0.7317 (t) cc_final: 0.6955 (m) REVERT: B 130 VAL cc_start: 0.7760 (t) cc_final: 0.7369 (p) REVERT: B 185 LYS cc_start: 0.6929 (tppp) cc_final: 0.6625 (mmmt) REVERT: B 188 ARG cc_start: 0.8252 (mtt-85) cc_final: 0.7793 (mtt90) REVERT: B 193 LYS cc_start: 0.8285 (ttpt) cc_final: 0.7918 (ttpt) REVERT: B 227 VAL cc_start: 0.8386 (m) cc_final: 0.8176 (p) REVERT: B 266 TYR cc_start: 0.7877 (m-80) cc_final: 0.7628 (m-80) REVERT: B 281 GLU cc_start: 0.7407 (pp20) cc_final: 0.7109 (pp20) REVERT: B 319 ARG cc_start: 0.8053 (ptp-110) cc_final: 0.7608 (mtp85) REVERT: B 355 ARG cc_start: 0.4773 (OUTLIER) cc_final: 0.4254 (tmt90) REVERT: B 537 LYS cc_start: 0.8173 (ttpt) cc_final: 0.7964 (ttpp) REVERT: B 591 SER cc_start: 0.8358 (OUTLIER) cc_final: 0.8088 (m) REVERT: B 603 ASN cc_start: 0.8063 (t0) cc_final: 0.7820 (t0) REVERT: B 619 GLU cc_start: 0.7618 (tt0) cc_final: 0.7379 (tt0) REVERT: B 644 GLN cc_start: 0.8156 (tp-100) cc_final: 0.7945 (tp40) REVERT: B 726 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8410 (mt) REVERT: B 747 THR cc_start: 0.8010 (OUTLIER) cc_final: 0.7754 (m) REVERT: B 751 ASN cc_start: 0.8441 (m-40) cc_final: 0.8160 (m110) REVERT: B 774 GLN cc_start: 0.7844 (mm-40) cc_final: 0.7601 (mm-40) REVERT: B 884 SER cc_start: 0.8817 (t) cc_final: 0.8426 (p) REVERT: B 902 MET cc_start: 0.7963 (tpp) cc_final: 0.7580 (tpp) REVERT: B 933 LYS cc_start: 0.7881 (mtmt) cc_final: 0.7599 (mtpp) REVERT: B 957 GLN cc_start: 0.7128 (OUTLIER) cc_final: 0.6926 (tm130) REVERT: B 964 LYS cc_start: 0.8424 (ttpp) cc_final: 0.8220 (ttmm) REVERT: B 980 ILE cc_start: 0.8462 (mt) cc_final: 0.8167 (mm) REVERT: B 1031 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7430 (mt-10) REVERT: B 1107 ARG cc_start: 0.7500 (mtt90) cc_final: 0.7240 (mtt180) REVERT: B 1118 ASP cc_start: 0.7378 (t70) cc_final: 0.7021 (t0) REVERT: B 1144 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7092 (mm-30) REVERT: C 51 THR cc_start: 0.8470 (t) cc_final: 0.8234 (p) REVERT: C 59 PHE cc_start: 0.8374 (m-10) cc_final: 0.7982 (m-80) REVERT: C 94 SER cc_start: 0.8396 (t) cc_final: 0.8168 (p) REVERT: C 95 ILE cc_start: 0.8437 (mt) cc_final: 0.8112 (mt) REVERT: C 104 TRP cc_start: 0.7091 (m-90) cc_final: 0.6823 (m-90) REVERT: C 105 ILE cc_start: 0.7897 (mt) cc_final: 0.7554 (mt) REVERT: C 106 PHE cc_start: 0.8151 (m-10) cc_final: 0.7837 (m-10) REVERT: C 190 PHE cc_start: 0.7458 (m-80) cc_final: 0.7215 (m-80) REVERT: C 240 THR cc_start: 0.7097 (t) cc_final: 0.6327 (p) REVERT: C 298 GLU cc_start: 0.7877 (tp30) cc_final: 0.7549 (tp30) REVERT: C 327 VAL cc_start: 0.8440 (t) cc_final: 0.8135 (m) REVERT: C 541 PHE cc_start: 0.7751 (p90) cc_final: 0.7332 (p90) REVERT: C 542 ASN cc_start: 0.8225 (t0) cc_final: 0.7912 (t0) REVERT: C 546 LEU cc_start: 0.7616 (tt) cc_final: 0.7409 (tt) REVERT: C 568 ASP cc_start: 0.6993 (p0) cc_final: 0.6195 (p0) REVERT: C 578 ASP cc_start: 0.7853 (t0) cc_final: 0.7556 (t0) REVERT: C 586 ASP cc_start: 0.7461 (t0) cc_final: 0.7175 (t0) REVERT: C 592 PHE cc_start: 0.7876 (p90) cc_final: 0.7548 (p90) REVERT: C 603 ASN cc_start: 0.8112 (t0) cc_final: 0.7703 (t0) REVERT: C 619 GLU cc_start: 0.7914 (tt0) cc_final: 0.7586 (tt0) REVERT: C 765 ARG cc_start: 0.8250 (ttm-80) cc_final: 0.7962 (ttp80) REVERT: C 773 GLU cc_start: 0.7868 (tt0) cc_final: 0.7501 (tt0) REVERT: C 821 LEU cc_start: 0.8002 (tp) cc_final: 0.7735 (tt) REVERT: C 900 MET cc_start: 0.7977 (ttm) cc_final: 0.7739 (ttm) REVERT: C 914 ASN cc_start: 0.8369 (p0) cc_final: 0.8154 (p0) REVERT: C 953 ASN cc_start: 0.8420 (m-40) cc_final: 0.7998 (m-40) REVERT: C 979 ASP cc_start: 0.6887 (OUTLIER) cc_final: 0.6624 (m-30) REVERT: C 993 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7687 (tt) REVERT: C 994 ASP cc_start: 0.7645 (m-30) cc_final: 0.7226 (t0) REVERT: C 1014 ARG cc_start: 0.7991 (tpp80) cc_final: 0.7686 (mtt90) REVERT: C 1017 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7690 (tm-30) REVERT: C 1073 LYS cc_start: 0.7984 (ttpp) cc_final: 0.7778 (ttmm) REVERT: C 1081 ILE cc_start: 0.8470 (OUTLIER) cc_final: 0.8112 (mt) REVERT: C 1097 SER cc_start: 0.8851 (t) cc_final: 0.8492 (p) REVERT: C 1111 GLU cc_start: 0.8159 (tt0) cc_final: 0.7921 (tt0) REVERT: C 1122 VAL cc_start: 0.8136 (t) cc_final: 0.7890 (m) REVERT: C 1125 ASN cc_start: 0.8032 (p0) cc_final: 0.7404 (p0) REVERT: C 1129 VAL cc_start: 0.8332 (OUTLIER) cc_final: 0.8065 (p) REVERT: D 111 LEU cc_start: -0.1473 (OUTLIER) cc_final: -0.2120 (tm) REVERT: D 205 TYR cc_start: 0.5046 (OUTLIER) cc_final: 0.4643 (p90) outliers start: 169 outliers final: 99 residues processed: 667 average time/residue: 0.4471 time to fit residues: 474.0145 Evaluate side-chains 608 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 496 time to evaluate : 3.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 51 THR 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 267 VAL Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 547 LYS Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 993 ILE 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 1129 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 111 LEU Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 221 CYS Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 201 ASN Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 193 PHE Chi-restraints excluded: chain F residue 205 TYR Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 247 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 38 optimal weight: 20.0000 chunk 127 optimal weight: 0.6980 chunk 265 optimal weight: 0.7980 chunk 312 optimal weight: 50.0000 chunk 371 optimal weight: 30.0000 chunk 352 optimal weight: 50.0000 chunk 90 optimal weight: 2.9990 chunk 118 optimal weight: 10.0000 chunk 229 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 131 optimal weight: 0.3980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 895 GLN A 955 ASN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 239 GLN B 487 ASN ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN C 321 GLN C1088 HIS ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 ASN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.220857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.162196 restraints weight = 51186.674| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.68 r_work: 0.3539 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 32200 Z= 0.129 Angle : 0.571 13.701 43888 Z= 0.281 Chirality : 0.045 0.279 4965 Planarity : 0.004 0.072 5648 Dihedral : 7.068 81.836 4963 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 4.73 % Allowed : 15.73 % Favored : 79.54 % 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: -2.77 (0.12), residues: 3963 helix: 0.93 (0.21), residues: 661 sheet: -1.75 (0.17), residues: 863 loop : -2.84 (0.11), residues: 2439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 37 HIS 0.007 0.001 HIS A 66 PHE 0.032 0.001 PHE B 106 TYR 0.018 0.001 TYR A 91 ARG 0.003 0.000 ARG C1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00321 ( 23) link_NAG-ASN : angle 1.91395 ( 69) hydrogen bonds : bond 0.03350 ( 847) hydrogen bonds : angle 4.71970 ( 2271) SS BOND : bond 0.00289 ( 47) SS BOND : angle 1.57406 ( 94) covalent geometry : bond 0.00292 (32130) covalent geometry : angle 0.56192 (43725) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 516 time to evaluate : 2.898 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: A 43 PHE cc_start: 0.8712 (t80) cc_final: 0.8509 (t80) REVERT: A 51 THR cc_start: 0.8356 (t) cc_final: 0.7883 (p) REVERT: A 63 THR cc_start: 0.8307 (OUTLIER) cc_final: 0.7638 (m) REVERT: A 129 LYS cc_start: 0.7989 (ttmm) cc_final: 0.7639 (ttmm) REVERT: A 224 GLU cc_start: 0.8209 (pm20) cc_final: 0.7478 (mp0) REVERT: A 238 PHE cc_start: 0.8206 (p90) cc_final: 0.7987 (p90) REVERT: A 541 PHE cc_start: 0.7981 (p90) cc_final: 0.7698 (p90) REVERT: A 563 GLN cc_start: 0.7645 (mm-40) cc_final: 0.7387 (mt0) REVERT: A 596 SER cc_start: 0.8686 (m) cc_final: 0.8345 (p) REVERT: A 711 SER cc_start: 0.8380 (m) cc_final: 0.8155 (p) REVERT: A 749 CYS cc_start: 0.6090 (t) cc_final: 0.5757 (t) REVERT: A 765 ARG cc_start: 0.7841 (ttp-110) cc_final: 0.7522 (ttp-170) REVERT: A 854 LYS cc_start: 0.7816 (ttpp) cc_final: 0.7542 (tttp) REVERT: A 914 ASN cc_start: 0.7948 (p0) cc_final: 0.7707 (p0) REVERT: A 950 ASP cc_start: 0.7600 (t70) cc_final: 0.7088 (t0) REVERT: A 964 LYS cc_start: 0.8539 (tmtm) cc_final: 0.8210 (ttmm) REVERT: A 1002 GLN cc_start: 0.7716 (tp-100) cc_final: 0.7470 (tp-100) REVERT: A 1091 ARG cc_start: 0.7931 (ttm170) cc_final: 0.7599 (ttm-80) REVERT: A 1097 SER cc_start: 0.8673 (t) cc_final: 0.8373 (p) REVERT: B 33 THR cc_start: 0.8646 (m) cc_final: 0.8283 (t) REVERT: B 54 LEU cc_start: 0.8480 (mt) cc_final: 0.8266 (mt) REVERT: B 126 VAL cc_start: 0.7336 (t) cc_final: 0.6957 (m) REVERT: B 130 VAL cc_start: 0.7728 (t) cc_final: 0.7289 (p) REVERT: B 188 ARG cc_start: 0.8150 (mtt-85) cc_final: 0.7777 (mtt90) REVERT: B 193 LYS cc_start: 0.8279 (ttpt) cc_final: 0.7938 (ttpt) REVERT: B 265 TYR cc_start: 0.7987 (p90) cc_final: 0.7779 (p90) REVERT: B 281 GLU cc_start: 0.7417 (pp20) cc_final: 0.7123 (pp20) REVERT: B 319 ARG cc_start: 0.8034 (ptp-110) cc_final: 0.7653 (mtp85) REVERT: B 355 ARG cc_start: 0.4753 (OUTLIER) cc_final: 0.4254 (tmt90) REVERT: B 537 LYS cc_start: 0.8220 (ttpt) cc_final: 0.7768 (ptmm) REVERT: B 603 ASN cc_start: 0.8260 (t0) cc_final: 0.8032 (t0) REVERT: B 726 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8421 (mt) REVERT: B 747 THR cc_start: 0.7930 (OUTLIER) cc_final: 0.7682 (p) REVERT: B 751 ASN cc_start: 0.8452 (m-40) cc_final: 0.8139 (m110) REVERT: B 774 GLN cc_start: 0.7835 (mm-40) cc_final: 0.7604 (mm-40) REVERT: B 884 SER cc_start: 0.8812 (t) cc_final: 0.8469 (p) REVERT: B 902 MET cc_start: 0.7917 (tpp) cc_final: 0.7623 (tpp) REVERT: B 933 LYS cc_start: 0.7840 (mtmt) cc_final: 0.7539 (mtpp) REVERT: B 957 GLN cc_start: 0.7127 (OUTLIER) cc_final: 0.6650 (tm130) REVERT: B 964 LYS cc_start: 0.8419 (ttpp) cc_final: 0.8213 (ttmm) REVERT: B 980 ILE cc_start: 0.8540 (mt) cc_final: 0.8288 (mm) REVERT: B 1107 ARG cc_start: 0.7462 (mtt90) cc_final: 0.7147 (mtt180) REVERT: B 1118 ASP cc_start: 0.7379 (t70) cc_final: 0.7005 (t0) REVERT: B 1127 ASP cc_start: 0.6972 (p0) cc_final: 0.6691 (p0) REVERT: B 1144 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7139 (mm-30) REVERT: C 51 THR cc_start: 0.8493 (t) cc_final: 0.8232 (p) REVERT: C 52 GLN cc_start: 0.7789 (tm-30) cc_final: 0.7065 (tm-30) REVERT: C 95 ILE cc_start: 0.8488 (mt) cc_final: 0.7983 (mt) REVERT: C 105 ILE cc_start: 0.7930 (mt) cc_final: 0.7617 (mt) REVERT: C 189 GLU cc_start: 0.7673 (mp0) cc_final: 0.7234 (mp0) REVERT: C 203 SER cc_start: 0.8636 (t) cc_final: 0.8177 (m) REVERT: C 287 ASP cc_start: 0.7619 (p0) cc_final: 0.7305 (p0) REVERT: C 327 VAL cc_start: 0.8373 (t) cc_final: 0.8153 (m) REVERT: C 541 PHE cc_start: 0.7725 (p90) cc_final: 0.7332 (p90) REVERT: C 542 ASN cc_start: 0.8201 (t0) cc_final: 0.7915 (t0) REVERT: C 546 LEU cc_start: 0.7632 (tt) cc_final: 0.7430 (tt) REVERT: C 578 ASP cc_start: 0.7886 (t0) cc_final: 0.7380 (t0) REVERT: C 586 ASP cc_start: 0.7431 (t0) cc_final: 0.7114 (t0) REVERT: C 592 PHE cc_start: 0.7976 (p90) cc_final: 0.7659 (p90) REVERT: C 603 ASN cc_start: 0.8158 (t0) cc_final: 0.7746 (t0) REVERT: C 619 GLU cc_start: 0.7879 (tt0) cc_final: 0.7551 (tt0) REVERT: C 723 THR cc_start: 0.8529 (t) cc_final: 0.8284 (p) REVERT: C 765 ARG cc_start: 0.8261 (ttm-80) cc_final: 0.7935 (ttp80) REVERT: C 773 GLU cc_start: 0.7895 (tt0) cc_final: 0.7542 (tt0) REVERT: C 821 LEU cc_start: 0.7928 (tp) cc_final: 0.7676 (tt) REVERT: C 900 MET cc_start: 0.7990 (ttm) cc_final: 0.7733 (ttm) REVERT: C 953 ASN cc_start: 0.8381 (m-40) cc_final: 0.7967 (m-40) REVERT: C 979 ASP cc_start: 0.6874 (OUTLIER) cc_final: 0.6568 (m-30) REVERT: C 990 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.6973 (mp0) REVERT: C 994 ASP cc_start: 0.7555 (m-30) cc_final: 0.7249 (t0) REVERT: C 1014 ARG cc_start: 0.8150 (tpp80) cc_final: 0.7828 (mtt90) REVERT: C 1068 VAL cc_start: 0.7908 (t) cc_final: 0.7706 (m) REVERT: C 1073 LYS cc_start: 0.8007 (ttpp) cc_final: 0.7798 (ttmm) REVERT: C 1081 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.8180 (pt) REVERT: C 1097 SER cc_start: 0.8820 (t) cc_final: 0.8524 (p) REVERT: C 1111 GLU cc_start: 0.8127 (tt0) cc_final: 0.7891 (tt0) REVERT: C 1129 VAL cc_start: 0.8276 (OUTLIER) cc_final: 0.8009 (p) REVERT: D 111 LEU cc_start: -0.1174 (OUTLIER) cc_final: -0.1687 (tm) outliers start: 162 outliers final: 110 residues processed: 653 average time/residue: 0.4389 time to fit residues: 456.0348 Evaluate side-chains 619 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 499 time to evaluate : 3.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 29 THR 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 229 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 183 ASN Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 979 ASP 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 1129 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 111 LEU Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 221 CYS Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 238 MET Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 193 PHE Chi-restraints excluded: chain F residue 205 TYR Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain G residue 247 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 382 optimal weight: 30.0000 chunk 86 optimal weight: 0.9980 chunk 179 optimal weight: 3.9990 chunk 130 optimal weight: 20.0000 chunk 167 optimal weight: 0.5980 chunk 362 optimal weight: 8.9990 chunk 298 optimal weight: 0.2980 chunk 205 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 336 optimal weight: 0.0980 chunk 220 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 824 ASN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 544 ASN ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN C 218 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.220858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.161802 restraints weight = 51021.019| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 2.75 r_work: 0.3516 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32200 Z= 0.114 Angle : 0.566 13.862 43888 Z= 0.278 Chirality : 0.044 0.286 4965 Planarity : 0.004 0.066 5648 Dihedral : 6.983 81.838 4960 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 4.76 % Allowed : 16.08 % Favored : 79.17 % 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: -2.58 (0.13), residues: 3963 helix: 1.15 (0.21), residues: 657 sheet: -1.63 (0.17), residues: 882 loop : -2.74 (0.11), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 64 HIS 0.008 0.001 HIS B1048 PHE 0.028 0.001 PHE A 592 TYR 0.019 0.001 TYR A 91 ARG 0.004 0.000 ARG A 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00255 ( 23) link_NAG-ASN : angle 1.83106 ( 69) hydrogen bonds : bond 0.03171 ( 847) hydrogen bonds : angle 4.64311 ( 2271) SS BOND : bond 0.00364 ( 47) SS BOND : angle 1.60814 ( 94) covalent geometry : bond 0.00259 (32130) covalent geometry : angle 0.55707 (43725) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 513 time to evaluate : 2.939 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: A 51 THR cc_start: 0.8365 (t) cc_final: 0.7899 (p) REVERT: A 186 ASN cc_start: 0.6797 (OUTLIER) cc_final: 0.6070 (p0) REVERT: A 188 ARG cc_start: 0.8426 (ptp-170) cc_final: 0.8142 (ptp90) REVERT: A 224 GLU cc_start: 0.8203 (pm20) cc_final: 0.7834 (pm20) REVERT: A 238 PHE cc_start: 0.8176 (p90) cc_final: 0.7897 (p90) REVERT: A 541 PHE cc_start: 0.7978 (p90) cc_final: 0.7707 (p90) REVERT: A 547 LYS cc_start: 0.8387 (mttm) cc_final: 0.8169 (mmtt) REVERT: A 563 GLN cc_start: 0.7698 (mm-40) cc_final: 0.7341 (mt0) REVERT: A 589 PRO cc_start: 0.8614 (Cg_endo) cc_final: 0.8390 (Cg_exo) REVERT: A 596 SER cc_start: 0.8639 (m) cc_final: 0.8338 (p) REVERT: A 655 TYR cc_start: 0.7797 (t80) cc_final: 0.7586 (t80) REVERT: A 765 ARG cc_start: 0.7976 (ttp-110) cc_final: 0.7668 (ttp-170) REVERT: A 854 LYS cc_start: 0.7840 (ttpp) cc_final: 0.7553 (tttp) REVERT: A 945 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8214 (mm) REVERT: A 950 ASP cc_start: 0.7618 (t70) cc_final: 0.7122 (t0) REVERT: A 964 LYS cc_start: 0.8563 (tmtm) cc_final: 0.8218 (ttmm) REVERT: A 984 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7596 (tt) REVERT: A 1002 GLN cc_start: 0.7731 (tp-100) cc_final: 0.7496 (tp-100) REVERT: A 1091 ARG cc_start: 0.7940 (ttm170) cc_final: 0.7605 (ttm-80) REVERT: A 1097 SER cc_start: 0.8653 (t) cc_final: 0.8378 (p) REVERT: B 33 THR cc_start: 0.8655 (m) cc_final: 0.8302 (t) REVERT: B 54 LEU cc_start: 0.8517 (mt) cc_final: 0.8292 (mt) REVERT: B 126 VAL cc_start: 0.7281 (t) cc_final: 0.6898 (t) REVERT: B 129 LYS cc_start: 0.8621 (ptpt) cc_final: 0.8421 (ptpp) REVERT: B 130 VAL cc_start: 0.7735 (t) cc_final: 0.7277 (p) REVERT: B 187 LEU cc_start: 0.8233 (tp) cc_final: 0.8021 (tp) REVERT: B 188 ARG cc_start: 0.8193 (mtt-85) cc_final: 0.7716 (mtt90) REVERT: B 193 LYS cc_start: 0.8322 (ttpt) cc_final: 0.7982 (ttpt) REVERT: B 281 GLU cc_start: 0.7466 (pp20) cc_final: 0.7181 (pp20) REVERT: B 319 ARG cc_start: 0.8055 (ptp-110) cc_final: 0.7608 (mtp85) REVERT: B 355 ARG cc_start: 0.4761 (OUTLIER) cc_final: 0.4232 (tmt90) REVERT: B 537 LYS cc_start: 0.8275 (ttpt) cc_final: 0.7813 (ptmm) REVERT: B 619 GLU cc_start: 0.7538 (tt0) cc_final: 0.7232 (tt0) REVERT: B 726 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8426 (mt) REVERT: B 747 THR cc_start: 0.7932 (OUTLIER) cc_final: 0.7668 (p) REVERT: B 751 ASN cc_start: 0.8514 (m-40) cc_final: 0.8248 (m110) REVERT: B 774 GLN cc_start: 0.7804 (mm-40) cc_final: 0.7575 (mm-40) REVERT: B 884 SER cc_start: 0.8871 (t) cc_final: 0.8560 (p) REVERT: B 902 MET cc_start: 0.7890 (tpp) cc_final: 0.7508 (tpp) REVERT: B 933 LYS cc_start: 0.7817 (mtmt) cc_final: 0.7519 (mtpp) REVERT: B 957 GLN cc_start: 0.7106 (OUTLIER) cc_final: 0.6789 (tm130) REVERT: B 964 LYS cc_start: 0.8446 (ttpp) cc_final: 0.8241 (ttmm) REVERT: B 980 ILE cc_start: 0.8616 (mt) cc_final: 0.8373 (mm) REVERT: B 1050 MET cc_start: 0.7896 (mtm) cc_final: 0.7692 (mtp) REVERT: B 1107 ARG cc_start: 0.7568 (mtt90) cc_final: 0.7295 (mtt180) REVERT: B 1113 GLN cc_start: 0.8280 (mt0) cc_final: 0.8072 (mt0) REVERT: B 1118 ASP cc_start: 0.7430 (t70) cc_final: 0.7016 (t0) REVERT: B 1127 ASP cc_start: 0.7055 (p0) cc_final: 0.6797 (p0) REVERT: B 1144 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7086 (mm-30) REVERT: C 51 THR cc_start: 0.8479 (t) cc_final: 0.8198 (p) REVERT: C 94 SER cc_start: 0.8402 (t) cc_final: 0.8180 (p) REVERT: C 105 ILE cc_start: 0.8038 (mt) cc_final: 0.7794 (mt) REVERT: C 106 PHE cc_start: 0.8178 (m-10) cc_final: 0.7974 (m-10) REVERT: C 190 PHE cc_start: 0.7548 (m-80) cc_final: 0.7269 (m-80) REVERT: C 203 SER cc_start: 0.8576 (t) cc_final: 0.8172 (m) REVERT: C 287 ASP cc_start: 0.7602 (p0) cc_final: 0.7399 (p0) REVERT: C 298 GLU cc_start: 0.7928 (tp30) cc_final: 0.7585 (tp30) REVERT: C 328 ARG cc_start: 0.7822 (tpp80) cc_final: 0.7587 (mtm-85) REVERT: C 541 PHE cc_start: 0.7667 (p90) cc_final: 0.7204 (p90) REVERT: C 542 ASN cc_start: 0.8209 (t0) cc_final: 0.7950 (t0) REVERT: C 568 ASP cc_start: 0.7177 (p0) cc_final: 0.6259 (p0) REVERT: C 578 ASP cc_start: 0.7854 (t0) cc_final: 0.7523 (t0) REVERT: C 592 PHE cc_start: 0.8112 (p90) cc_final: 0.7859 (p90) REVERT: C 603 ASN cc_start: 0.8223 (t0) cc_final: 0.7793 (t0) REVERT: C 619 GLU cc_start: 0.7980 (tt0) cc_final: 0.7601 (tt0) REVERT: C 723 THR cc_start: 0.8541 (t) cc_final: 0.8298 (p) REVERT: C 765 ARG cc_start: 0.8358 (ttm-80) cc_final: 0.8045 (ttp80) REVERT: C 773 GLU cc_start: 0.7845 (tt0) cc_final: 0.7485 (tt0) REVERT: C 808 ASP cc_start: 0.7818 (t0) cc_final: 0.7511 (m-30) REVERT: C 821 LEU cc_start: 0.7948 (tp) cc_final: 0.7739 (tt) REVERT: C 900 MET cc_start: 0.7961 (ttm) cc_final: 0.7680 (ttm) REVERT: C 902 MET cc_start: 0.7877 (mmm) cc_final: 0.7256 (tpt) REVERT: C 953 ASN cc_start: 0.8328 (m-40) cc_final: 0.7913 (m-40) REVERT: C 979 ASP cc_start: 0.6854 (OUTLIER) cc_final: 0.6471 (m-30) REVERT: C 990 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.7091 (mp0) REVERT: C 994 ASP cc_start: 0.7605 (m-30) cc_final: 0.7272 (t0) REVERT: C 1014 ARG cc_start: 0.8205 (tpp80) cc_final: 0.7857 (mtt90) REVERT: C 1068 VAL cc_start: 0.7902 (t) cc_final: 0.7690 (m) REVERT: C 1073 LYS cc_start: 0.8027 (ttpp) cc_final: 0.7780 (ttmm) REVERT: C 1097 SER cc_start: 0.8814 (t) cc_final: 0.8518 (p) REVERT: C 1111 GLU cc_start: 0.8101 (tt0) cc_final: 0.7845 (tt0) REVERT: C 1129 VAL cc_start: 0.8222 (OUTLIER) cc_final: 0.7946 (p) REVERT: D 111 LEU cc_start: -0.1309 (OUTLIER) cc_final: -0.2112 (tm) outliers start: 163 outliers final: 116 residues processed: 643 average time/residue: 0.4316 time to fit residues: 440.9847 Evaluate side-chains 616 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 489 time to evaluate : 3.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 29 THR 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 229 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 547 LYS Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 LYS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 979 ASP 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 1072 GLU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1144 GLU 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 111 LEU Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 221 CYS Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 238 MET Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 193 PHE Chi-restraints excluded: chain F residue 205 TYR Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 247 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 139 optimal weight: 1.9990 chunk 307 optimal weight: 50.0000 chunk 366 optimal weight: 10.0000 chunk 200 optimal weight: 0.8980 chunk 327 optimal weight: 0.0070 chunk 18 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 175 optimal weight: 9.9990 chunk 51 optimal weight: 0.0980 chunk 55 optimal weight: 0.0970 chunk 73 optimal weight: 2.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 824 ASN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN B 544 ASN ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 935 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN C 536 ASN C 690 GLN C 901 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.220316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.160520 restraints weight = 50868.550| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.94 r_work: 0.3532 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 32200 Z= 0.119 Angle : 0.569 14.688 43888 Z= 0.279 Chirality : 0.045 0.485 4965 Planarity : 0.004 0.068 5648 Dihedral : 6.993 81.742 4960 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 4.84 % Allowed : 16.08 % Favored : 79.08 % 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: -2.46 (0.13), residues: 3963 helix: 1.20 (0.21), residues: 661 sheet: -1.56 (0.17), residues: 860 loop : -2.64 (0.11), residues: 2442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 98 HIS 0.013 0.001 HIS B1048 PHE 0.022 0.001 PHE A 190 TYR 0.018 0.001 TYR A 91 ARG 0.008 0.000 ARG G 143 Details of bonding type rmsd link_NAG-ASN : bond 0.00246 ( 23) link_NAG-ASN : angle 2.45755 ( 69) hydrogen bonds : bond 0.03143 ( 847) hydrogen bonds : angle 4.58528 ( 2271) SS BOND : bond 0.00294 ( 47) SS BOND : angle 1.35330 ( 94) covalent geometry : bond 0.00271 (32130) covalent geometry : angle 0.55814 (43725) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 512 time to evaluate : 3.051 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: A 51 THR cc_start: 0.8374 (t) cc_final: 0.7902 (p) REVERT: A 129 LYS cc_start: 0.8039 (ttmm) cc_final: 0.7644 (ttmm) REVERT: A 130 VAL cc_start: 0.7967 (OUTLIER) cc_final: 0.7761 (p) REVERT: A 186 ASN cc_start: 0.6763 (OUTLIER) cc_final: 0.6075 (p0) REVERT: A 188 ARG cc_start: 0.8453 (ptp-170) cc_final: 0.8009 (ptp90) REVERT: A 189 GLU cc_start: 0.7689 (pm20) cc_final: 0.7454 (pm20) REVERT: A 224 GLU cc_start: 0.8169 (pm20) cc_final: 0.7787 (pm20) REVERT: A 238 PHE cc_start: 0.8208 (p90) cc_final: 0.7854 (p90) REVERT: A 541 PHE cc_start: 0.8016 (p90) cc_final: 0.7747 (p90) REVERT: A 563 GLN cc_start: 0.7728 (mm-40) cc_final: 0.7397 (mt0) REVERT: A 596 SER cc_start: 0.8685 (m) cc_final: 0.8344 (p) REVERT: A 749 CYS cc_start: 0.6065 (t) cc_final: 0.5696 (t) REVERT: A 765 ARG cc_start: 0.7970 (ttp-110) cc_final: 0.7637 (ttp-170) REVERT: A 854 LYS cc_start: 0.7889 (ttpp) cc_final: 0.7562 (tttp) REVERT: A 904 TYR cc_start: 0.7268 (m-10) cc_final: 0.6055 (m-10) REVERT: A 950 ASP cc_start: 0.7702 (t70) cc_final: 0.7260 (t0) REVERT: A 964 LYS cc_start: 0.8544 (tmtm) cc_final: 0.8217 (ttmm) REVERT: A 984 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7591 (tt) REVERT: A 1002 GLN cc_start: 0.7817 (tp-100) cc_final: 0.7545 (tp-100) REVERT: A 1091 ARG cc_start: 0.7990 (ttm170) cc_final: 0.7643 (ttm-80) REVERT: A 1097 SER cc_start: 0.8680 (t) cc_final: 0.8387 (p) REVERT: B 33 THR cc_start: 0.8663 (m) cc_final: 0.8294 (t) REVERT: B 54 LEU cc_start: 0.8512 (mt) cc_final: 0.8303 (mt) REVERT: B 126 VAL cc_start: 0.7245 (t) cc_final: 0.6754 (t) REVERT: B 129 LYS cc_start: 0.8551 (ptpt) cc_final: 0.8349 (ptpp) REVERT: B 130 VAL cc_start: 0.7847 (t) cc_final: 0.7354 (p) REVERT: B 188 ARG cc_start: 0.8283 (mtt-85) cc_final: 0.7994 (mtt-85) REVERT: B 193 LYS cc_start: 0.8369 (ttpt) cc_final: 0.7993 (ttpt) REVERT: B 281 GLU cc_start: 0.7426 (pp20) cc_final: 0.7147 (pp20) REVERT: B 319 ARG cc_start: 0.8024 (ptp-110) cc_final: 0.7590 (mtp85) REVERT: B 355 ARG cc_start: 0.4720 (OUTLIER) cc_final: 0.4225 (tmt90) REVERT: B 362 VAL cc_start: 0.6109 (OUTLIER) cc_final: 0.5680 (p) REVERT: B 537 LYS cc_start: 0.8313 (ttpt) cc_final: 0.7871 (ptmm) REVERT: B 558 LYS cc_start: 0.8276 (mtpp) cc_final: 0.7944 (mtpp) REVERT: B 603 ASN cc_start: 0.8321 (t0) cc_final: 0.8067 (t0) REVERT: B 619 GLU cc_start: 0.7323 (tt0) cc_final: 0.7055 (tt0) REVERT: B 726 ILE cc_start: 0.8707 (OUTLIER) cc_final: 0.8419 (mt) REVERT: B 747 THR cc_start: 0.7952 (OUTLIER) cc_final: 0.7660 (p) REVERT: B 751 ASN cc_start: 0.8565 (m-40) cc_final: 0.8284 (m110) REVERT: B 774 GLN cc_start: 0.7848 (mm-40) cc_final: 0.7609 (mm-40) REVERT: B 884 SER cc_start: 0.8830 (t) cc_final: 0.8547 (p) REVERT: B 902 MET cc_start: 0.7960 (tpp) cc_final: 0.7531 (tpp) REVERT: B 933 LYS cc_start: 0.7779 (mtmt) cc_final: 0.7481 (mtpp) REVERT: B 957 GLN cc_start: 0.7088 (OUTLIER) cc_final: 0.6712 (tm130) REVERT: B 970 PHE cc_start: 0.7583 (m-80) cc_final: 0.7347 (m-80) REVERT: B 980 ILE cc_start: 0.8602 (mt) cc_final: 0.8380 (mm) REVERT: B 1084 ASP cc_start: 0.7477 (p0) cc_final: 0.7006 (p0) REVERT: B 1107 ARG cc_start: 0.7570 (mtt90) cc_final: 0.6481 (mtt180) REVERT: B 1118 ASP cc_start: 0.7417 (t70) cc_final: 0.7045 (t0) REVERT: B 1127 ASP cc_start: 0.7085 (p0) cc_final: 0.6833 (p0) REVERT: B 1144 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7071 (mm-30) REVERT: C 51 THR cc_start: 0.8467 (OUTLIER) cc_final: 0.8189 (p) REVERT: C 52 GLN cc_start: 0.7806 (tm-30) cc_final: 0.7132 (tm-30) REVERT: C 94 SER cc_start: 0.8391 (t) cc_final: 0.8151 (p) REVERT: C 95 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8186 (mt) REVERT: C 104 TRP cc_start: 0.7630 (m-90) cc_final: 0.7371 (m-90) REVERT: C 105 ILE cc_start: 0.8104 (mt) cc_final: 0.7867 (mt) REVERT: C 106 PHE cc_start: 0.8176 (m-10) cc_final: 0.7963 (m-10) REVERT: C 168 PHE cc_start: 0.8423 (t80) cc_final: 0.7730 (t80) REVERT: C 190 PHE cc_start: 0.7627 (m-80) cc_final: 0.7283 (m-80) REVERT: C 203 SER cc_start: 0.8597 (t) cc_final: 0.8182 (m) REVERT: C 298 GLU cc_start: 0.7967 (tp30) cc_final: 0.7622 (tp30) REVERT: C 328 ARG cc_start: 0.7823 (tpp80) cc_final: 0.7601 (mtm-85) REVERT: C 541 PHE cc_start: 0.7703 (p90) cc_final: 0.7178 (p90) REVERT: C 542 ASN cc_start: 0.8178 (t0) cc_final: 0.7836 (t0) REVERT: C 568 ASP cc_start: 0.7040 (p0) cc_final: 0.6291 (p0) REVERT: C 578 ASP cc_start: 0.7865 (t0) cc_final: 0.7427 (t0) REVERT: C 586 ASP cc_start: 0.7263 (t70) cc_final: 0.6898 (t0) REVERT: C 592 PHE cc_start: 0.8147 (p90) cc_final: 0.7936 (p90) REVERT: C 603 ASN cc_start: 0.8258 (t0) cc_final: 0.7822 (t0) REVERT: C 619 GLU cc_start: 0.8036 (tt0) cc_final: 0.7622 (tt0) REVERT: C 643 PHE cc_start: 0.6813 (t80) cc_final: 0.6354 (t80) REVERT: C 645 THR cc_start: 0.8466 (t) cc_final: 0.7984 (p) REVERT: C 740 MET cc_start: 0.7447 (ttm) cc_final: 0.7232 (ttp) REVERT: C 765 ARG cc_start: 0.8298 (ttm-80) cc_final: 0.8013 (ttp80) REVERT: C 773 GLU cc_start: 0.7922 (tt0) cc_final: 0.7559 (tt0) REVERT: C 808 ASP cc_start: 0.7862 (t0) cc_final: 0.7568 (m-30) REVERT: C 821 LEU cc_start: 0.7910 (tp) cc_final: 0.7649 (tt) REVERT: C 900 MET cc_start: 0.7999 (ttm) cc_final: 0.7707 (ttm) REVERT: C 902 MET cc_start: 0.7950 (mmm) cc_final: 0.7276 (tpt) REVERT: C 934 ILE cc_start: 0.7877 (tp) cc_final: 0.7626 (tt) REVERT: C 979 ASP cc_start: 0.6850 (OUTLIER) cc_final: 0.6443 (m-30) REVERT: C 990 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7008 (mp0) REVERT: C 994 ASP cc_start: 0.7553 (m-30) cc_final: 0.7223 (t0) REVERT: C 1014 ARG cc_start: 0.8169 (tpp80) cc_final: 0.7800 (mtt90) REVERT: C 1068 VAL cc_start: 0.7947 (t) cc_final: 0.7720 (m) REVERT: C 1073 LYS cc_start: 0.8073 (ttpp) cc_final: 0.7815 (ttmm) REVERT: C 1097 SER cc_start: 0.8851 (t) cc_final: 0.8473 (p) REVERT: C 1111 GLU cc_start: 0.8051 (tt0) cc_final: 0.7836 (tt0) REVERT: C 1129 VAL cc_start: 0.8214 (OUTLIER) cc_final: 0.7955 (p) REVERT: D 111 LEU cc_start: -0.1424 (OUTLIER) cc_final: -0.2246 (tm) outliers start: 166 outliers final: 122 residues processed: 641 average time/residue: 0.4313 time to fit residues: 439.2301 Evaluate side-chains 632 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 496 time to evaluate : 3.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 LYS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 979 ASP 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 1072 GLU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1144 GLU 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 111 LEU Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 221 CYS Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 238 MET Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 193 PHE Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain G residue 28 ASN Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 247 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 22 optimal weight: 4.9990 chunk 19 optimal weight: 10.0000 chunk 223 optimal weight: 3.9990 chunk 43 optimal weight: 50.0000 chunk 90 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 270 optimal weight: 0.9980 chunk 230 optimal weight: 2.9990 chunk 349 optimal weight: 50.0000 chunk 79 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 824 ASN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 544 ASN ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.216753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.155263 restraints weight = 50321.445| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.80 r_work: 0.3450 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.109 32200 Z= 0.307 Angle : 0.707 15.628 43888 Z= 0.353 Chirality : 0.050 0.532 4965 Planarity : 0.005 0.071 5648 Dihedral : 7.389 81.474 4956 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.30 % Favored : 89.70 % Rotamer: Outliers : 5.19 % Allowed : 16.57 % Favored : 78.23 % 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: -2.54 (0.13), residues: 3963 helix: 0.73 (0.21), residues: 660 sheet: -1.55 (0.17), residues: 853 loop : -2.58 (0.11), residues: 2450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 64 HIS 0.018 0.001 HIS B1048 PHE 0.036 0.002 PHE A 592 TYR 0.045 0.002 TYR B1067 ARG 0.008 0.000 ARG A 34 Details of bonding type rmsd link_NAG-ASN : bond 0.01034 ( 23) link_NAG-ASN : angle 3.25572 ( 69) hydrogen bonds : bond 0.04435 ( 847) hydrogen bonds : angle 4.96535 ( 2271) SS BOND : bond 0.00540 ( 47) SS BOND : angle 1.90043 ( 94) covalent geometry : bond 0.00688 (32130) covalent geometry : angle 0.69043 (43725) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 544 time to evaluate : 3.261 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: A 51 THR cc_start: 0.8298 (t) cc_final: 0.7806 (p) REVERT: A 117 LEU cc_start: 0.7898 (mt) cc_final: 0.7612 (mt) REVERT: A 129 LYS cc_start: 0.8208 (ttmm) cc_final: 0.7748 (ttmm) REVERT: A 130 VAL cc_start: 0.8012 (OUTLIER) cc_final: 0.7765 (p) REVERT: A 186 ASN cc_start: 0.6832 (OUTLIER) cc_final: 0.6120 (p0) REVERT: A 196 ASP cc_start: 0.7284 (p0) cc_final: 0.6609 (m-30) REVERT: A 204 LYS cc_start: 0.8341 (tptm) cc_final: 0.8009 (tptm) REVERT: A 224 GLU cc_start: 0.8248 (pm20) cc_final: 0.7556 (pt0) REVERT: A 298 GLU cc_start: 0.7628 (tt0) cc_final: 0.7254 (tt0) REVERT: A 315 THR cc_start: 0.8666 (OUTLIER) cc_final: 0.8340 (m) REVERT: A 541 PHE cc_start: 0.8135 (p90) cc_final: 0.7916 (p90) REVERT: A 547 LYS cc_start: 0.8456 (mmtt) cc_final: 0.8102 (mmtm) REVERT: A 563 GLN cc_start: 0.7797 (mm-40) cc_final: 0.7503 (mt0) REVERT: A 574 ASP cc_start: 0.7810 (t70) cc_final: 0.7475 (t0) REVERT: A 584 ILE cc_start: 0.6929 (OUTLIER) cc_final: 0.6638 (pt) REVERT: A 596 SER cc_start: 0.8732 (m) cc_final: 0.8379 (p) REVERT: A 602 THR cc_start: 0.8172 (m) cc_final: 0.7928 (p) REVERT: A 654 GLU cc_start: 0.7929 (pt0) cc_final: 0.7632 (pt0) REVERT: A 670 ILE cc_start: 0.8656 (mm) cc_final: 0.8423 (mt) REVERT: A 749 CYS cc_start: 0.6251 (t) cc_final: 0.5871 (t) REVERT: A 765 ARG cc_start: 0.8039 (ttp-110) cc_final: 0.7729 (ttp-170) REVERT: A 854 LYS cc_start: 0.8056 (ttpp) cc_final: 0.7788 (tttm) REVERT: A 904 TYR cc_start: 0.7421 (m-10) cc_final: 0.6440 (m-10) REVERT: A 950 ASP cc_start: 0.7682 (t70) cc_final: 0.7205 (t0) REVERT: A 957 GLN cc_start: 0.7907 (mt0) cc_final: 0.7641 (mt0) REVERT: A 964 LYS cc_start: 0.8526 (tmtm) cc_final: 0.8197 (ttmm) REVERT: A 965 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.8043 (mt0) REVERT: A 984 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7843 (tt) REVERT: A 1002 GLN cc_start: 0.7914 (tp-100) cc_final: 0.7654 (tp-100) REVERT: A 1017 GLU cc_start: 0.7775 (tm-30) cc_final: 0.7544 (tm-30) REVERT: A 1086 LYS cc_start: 0.7816 (mtmm) cc_final: 0.7428 (mtmm) REVERT: A 1097 SER cc_start: 0.8668 (t) cc_final: 0.8339 (p) REVERT: B 33 THR cc_start: 0.8632 (m) cc_final: 0.8223 (t) REVERT: B 54 LEU cc_start: 0.8546 (mt) cc_final: 0.8296 (mt) REVERT: B 105 ILE cc_start: 0.8475 (mm) cc_final: 0.8255 (mp) REVERT: B 129 LYS cc_start: 0.8664 (ptpt) cc_final: 0.8419 (ptpp) REVERT: B 130 VAL cc_start: 0.8018 (t) cc_final: 0.7476 (p) REVERT: B 193 LYS cc_start: 0.8329 (ttpt) cc_final: 0.8025 (ttpt) REVERT: B 281 GLU cc_start: 0.7478 (pp20) cc_final: 0.7147 (pp20) REVERT: B 355 ARG cc_start: 0.4734 (OUTLIER) cc_final: 0.4259 (tmt90) REVERT: B 362 VAL cc_start: 0.6526 (OUTLIER) cc_final: 0.6116 (p) REVERT: B 537 LYS cc_start: 0.8591 (ttpt) cc_final: 0.8168 (ptmm) REVERT: B 558 LYS cc_start: 0.8346 (mtpp) cc_final: 0.7990 (mtpp) REVERT: B 619 GLU cc_start: 0.7654 (tt0) cc_final: 0.7381 (tt0) REVERT: B 726 ILE cc_start: 0.8766 (OUTLIER) cc_final: 0.7737 (mt) REVERT: B 747 THR cc_start: 0.7760 (OUTLIER) cc_final: 0.7520 (p) REVERT: B 751 ASN cc_start: 0.8478 (m-40) cc_final: 0.8157 (m110) REVERT: B 774 GLN cc_start: 0.8098 (mm-40) cc_final: 0.7860 (mm-40) REVERT: B 884 SER cc_start: 0.8890 (t) cc_final: 0.8514 (p) REVERT: B 902 MET cc_start: 0.8164 (tpp) cc_final: 0.7671 (tpp) REVERT: B 933 LYS cc_start: 0.8080 (mtmt) cc_final: 0.7755 (mtpp) REVERT: B 957 GLN cc_start: 0.7184 (OUTLIER) cc_final: 0.6765 (tm130) REVERT: B 1002 GLN cc_start: 0.8094 (tp40) cc_final: 0.7228 (tp40) REVERT: B 1107 ARG cc_start: 0.7524 (mtt90) cc_final: 0.6503 (mtt180) REVERT: B 1118 ASP cc_start: 0.7534 (t70) cc_final: 0.7083 (t0) REVERT: B 1127 ASP cc_start: 0.7210 (p0) cc_final: 0.6845 (p0) REVERT: C 62 VAL cc_start: 0.8383 (OUTLIER) cc_final: 0.8047 (m) REVERT: C 87 ASN cc_start: 0.7318 (OUTLIER) cc_final: 0.6802 (p0) REVERT: C 94 SER cc_start: 0.8541 (t) cc_final: 0.8169 (p) REVERT: C 95 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8344 (mt) REVERT: C 105 ILE cc_start: 0.8182 (mt) cc_final: 0.7606 (tt) REVERT: C 135 PHE cc_start: 0.5120 (OUTLIER) cc_final: 0.4829 (t80) REVERT: C 227 VAL cc_start: 0.8518 (p) cc_final: 0.8278 (t) REVERT: C 269 TYR cc_start: 0.8267 (m-10) cc_final: 0.7703 (m-80) REVERT: C 541 PHE cc_start: 0.7741 (p90) cc_final: 0.7415 (p90) REVERT: C 542 ASN cc_start: 0.8333 (t0) cc_final: 0.7922 (t0) REVERT: C 547 LYS cc_start: 0.8229 (mtmm) cc_final: 0.7984 (mttp) REVERT: C 568 ASP cc_start: 0.7147 (p0) cc_final: 0.6419 (p0) REVERT: C 578 ASP cc_start: 0.7979 (t0) cc_final: 0.7591 (t0) REVERT: C 603 ASN cc_start: 0.8371 (t0) cc_final: 0.7942 (t0) REVERT: C 723 THR cc_start: 0.8503 (t) cc_final: 0.8261 (p) REVERT: C 752 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8343 (tt) REVERT: C 765 ARG cc_start: 0.8441 (ttm-80) cc_final: 0.8035 (ttp80) REVERT: C 773 GLU cc_start: 0.7984 (tt0) cc_final: 0.7564 (tt0) REVERT: C 821 LEU cc_start: 0.7887 (tp) cc_final: 0.7608 (tt) REVERT: C 979 ASP cc_start: 0.6828 (OUTLIER) cc_final: 0.6414 (m-30) REVERT: C 990 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7020 (mp0) REVERT: C 1002 GLN cc_start: 0.7488 (mt0) cc_final: 0.7235 (mt0) REVERT: C 1014 ARG cc_start: 0.8214 (tpp80) cc_final: 0.7782 (mtm-85) REVERT: C 1073 LYS cc_start: 0.8154 (ttpp) cc_final: 0.7896 (ttmm) REVERT: C 1097 SER cc_start: 0.8859 (t) cc_final: 0.8366 (p) REVERT: C 1107 ARG cc_start: 0.7580 (mtt180) cc_final: 0.7380 (mtt90) REVERT: C 1129 VAL cc_start: 0.8321 (OUTLIER) cc_final: 0.8106 (p) REVERT: C 1137 VAL cc_start: 0.8983 (t) cc_final: 0.8677 (m) outliers start: 178 outliers final: 122 residues processed: 672 average time/residue: 0.4322 time to fit residues: 466.3885 Evaluate side-chains 673 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 532 time to evaluate : 3.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 51 THR 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 229 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1129 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 111 LEU Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 221 CYS Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 238 MET Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 193 PHE Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain G residue 28 ASN Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 247 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 387 optimal weight: 50.0000 chunk 373 optimal weight: 0.8980 chunk 193 optimal weight: 1.9990 chunk 250 optimal weight: 0.8980 chunk 311 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 123 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 308 optimal weight: 0.9990 chunk 157 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 641 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 ASN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 239 GLN B 564 GLN B 675 GLN B 824 ASN B 901 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1113 GLN C 239 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 GLN F 207 GLN F 209 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.217513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.156395 restraints weight = 51111.346| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.95 r_work: 0.3415 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32200 Z= 0.144 Angle : 0.632 14.498 43888 Z= 0.311 Chirality : 0.046 0.492 4965 Planarity : 0.005 0.082 5648 Dihedral : 7.123 81.307 4950 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 4.55 % Allowed : 17.86 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.34 (0.13), residues: 3963 helix: 1.06 (0.21), residues: 661 sheet: -1.40 (0.18), residues: 827 loop : -2.50 (0.11), residues: 2475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 104 HIS 0.017 0.001 HIS B1048 PHE 0.040 0.002 PHE C 106 TYR 0.019 0.001 TYR B1067 ARG 0.007 0.000 ARG A 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00454 ( 23) link_NAG-ASN : angle 2.95519 ( 69) hydrogen bonds : bond 0.03494 ( 847) hydrogen bonds : angle 4.77805 ( 2271) SS BOND : bond 0.00344 ( 47) SS BOND : angle 1.81832 ( 94) covalent geometry : bond 0.00324 (32130) covalent geometry : angle 0.61616 (43725) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 525 time to evaluate : 5.149 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: A 51 THR cc_start: 0.8345 (t) cc_final: 0.7855 (p) REVERT: A 52 GLN cc_start: 0.8375 (tp40) cc_final: 0.8155 (tp40) REVERT: A 105 ILE cc_start: 0.8243 (OUTLIER) cc_final: 0.7944 (mm) REVERT: A 117 LEU cc_start: 0.7825 (mt) cc_final: 0.7543 (mt) REVERT: A 129 LYS cc_start: 0.8078 (ttmm) cc_final: 0.7596 (ttmm) REVERT: A 186 ASN cc_start: 0.6898 (OUTLIER) cc_final: 0.6127 (p0) REVERT: A 188 ARG cc_start: 0.8517 (ptp-170) cc_final: 0.8289 (ptp-170) REVERT: A 224 GLU cc_start: 0.8260 (pm20) cc_final: 0.7509 (pt0) REVERT: A 287 ASP cc_start: 0.7859 (t70) cc_final: 0.7652 (m-30) REVERT: A 290 ASP cc_start: 0.7714 (p0) cc_final: 0.7504 (p0) REVERT: A 563 GLN cc_start: 0.7833 (mm-40) cc_final: 0.7481 (mt0) REVERT: A 574 ASP cc_start: 0.7778 (t70) cc_final: 0.7347 (t0) REVERT: A 596 SER cc_start: 0.8666 (m) cc_final: 0.8299 (p) REVERT: A 602 THR cc_start: 0.8223 (m) cc_final: 0.7922 (p) REVERT: A 654 GLU cc_start: 0.7926 (pt0) cc_final: 0.7651 (pt0) REVERT: A 749 CYS cc_start: 0.6354 (t) cc_final: 0.5967 (t) REVERT: A 765 ARG cc_start: 0.7920 (ttp-110) cc_final: 0.7630 (ttp-170) REVERT: A 854 LYS cc_start: 0.8006 (ttpp) cc_final: 0.7775 (tttm) REVERT: A 867 ASP cc_start: 0.7408 (m-30) cc_final: 0.7176 (t0) REVERT: A 904 TYR cc_start: 0.7458 (m-10) cc_final: 0.6538 (m-10) REVERT: A 950 ASP cc_start: 0.7867 (t70) cc_final: 0.7375 (t0) REVERT: A 964 LYS cc_start: 0.8544 (tmtm) cc_final: 0.8219 (ttmm) REVERT: A 965 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.8313 (mt0) REVERT: A 984 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7741 (tt) REVERT: A 994 ASP cc_start: 0.7866 (t0) cc_final: 0.7635 (t0) REVERT: A 1002 GLN cc_start: 0.7865 (tp-100) cc_final: 0.7535 (tp-100) REVERT: A 1038 LYS cc_start: 0.8391 (mtmp) cc_final: 0.8130 (mtmm) REVERT: A 1086 LYS cc_start: 0.7657 (mtmm) cc_final: 0.7317 (mtmm) REVERT: A 1091 ARG cc_start: 0.8106 (ttm170) cc_final: 0.7738 (ttm-80) REVERT: A 1097 SER cc_start: 0.8672 (t) cc_final: 0.8348 (p) REVERT: B 33 THR cc_start: 0.8530 (m) cc_final: 0.8132 (t) REVERT: B 41 LYS cc_start: 0.8280 (mtpp) cc_final: 0.7937 (mtpp) REVERT: B 54 LEU cc_start: 0.8571 (mt) cc_final: 0.8343 (mt) REVERT: B 105 ILE cc_start: 0.8422 (mm) cc_final: 0.8206 (mp) REVERT: B 129 LYS cc_start: 0.8615 (ptpt) cc_final: 0.8310 (ptpp) REVERT: B 130 VAL cc_start: 0.7872 (t) cc_final: 0.7343 (p) REVERT: B 188 ARG cc_start: 0.8406 (mtt-85) cc_final: 0.8013 (mtt-85) REVERT: B 193 LYS cc_start: 0.8378 (ttpt) cc_final: 0.8059 (ttpt) REVERT: B 228 ASP cc_start: 0.7930 (t70) cc_final: 0.7621 (t70) REVERT: B 281 GLU cc_start: 0.7409 (pp20) cc_final: 0.7096 (pp20) REVERT: B 319 ARG cc_start: 0.8196 (ptp-110) cc_final: 0.7514 (mtp85) REVERT: B 355 ARG cc_start: 0.4729 (OUTLIER) cc_final: 0.4233 (tmt90) REVERT: B 362 VAL cc_start: 0.6480 (OUTLIER) cc_final: 0.6074 (p) REVERT: B 537 LYS cc_start: 0.8440 (ttpt) cc_final: 0.8041 (ptmm) REVERT: B 544 ASN cc_start: 0.7653 (t0) cc_final: 0.7241 (t0) REVERT: B 558 LYS cc_start: 0.8291 (mtpp) cc_final: 0.7927 (mtpp) REVERT: B 619 GLU cc_start: 0.7472 (tt0) cc_final: 0.7155 (tt0) REVERT: B 747 THR cc_start: 0.7566 (OUTLIER) cc_final: 0.7351 (p) REVERT: B 751 ASN cc_start: 0.8476 (m-40) cc_final: 0.8161 (m110) REVERT: B 774 GLN cc_start: 0.7879 (mm-40) cc_final: 0.7668 (mm-40) REVERT: B 884 SER cc_start: 0.8783 (t) cc_final: 0.8544 (p) REVERT: B 902 MET cc_start: 0.8091 (tpp) cc_final: 0.7661 (tpp) REVERT: B 914 ASN cc_start: 0.8479 (p0) cc_final: 0.8269 (p0) REVERT: B 933 LYS cc_start: 0.7904 (mtmt) cc_final: 0.7591 (mtpp) REVERT: B 957 GLN cc_start: 0.7255 (OUTLIER) cc_final: 0.6908 (tm130) REVERT: B 1107 ARG cc_start: 0.7662 (mtt90) cc_final: 0.6580 (mtt180) REVERT: B 1118 ASP cc_start: 0.7609 (t70) cc_final: 0.7243 (t0) REVERT: B 1127 ASP cc_start: 0.7185 (p0) cc_final: 0.6822 (p0) REVERT: C 51 THR cc_start: 0.8476 (OUTLIER) cc_final: 0.8084 (p) REVERT: C 94 SER cc_start: 0.8449 (t) cc_final: 0.8118 (p) REVERT: C 95 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8425 (mt) REVERT: C 105 ILE cc_start: 0.8199 (mt) cc_final: 0.7668 (tt) REVERT: C 135 PHE cc_start: 0.5037 (OUTLIER) cc_final: 0.4808 (t80) REVERT: C 168 PHE cc_start: 0.8637 (t80) cc_final: 0.8066 (t80) REVERT: C 189 GLU cc_start: 0.7735 (mp0) cc_final: 0.7189 (mp0) REVERT: C 203 SER cc_start: 0.8765 (t) cc_final: 0.8336 (m) REVERT: C 227 VAL cc_start: 0.8540 (p) cc_final: 0.8294 (t) REVERT: C 228 ASP cc_start: 0.7081 (t70) cc_final: 0.6798 (t0) REVERT: C 239 GLN cc_start: 0.7360 (tp-100) cc_final: 0.6865 (tp-100) REVERT: C 541 PHE cc_start: 0.7706 (p90) cc_final: 0.7306 (p90) REVERT: C 542 ASN cc_start: 0.8307 (t0) cc_final: 0.7896 (t0) REVERT: C 547 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7927 (mttp) REVERT: C 568 ASP cc_start: 0.7073 (p0) cc_final: 0.6341 (p0) REVERT: C 578 ASP cc_start: 0.7863 (t0) cc_final: 0.7419 (t0) REVERT: C 603 ASN cc_start: 0.8288 (t0) cc_final: 0.7854 (t0) REVERT: C 616 ASN cc_start: 0.7441 (t0) cc_final: 0.7058 (t0) REVERT: C 723 THR cc_start: 0.8535 (t) cc_final: 0.8312 (p) REVERT: C 752 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8308 (tt) REVERT: C 762 GLN cc_start: 0.7933 (pt0) cc_final: 0.7671 (pt0) REVERT: C 773 GLU cc_start: 0.8032 (tt0) cc_final: 0.7684 (tt0) REVERT: C 821 LEU cc_start: 0.7904 (tp) cc_final: 0.7629 (tt) REVERT: C 934 ILE cc_start: 0.7890 (tt) cc_final: 0.7618 (tt) REVERT: C 979 ASP cc_start: 0.6859 (OUTLIER) cc_final: 0.6242 (m-30) REVERT: C 983 ARG cc_start: 0.7627 (ptp-110) cc_final: 0.7301 (ptp-110) REVERT: C 990 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7107 (mp0) REVERT: C 994 ASP cc_start: 0.7444 (t0) cc_final: 0.7216 (t0) REVERT: C 1014 ARG cc_start: 0.8248 (tpp80) cc_final: 0.7901 (mtm-85) REVERT: C 1017 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7783 (tm-30) REVERT: C 1073 LYS cc_start: 0.8125 (ttpp) cc_final: 0.7877 (ttmm) REVERT: C 1097 SER cc_start: 0.8841 (t) cc_final: 0.8345 (p) REVERT: C 1129 VAL cc_start: 0.8267 (OUTLIER) cc_final: 0.8037 (p) REVERT: D 49 MET cc_start: 0.2378 (ppp) cc_final: 0.2081 (ppp) outliers start: 156 outliers final: 112 residues processed: 644 average time/residue: 0.6105 time to fit residues: 635.0902 Evaluate side-chains 647 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 519 time to evaluate : 3.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 LYS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1129 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 111 LEU Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 221 CYS Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 238 MET Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 129 GLN Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 193 PHE 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 28 ASN Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 247 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 214 optimal weight: 4.9990 chunk 382 optimal weight: 10.0000 chunk 374 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 chunk 291 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 372 optimal weight: 0.5980 chunk 329 optimal weight: 0.3980 chunk 80 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 268 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 641 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 ASN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 675 GLN B 901 GLN C 87 ASN C 239 GLN C 317 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.217768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.156332 restraints weight = 50745.924| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.76 r_work: 0.3450 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32200 Z= 0.136 Angle : 0.633 15.311 43888 Z= 0.311 Chirality : 0.046 0.446 4965 Planarity : 0.005 0.056 5648 Dihedral : 7.053 81.200 4946 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 4.26 % Allowed : 18.44 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.26 (0.13), residues: 3963 helix: 1.22 (0.21), residues: 660 sheet: -1.41 (0.18), residues: 825 loop : -2.45 (0.11), residues: 2478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 104 HIS 0.019 0.001 HIS B1048 PHE 0.039 0.001 PHE A 541 TYR 0.020 0.001 TYR C 91 ARG 0.010 0.000 ARG C 188 Details of bonding type rmsd link_NAG-ASN : bond 0.00408 ( 23) link_NAG-ASN : angle 2.66644 ( 69) hydrogen bonds : bond 0.03414 ( 847) hydrogen bonds : angle 4.70960 ( 2271) SS BOND : bond 0.00344 ( 47) SS BOND : angle 1.67517 ( 94) covalent geometry : bond 0.00311 (32130) covalent geometry : angle 0.62021 (43725) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 537 time to evaluate : 4.790 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: A 52 GLN cc_start: 0.8332 (tp40) cc_final: 0.8119 (tp40) REVERT: A 105 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7840 (mt) REVERT: A 129 LYS cc_start: 0.8014 (ttmm) cc_final: 0.7529 (ttmm) REVERT: A 169 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7528 (tm-30) REVERT: A 186 ASN cc_start: 0.6909 (OUTLIER) cc_final: 0.6185 (p0) REVERT: A 188 ARG cc_start: 0.8553 (ptp-170) cc_final: 0.8123 (ptp-170) REVERT: A 189 GLU cc_start: 0.7847 (pm20) cc_final: 0.7473 (pm20) REVERT: A 204 LYS cc_start: 0.8263 (tptm) cc_final: 0.7847 (tptp) REVERT: A 298 GLU cc_start: 0.7425 (tt0) cc_final: 0.7183 (tt0) REVERT: A 537 LYS cc_start: 0.8202 (tttt) cc_final: 0.7943 (tttt) REVERT: A 547 LYS cc_start: 0.8485 (mmtt) cc_final: 0.8235 (mmtm) REVERT: A 563 GLN cc_start: 0.7852 (mm-40) cc_final: 0.7568 (mt0) REVERT: A 574 ASP cc_start: 0.7765 (t70) cc_final: 0.7340 (t0) REVERT: A 577 ARG cc_start: 0.8425 (ttm-80) cc_final: 0.8208 (ttm-80) REVERT: A 596 SER cc_start: 0.8624 (m) cc_final: 0.8213 (p) REVERT: A 602 THR cc_start: 0.8189 (m) cc_final: 0.7923 (p) REVERT: A 658 ASN cc_start: 0.7695 (m-40) cc_final: 0.7166 (p0) REVERT: A 746 SER cc_start: 0.8469 (OUTLIER) cc_final: 0.8182 (t) REVERT: A 749 CYS cc_start: 0.6260 (t) cc_final: 0.5984 (t) REVERT: A 765 ARG cc_start: 0.7866 (ttp-110) cc_final: 0.7571 (ttp-170) REVERT: A 854 LYS cc_start: 0.8028 (ttpp) cc_final: 0.7742 (tttm) REVERT: A 904 TYR cc_start: 0.7460 (m-10) cc_final: 0.6502 (m-10) REVERT: A 950 ASP cc_start: 0.7839 (t70) cc_final: 0.7449 (t70) REVERT: A 964 LYS cc_start: 0.8522 (tmtm) cc_final: 0.8187 (ttmm) REVERT: A 965 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.8278 (mt0) REVERT: A 984 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7704 (tt) REVERT: A 1002 GLN cc_start: 0.7866 (tp-100) cc_final: 0.7484 (tp-100) REVERT: A 1031 GLU cc_start: 0.7862 (tt0) cc_final: 0.7505 (mm-30) REVERT: A 1038 LYS cc_start: 0.8340 (mtmp) cc_final: 0.8107 (mtmm) REVERT: A 1086 LYS cc_start: 0.7658 (mtmm) cc_final: 0.7309 (mtmm) REVERT: A 1091 ARG cc_start: 0.8096 (ttm170) cc_final: 0.7754 (ttm-80) REVERT: A 1097 SER cc_start: 0.8645 (t) cc_final: 0.8311 (p) REVERT: B 33 THR cc_start: 0.8513 (m) cc_final: 0.8105 (t) REVERT: B 41 LYS cc_start: 0.8228 (mtpp) cc_final: 0.7906 (mtpp) REVERT: B 54 LEU cc_start: 0.8560 (mt) cc_final: 0.8325 (mt) REVERT: B 105 ILE cc_start: 0.8419 (mm) cc_final: 0.8186 (mp) REVERT: B 130 VAL cc_start: 0.7854 (t) cc_final: 0.7306 (p) REVERT: B 188 ARG cc_start: 0.8342 (mtt-85) cc_final: 0.8019 (mtt-85) REVERT: B 193 LYS cc_start: 0.8380 (ttpt) cc_final: 0.8054 (ttpt) REVERT: B 200 LYS cc_start: 0.8597 (mttm) cc_final: 0.8371 (mttp) REVERT: B 224 GLU cc_start: 0.7047 (mp0) cc_final: 0.6810 (mp0) REVERT: B 228 ASP cc_start: 0.7887 (t70) cc_final: 0.7349 (t0) REVERT: B 281 GLU cc_start: 0.7305 (pp20) cc_final: 0.7023 (pp20) REVERT: B 319 ARG cc_start: 0.8158 (ptp-110) cc_final: 0.7492 (mtp85) REVERT: B 355 ARG cc_start: 0.4733 (OUTLIER) cc_final: 0.4261 (tmt90) REVERT: B 362 VAL cc_start: 0.6496 (OUTLIER) cc_final: 0.6060 (p) REVERT: B 537 LYS cc_start: 0.8383 (ttpt) cc_final: 0.7965 (ptmm) REVERT: B 544 ASN cc_start: 0.7619 (t0) cc_final: 0.7232 (t0) REVERT: B 558 LYS cc_start: 0.8307 (mtpp) cc_final: 0.7941 (mtpp) REVERT: B 619 GLU cc_start: 0.7456 (tt0) cc_final: 0.7128 (tt0) REVERT: B 747 THR cc_start: 0.7495 (OUTLIER) cc_final: 0.7196 (p) REVERT: B 751 ASN cc_start: 0.8384 (m-40) cc_final: 0.8120 (m110) REVERT: B 765 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7864 (mtm110) REVERT: B 774 GLN cc_start: 0.7800 (mm-40) cc_final: 0.7572 (mm-40) REVERT: B 884 SER cc_start: 0.8747 (t) cc_final: 0.8530 (p) REVERT: B 902 MET cc_start: 0.8063 (tpp) cc_final: 0.7606 (tpp) REVERT: B 933 LYS cc_start: 0.7878 (mtmt) cc_final: 0.7554 (mtpp) REVERT: B 957 GLN cc_start: 0.7207 (OUTLIER) cc_final: 0.6831 (tm130) REVERT: B 1084 ASP cc_start: 0.7697 (p0) cc_final: 0.7193 (p0) REVERT: B 1107 ARG cc_start: 0.7548 (mtt90) cc_final: 0.6449 (mtt180) REVERT: B 1118 ASP cc_start: 0.7566 (t70) cc_final: 0.7132 (t0) REVERT: B 1127 ASP cc_start: 0.7144 (p0) cc_final: 0.6794 (p0) REVERT: C 51 THR cc_start: 0.8456 (OUTLIER) cc_final: 0.8033 (p) REVERT: C 94 SER cc_start: 0.8463 (t) cc_final: 0.8158 (p) REVERT: C 129 LYS cc_start: 0.8281 (ttmt) cc_final: 0.7886 (ttmt) REVERT: C 168 PHE cc_start: 0.8550 (t80) cc_final: 0.7950 (t80) REVERT: C 187 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7389 (mt) REVERT: C 189 GLU cc_start: 0.7493 (mp0) cc_final: 0.7112 (mp0) REVERT: C 190 PHE cc_start: 0.7713 (m-80) cc_final: 0.7507 (m-80) REVERT: C 203 SER cc_start: 0.8738 (t) cc_final: 0.8266 (m) REVERT: C 227 VAL cc_start: 0.8530 (p) cc_final: 0.8280 (t) REVERT: C 228 ASP cc_start: 0.6988 (t70) cc_final: 0.6696 (t0) REVERT: C 537 LYS cc_start: 0.8424 (ttmm) cc_final: 0.8039 (mtpp) REVERT: C 541 PHE cc_start: 0.7637 (p90) cc_final: 0.7250 (p90) REVERT: C 542 ASN cc_start: 0.8330 (t0) cc_final: 0.7944 (t0) REVERT: C 547 LYS cc_start: 0.8131 (mtmm) cc_final: 0.7886 (mttp) REVERT: C 578 ASP cc_start: 0.7998 (t0) cc_final: 0.7429 (t0) REVERT: C 603 ASN cc_start: 0.8309 (t0) cc_final: 0.7882 (t0) REVERT: C 616 ASN cc_start: 0.7147 (t0) cc_final: 0.6934 (t0) REVERT: C 645 THR cc_start: 0.8213 (t) cc_final: 0.7926 (p) REVERT: C 723 THR cc_start: 0.8483 (t) cc_final: 0.8260 (p) REVERT: C 725 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7325 (tm-30) REVERT: C 752 LEU cc_start: 0.8536 (tp) cc_final: 0.8288 (tt) REVERT: C 762 GLN cc_start: 0.7909 (pt0) cc_final: 0.7633 (pt0) REVERT: C 773 GLU cc_start: 0.7955 (tt0) cc_final: 0.7626 (tt0) REVERT: C 821 LEU cc_start: 0.7867 (tp) cc_final: 0.7599 (tt) REVERT: C 934 ILE cc_start: 0.7806 (tt) cc_final: 0.7558 (tt) REVERT: C 979 ASP cc_start: 0.6848 (OUTLIER) cc_final: 0.6438 (m-30) REVERT: C 1014 ARG cc_start: 0.8193 (tpp80) cc_final: 0.7862 (mtm-85) REVERT: C 1017 GLU cc_start: 0.7951 (tm-30) cc_final: 0.7700 (tm-30) REVERT: C 1073 LYS cc_start: 0.8120 (ttpp) cc_final: 0.7861 (ttmm) REVERT: C 1097 SER cc_start: 0.8827 (t) cc_final: 0.8330 (p) REVERT: C 1129 VAL cc_start: 0.8224 (OUTLIER) cc_final: 0.7997 (p) REVERT: D 49 MET cc_start: 0.2428 (ppp) cc_final: 0.1998 (ppp) outliers start: 146 outliers final: 113 residues processed: 653 average time/residue: 0.4701 time to fit residues: 489.8026 Evaluate side-chains 650 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 523 time to evaluate : 3.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1129 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 111 LEU Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 221 CYS Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 129 GLN Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 193 PHE 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 28 ASN Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 247 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 309 optimal weight: 6.9990 chunk 189 optimal weight: 0.0060 chunk 67 optimal weight: 2.9990 chunk 307 optimal weight: 8.9990 chunk 353 optimal weight: 10.0000 chunk 351 optimal weight: 0.0570 chunk 110 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 193 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 287 optimal weight: 3.9990 overall best weight: 1.2120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 ASN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 675 GLN B 901 GLN C 87 ASN ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.217446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.153937 restraints weight = 49836.631| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.81 r_work: 0.3412 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 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 0.055 32200 Z= 0.188 Angle : 0.658 15.878 43888 Z= 0.326 Chirality : 0.047 0.392 4965 Planarity : 0.005 0.046 5648 Dihedral : 7.091 81.056 4943 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Rotamer: Outliers : 3.97 % Allowed : 18.76 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.26 (0.13), residues: 3963 helix: 1.14 (0.21), residues: 661 sheet: -1.42 (0.18), residues: 828 loop : -2.42 (0.11), residues: 2474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 64 HIS 0.022 0.001 HIS B1048 PHE 0.035 0.002 PHE A 541 TYR 0.028 0.001 TYR B1067 ARG 0.009 0.000 ARG C 188 Details of bonding type rmsd link_NAG-ASN : bond 0.00451 ( 23) link_NAG-ASN : angle 2.55754 ( 69) hydrogen bonds : bond 0.03697 ( 847) hydrogen bonds : angle 4.75883 ( 2271) SS BOND : bond 0.00428 ( 47) SS BOND : angle 1.81021 ( 94) covalent geometry : bond 0.00429 (32130) covalent geometry : angle 0.64588 (43725) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 536 time to evaluate : 3.123 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: A 105 ILE cc_start: 0.8259 (OUTLIER) cc_final: 0.7945 (mt) REVERT: A 129 LYS cc_start: 0.8087 (ttmm) cc_final: 0.7638 (ttmm) REVERT: A 168 PHE cc_start: 0.7789 (t80) cc_final: 0.7473 (t80) REVERT: A 186 ASN cc_start: 0.6934 (OUTLIER) cc_final: 0.6179 (p0) REVERT: A 189 GLU cc_start: 0.7817 (pm20) cc_final: 0.7499 (pm20) REVERT: A 204 LYS cc_start: 0.8283 (tptm) cc_final: 0.7850 (tptp) REVERT: A 224 GLU cc_start: 0.8229 (pm20) cc_final: 0.7598 (pt0) REVERT: A 298 GLU cc_start: 0.7486 (tt0) cc_final: 0.7266 (tt0) REVERT: A 547 LYS cc_start: 0.8562 (mmtt) cc_final: 0.8207 (mmtm) REVERT: A 563 GLN cc_start: 0.7871 (mm-40) cc_final: 0.7563 (mt0) REVERT: A 574 ASP cc_start: 0.7852 (t70) cc_final: 0.7465 (t0) REVERT: A 596 SER cc_start: 0.8629 (m) cc_final: 0.8232 (p) REVERT: A 602 THR cc_start: 0.8242 (m) cc_final: 0.7925 (p) REVERT: A 654 GLU cc_start: 0.7870 (pt0) cc_final: 0.7546 (pt0) REVERT: A 658 ASN cc_start: 0.7706 (m-40) cc_final: 0.7191 (p0) REVERT: A 746 SER cc_start: 0.8501 (OUTLIER) cc_final: 0.8239 (t) REVERT: A 749 CYS cc_start: 0.6298 (t) cc_final: 0.6012 (t) REVERT: A 765 ARG cc_start: 0.7978 (ttp-110) cc_final: 0.7681 (ttp-170) REVERT: A 854 LYS cc_start: 0.8164 (ttpp) cc_final: 0.7843 (tttp) REVERT: A 904 TYR cc_start: 0.7482 (m-10) cc_final: 0.6550 (m-10) REVERT: A 950 ASP cc_start: 0.7812 (t70) cc_final: 0.7436 (t70) REVERT: A 964 LYS cc_start: 0.8559 (tmtm) cc_final: 0.8240 (ttmm) REVERT: A 965 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.8293 (mt0) REVERT: A 984 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7695 (tt) REVERT: A 1002 GLN cc_start: 0.7913 (tp-100) cc_final: 0.7523 (tp-100) REVERT: A 1038 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.8100 (mtmm) REVERT: A 1086 LYS cc_start: 0.7635 (mtmm) cc_final: 0.7312 (mtmm) REVERT: A 1091 ARG cc_start: 0.8065 (ttm170) cc_final: 0.7733 (ttm-80) REVERT: A 1097 SER cc_start: 0.8644 (t) cc_final: 0.8308 (p) REVERT: B 33 THR cc_start: 0.8528 (m) cc_final: 0.8122 (t) REVERT: B 41 LYS cc_start: 0.8220 (mtpp) cc_final: 0.7916 (mtpp) REVERT: B 54 LEU cc_start: 0.8550 (mt) cc_final: 0.8311 (mt) REVERT: B 105 ILE cc_start: 0.8406 (mm) cc_final: 0.8182 (mp) REVERT: B 129 LYS cc_start: 0.8618 (ptpt) cc_final: 0.8310 (ptpp) REVERT: B 130 VAL cc_start: 0.7886 (t) cc_final: 0.7333 (p) REVERT: B 188 ARG cc_start: 0.8403 (mtt-85) cc_final: 0.8040 (mtt-85) REVERT: B 193 LYS cc_start: 0.8370 (ttpt) cc_final: 0.8051 (ttpt) REVERT: B 200 LYS cc_start: 0.8614 (mttm) cc_final: 0.8393 (mttp) REVERT: B 224 GLU cc_start: 0.7099 (mp0) cc_final: 0.6856 (mp0) REVERT: B 228 ASP cc_start: 0.7920 (t70) cc_final: 0.7416 (t0) REVERT: B 281 GLU cc_start: 0.7438 (pp20) cc_final: 0.7153 (pp20) REVERT: B 319 ARG cc_start: 0.8169 (ptp-110) cc_final: 0.7533 (mtp85) REVERT: B 328 ARG cc_start: 0.7979 (mmm-85) cc_final: 0.7555 (mmm160) REVERT: B 355 ARG cc_start: 0.4858 (OUTLIER) cc_final: 0.4308 (tmt90) REVERT: B 362 VAL cc_start: 0.6572 (OUTLIER) cc_final: 0.6157 (p) REVERT: B 537 LYS cc_start: 0.8405 (ttpt) cc_final: 0.8006 (ptmm) REVERT: B 544 ASN cc_start: 0.7625 (t0) cc_final: 0.7233 (t0) REVERT: B 558 LYS cc_start: 0.8339 (mtpp) cc_final: 0.7986 (mtpp) REVERT: B 603 ASN cc_start: 0.8367 (t0) cc_final: 0.8111 (t0) REVERT: B 619 GLU cc_start: 0.7615 (tt0) cc_final: 0.7269 (tt0) REVERT: B 737 ASP cc_start: 0.7476 (m-30) cc_final: 0.7116 (m-30) REVERT: B 747 THR cc_start: 0.7383 (OUTLIER) cc_final: 0.7098 (p) REVERT: B 751 ASN cc_start: 0.8415 (m-40) cc_final: 0.8138 (m110) REVERT: B 765 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7865 (mtm110) REVERT: B 774 GLN cc_start: 0.7905 (mm-40) cc_final: 0.7705 (mm-40) REVERT: B 803 SER cc_start: 0.8652 (m) cc_final: 0.8259 (p) REVERT: B 884 SER cc_start: 0.8786 (t) cc_final: 0.8551 (p) REVERT: B 902 MET cc_start: 0.8112 (tpp) cc_final: 0.7624 (tpp) REVERT: B 933 LYS cc_start: 0.7935 (mtmt) cc_final: 0.7616 (mtpp) REVERT: B 957 GLN cc_start: 0.7276 (OUTLIER) cc_final: 0.6908 (tm130) REVERT: B 1084 ASP cc_start: 0.7740 (p0) cc_final: 0.7234 (p0) REVERT: B 1107 ARG cc_start: 0.7558 (mtt90) cc_final: 0.6482 (mtt180) REVERT: B 1118 ASP cc_start: 0.7506 (t70) cc_final: 0.7128 (t0) REVERT: C 62 VAL cc_start: 0.8305 (OUTLIER) cc_final: 0.8002 (m) REVERT: C 87 ASN cc_start: 0.7209 (OUTLIER) cc_final: 0.6514 (p0) REVERT: C 129 LYS cc_start: 0.8279 (ttmt) cc_final: 0.7938 (ttmt) REVERT: C 168 PHE cc_start: 0.8603 (t80) cc_final: 0.8032 (t80) REVERT: C 187 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7422 (mt) REVERT: C 189 GLU cc_start: 0.7478 (mp0) cc_final: 0.7056 (mp0) REVERT: C 190 PHE cc_start: 0.7777 (m-80) cc_final: 0.7536 (m-80) REVERT: C 203 SER cc_start: 0.8740 (t) cc_final: 0.8164 (p) REVERT: C 227 VAL cc_start: 0.8559 (p) cc_final: 0.8303 (t) REVERT: C 228 ASP cc_start: 0.7050 (t70) cc_final: 0.6758 (t0) REVERT: C 269 TYR cc_start: 0.8242 (m-10) cc_final: 0.7496 (m-80) REVERT: C 537 LYS cc_start: 0.8432 (ttmm) cc_final: 0.8225 (mtpt) REVERT: C 541 PHE cc_start: 0.7673 (p90) cc_final: 0.7278 (p90) REVERT: C 542 ASN cc_start: 0.8342 (t0) cc_final: 0.7930 (t0) REVERT: C 547 LYS cc_start: 0.8160 (mtmm) cc_final: 0.7926 (mttp) REVERT: C 578 ASP cc_start: 0.7941 (t0) cc_final: 0.7585 (t0) REVERT: C 603 ASN cc_start: 0.8337 (t0) cc_final: 0.7904 (t0) REVERT: C 616 ASN cc_start: 0.7417 (t0) cc_final: 0.7194 (t0) REVERT: C 619 GLU cc_start: 0.7795 (tt0) cc_final: 0.7492 (tt0) REVERT: C 645 THR cc_start: 0.8208 (t) cc_final: 0.7951 (p) REVERT: C 655 TYR cc_start: 0.8434 (t80) cc_final: 0.8212 (t80) REVERT: C 723 THR cc_start: 0.8492 (t) cc_final: 0.8272 (p) REVERT: C 725 GLU cc_start: 0.7793 (tm-30) cc_final: 0.7338 (tm-30) REVERT: C 752 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8359 (tt) REVERT: C 762 GLN cc_start: 0.7983 (pt0) cc_final: 0.7713 (pt0) REVERT: C 773 GLU cc_start: 0.8002 (tt0) cc_final: 0.7640 (tt0) REVERT: C 821 LEU cc_start: 0.7931 (tp) cc_final: 0.7664 (tt) REVERT: C 902 MET cc_start: 0.8152 (mmm) cc_final: 0.7555 (tpt) REVERT: C 934 ILE cc_start: 0.7904 (tt) cc_final: 0.7650 (tt) REVERT: C 979 ASP cc_start: 0.6899 (OUTLIER) cc_final: 0.6265 (m-30) REVERT: C 983 ARG cc_start: 0.7586 (ptp-110) cc_final: 0.7225 (ptp-110) REVERT: C 994 ASP cc_start: 0.7939 (t0) cc_final: 0.7558 (t0) REVERT: C 997 ILE cc_start: 0.8607 (mm) cc_final: 0.8276 (mt) REVERT: C 1014 ARG cc_start: 0.8210 (tpp80) cc_final: 0.7816 (mtm-85) REVERT: C 1073 LYS cc_start: 0.8125 (ttpp) cc_final: 0.7875 (ttmm) REVERT: C 1097 SER cc_start: 0.8834 (t) cc_final: 0.8315 (p) REVERT: C 1129 VAL cc_start: 0.8227 (OUTLIER) cc_final: 0.8013 (p) REVERT: D 49 MET cc_start: 0.2334 (ppp) cc_final: 0.1885 (ppp) REVERT: E 238 MET cc_start: -0.3283 (mtm) cc_final: -0.3500 (mtm) outliers start: 136 outliers final: 115 residues processed: 643 average time/residue: 0.4738 time to fit residues: 480.1609 Evaluate side-chains 658 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 526 time to evaluate : 3.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1129 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 128 VAL Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 221 CYS Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 193 PHE Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain G residue 28 ASN Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 247 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 282 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 chunk 189 optimal weight: 0.0170 chunk 32 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 118 optimal weight: 3.9990 chunk 199 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 148 optimal weight: 10.0000 chunk 350 optimal weight: 50.0000 chunk 357 optimal weight: 1.9990 overall best weight: 0.6220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 ASN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 901 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN ** C 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.217600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.153936 restraints weight = 49945.892| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.83 r_work: 0.3412 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.147 32200 Z= 0.209 Angle : 0.796 59.200 43888 Z= 0.427 Chirality : 0.047 0.484 4965 Planarity : 0.005 0.145 5648 Dihedral : 7.060 81.055 4941 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 4.09 % Allowed : 19.00 % Favored : 76.92 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.25 (0.13), residues: 3963 helix: 1.16 (0.21), residues: 661 sheet: -1.45 (0.17), residues: 836 loop : -2.41 (0.11), residues: 2466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 104 HIS 0.019 0.001 HIS B1048 PHE 0.031 0.002 PHE A 643 TYR 0.026 0.001 TYR B1067 ARG 0.010 0.000 ARG C 188 Details of bonding type rmsd link_NAG-ASN : bond 0.00433 ( 23) link_NAG-ASN : angle 2.55311 ( 69) hydrogen bonds : bond 0.03642 ( 847) hydrogen bonds : angle 4.75910 ( 2271) SS BOND : bond 0.00429 ( 47) SS BOND : angle 2.47621 ( 94) covalent geometry : bond 0.00450 (32130) covalent geometry : angle 0.78232 (43725) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19988.79 seconds wall clock time: 349 minutes 27.98 seconds (20967.98 seconds total)