Starting phenix.real_space_refine on Sun Jun 22 21:12:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7woq_32655/06_2025/7woq_32655.cif Found real_map, /net/cci-nas-00/data/ceres_data/7woq_32655/06_2025/7woq_32655.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/7woq_32655/06_2025/7woq_32655.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7woq_32655/06_2025/7woq_32655.map" model { file = "/net/cci-nas-00/data/ceres_data/7woq_32655/06_2025/7woq_32655.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7woq_32655/06_2025/7woq_32655.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= 0.002 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 119 5.16 5 C 16756 2.51 5 N 4322 2.21 5 O 5024 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 26221 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" 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: "B" 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: "C" 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: "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: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 14.22, per 1000 atoms: 0.54 Number of scatterers: 26221 At special positions: 0 Unit cell: (137.256, 134.064, 200.032, 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 119 16.00 O 5024 8.00 N 4322 7.00 C 16756 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, 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=2.04 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 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 616 " " NAG A1304 " - " ASN A 709 " " NAG A1305 " - " ASN A 717 " " NAG A1306 " - " ASN A 801 " " NAG A1307 " - " ASN A1098 " " NAG A1308 " - " ASN A1134 " " NAG A1309 " - " ASN A 61 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 717 " " NAG B1306 " - " ASN B 801 " " NAG B1307 " - " ASN B1074 " " NAG B1308 " - " ASN B1098 " " NAG B1309 " - " ASN B1134 " " NAG B1310 " - " ASN B 709 " " NAG C1301 " - " ASN C 234 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C 717 " " NAG C1307 " - " ASN C 801 " " NAG C1308 " - " ASN C1098 " " NAG C1309 " - " ASN C1134 " Time building additional restraints: 5.70 Conformation dependent library (CDL) restraints added in 3.1 seconds 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6220 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 52 sheets defined 20.5% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.04 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.214A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 removed outlier: 4.157A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 756 Processing helix chain 'A' and resid 761 through 782 removed outlier: 3.772A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) removed outlier: 3.894A 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 897 through 907 removed outlier: 4.029A pdb=" N ASN A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 939 removed outlier: 4.422A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.530A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 983 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.177A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU A1001 " --> pdb=" O ILE A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1147 removed outlier: 3.838A pdb=" N ASP A1146 " --> pdb=" O PRO A1143 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N SER A1147 " --> pdb=" O GLU A1144 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1143 through 1147' Processing helix chain 'B' and resid 294 through 302 Processing helix chain 'B' and resid 336 through 341 removed outlier: 4.137A pdb=" N ASP B 339 " --> pdb=" O CYS B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 Processing helix chain 'B' and resid 383 through 388 removed outlier: 3.862A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.606A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.694A 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 747 through 755 removed outlier: 3.582A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 778 removed outlier: 3.836A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 848 through 855 removed outlier: 3.608A pdb=" N LYS B 854 " --> pdb=" O ILE B 850 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 882 Processing helix chain 'B' and resid 897 through 907 removed outlier: 3.591A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG B 905 " --> pdb=" O GLN B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 938 removed outlier: 3.533A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.571A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN B 965 " --> pdb=" O THR B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 981 removed outlier: 4.327A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N PHE B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 976 through 981' Processing helix chain 'B' and resid 985 through 993 removed outlier: 4.259A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 1033 removed outlier: 3.606A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.905A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 367 through 371 removed outlier: 4.075A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.504A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 444 through 448 removed outlier: 3.855A pdb=" N GLY C 447 " --> pdb=" O LYS C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.693A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 783 removed outlier: 3.581A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.933A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 removed outlier: 3.502A pdb=" N ASN C 907 " --> pdb=" O ALA C 903 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY C 908 " --> pdb=" O TYR C 904 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY C 910 " --> pdb=" O PHE C 906 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 4.052A pdb=" N GLY C 932 " --> pdb=" O ASN C 928 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LYS C 933 " --> pdb=" O SER C 929 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.602A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 983 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.487A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 3.993A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.930A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 224 through 229 removed outlier: 6.365A pdb=" N SER A 203 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL A 227 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 201 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU A 229 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR A 198 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR A 91 " --> pdb=" O GLY A 268 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 120 through 122 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA8, first strand: chain 'A' and resid 318 through 319 Processing sheet with id=AA9, first strand: chain 'A' and resid 325 through 326 removed outlier: 3.748A pdb=" N PHE A 543 " --> pdb=" O LEU A 546 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.184A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 394 through 400 Processing sheet with id=AB3, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.773A 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: 5.762A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 712 through 718 removed outlier: 6.877A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 721 through 728 removed outlier: 7.156A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 735 Processing sheet with id=AB8, first strand: chain 'A' and resid 788 through 789 removed outlier: 5.503A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AC1, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.267A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU B 224 " --> pdb=" O SER B 203 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ILE B 201 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.516A pdb=" N ARG C 567 " --> pdb=" O PHE B 43 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.672A pdb=" N LYS B 278 " --> pdb=" O ASP B 287 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AC5, first strand: chain 'B' and resid 93 through 96 removed outlier: 3.925A pdb=" N SER B 94 " --> pdb=" O ARG B 188 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU B 96 " --> pdb=" O ASN B 186 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.989A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 325 through 326 removed outlier: 3.564A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 356 through 358 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 660 removed outlier: 5.709A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 712 through 713 Processing sheet with id=AD2, first strand: chain 'B' and resid 717 through 718 Processing sheet with id=AD3, first strand: chain 'B' and resid 721 through 728 removed outlier: 3.767A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 735 removed outlier: 4.533A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 788 through 789 removed outlier: 5.694A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.876A pdb=" N SER B1123 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD8, first strand: chain 'C' and resid 28 through 29 removed outlier: 3.524A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.921A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE2, first strand: chain 'C' and resid 90 through 93 removed outlier: 7.614A pdb=" N ILE C 201 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER C 203 " --> pdb=" O GLU C 224 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU C 224 " --> pdb=" O SER C 203 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 128 through 129 Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.979A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 325 through 326 Processing sheet with id=AE6, first strand: chain 'C' and resid 376 through 377 removed outlier: 3.863A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG C 509 " --> pdb=" O TRP C 436 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.323A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 712 through 722 removed outlier: 6.791A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 725 through 728 Processing sheet with id=AF2, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.294A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1121 Processing sheet with id=AF4, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF5, first strand: chain 'D' and resid 47 through 50 removed outlier: 6.165A pdb=" N LEU D 48 " --> pdb=" O GLN D 39 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N GLN D 39 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE D 50 " --> pdb=" O TRP D 37 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 64 through 69 removed outlier: 5.425A pdb=" N SER D 65 " --> pdb=" O THR D 76 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER D 67 " --> pdb=" O SER D 74 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 172 through 176 removed outlier: 6.127A pdb=" N TRP D 173 " --> pdb=" O ARG D 164 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ARG D 164 " --> pdb=" O TRP D 173 " (cutoff:3.500A) 750 hydrogen bonds defined for protein. 2004 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: 9.41 Time building geometry restraints manager: 6.91 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: 7262 1.33 - 1.45: 4990 1.45 - 1.57: 14433 1.57 - 1.70: 0 1.70 - 1.82: 150 Bond restraints: 26835 Sorted by residual: bond pdb=" CA ASN A 30 " pdb=" C ASN A 30 " ideal model delta sigma weight residual 1.523 1.421 0.102 1.28e-02 6.10e+03 6.37e+01 bond pdb=" CA ASN A 801 " pdb=" C ASN A 801 " ideal model delta sigma weight residual 1.522 1.468 0.054 1.14e-02 7.69e+03 2.24e+01 bond pdb=" CA ALA B 27 " pdb=" C ALA B 27 " ideal model delta sigma weight residual 1.523 1.474 0.049 1.34e-02 5.57e+03 1.36e+01 bond pdb=" CA ASN A 331 " pdb=" C ASN A 331 " ideal model delta sigma weight residual 1.524 1.478 0.046 1.28e-02 6.10e+03 1.32e+01 bond pdb=" N TYR B 28 " pdb=" CA TYR B 28 " ideal model delta sigma weight residual 1.458 1.416 0.042 1.16e-02 7.43e+03 1.28e+01 ... (remaining 26830 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 35818 1.79 - 3.59: 637 3.59 - 5.38: 64 5.38 - 7.18: 9 7.18 - 8.97: 5 Bond angle restraints: 36533 Sorted by residual: angle pdb=" C ASN A1135 " pdb=" N THR A1136 " pdb=" CA THR A1136 " ideal model delta sigma weight residual 120.82 129.70 -8.88 1.47e+00 4.63e-01 3.65e+01 angle pdb=" C PHE A 329 " pdb=" N PRO A 330 " pdb=" CA PRO A 330 " ideal model delta sigma weight residual 120.21 114.92 5.29 9.60e-01 1.09e+00 3.04e+01 angle pdb=" C ASN A 331 " pdb=" CA ASN A 331 " pdb=" CB ASN A 331 " ideal model delta sigma weight residual 110.92 103.52 7.40 1.59e+00 3.96e-01 2.16e+01 angle pdb=" N ASN B 30 " pdb=" CA ASN B 30 " pdb=" C ASN B 30 " ideal model delta sigma weight residual 109.94 117.04 -7.10 1.57e+00 4.06e-01 2.04e+01 angle pdb=" C ASN B 30 " pdb=" CA ASN B 30 " pdb=" CB ASN B 30 " ideal model delta sigma weight residual 112.63 103.66 8.97 2.16e+00 2.14e-01 1.73e+01 ... (remaining 36528 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 15553 17.27 - 34.54: 655 34.54 - 51.82: 110 51.82 - 69.09: 21 69.09 - 86.36: 2 Dihedral angle restraints: 16341 sinusoidal: 6664 harmonic: 9677 Sorted by residual: dihedral pdb=" CA ASN C1135 " pdb=" CB ASN C1135 " pdb=" CG ASN C1135 " pdb=" OD1 ASN C1135 " ideal model delta sinusoidal sigma weight residual 120.00 -173.94 -66.06 2 2.00e+01 2.50e-03 1.00e+01 dihedral pdb=" C ASN A 331 " pdb=" N ASN A 331 " pdb=" CA ASN A 331 " pdb=" CB ASN A 331 " ideal model delta harmonic sigma weight residual -122.60 -114.69 -7.91 0 2.50e+00 1.60e-01 1.00e+01 dihedral pdb=" CA ALA B 570 " pdb=" C ALA B 570 " pdb=" N ASP B 571 " pdb=" CA ASP B 571 " ideal model delta harmonic sigma weight residual 180.00 164.23 15.77 0 5.00e+00 4.00e-02 9.95e+00 ... (remaining 16338 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.136: 4195 0.136 - 0.272: 16 0.272 - 0.408: 3 0.408 - 0.544: 1 0.544 - 0.680: 1 Chirality restraints: 4216 Sorted by residual: chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.72 -0.68 2.00e-01 2.50e+01 1.16e+01 chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B 282 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.24e+00 chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 282 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.02e+00 ... (remaining 4213 not shown) Planarity restraints: 4725 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1308 " 0.355 2.00e-02 2.50e+03 3.06e-01 1.17e+03 pdb=" C7 NAG A1308 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG A1308 " 0.092 2.00e-02 2.50e+03 pdb=" N2 NAG A1308 " -0.542 2.00e-02 2.50e+03 pdb=" O7 NAG A1308 " 0.178 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1305 " -0.352 2.00e-02 2.50e+03 3.04e-01 1.15e+03 pdb=" C7 NAG C1305 " 0.083 2.00e-02 2.50e+03 pdb=" C8 NAG C1305 " -0.116 2.00e-02 2.50e+03 pdb=" N2 NAG C1305 " 0.541 2.00e-02 2.50e+03 pdb=" O7 NAG C1305 " -0.155 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1310 " 0.349 2.00e-02 2.50e+03 3.00e-01 1.13e+03 pdb=" C7 NAG B1310 " -0.082 2.00e-02 2.50e+03 pdb=" C8 NAG B1310 " 0.123 2.00e-02 2.50e+03 pdb=" N2 NAG B1310 " -0.535 2.00e-02 2.50e+03 pdb=" O7 NAG B1310 " 0.146 2.00e-02 2.50e+03 ... (remaining 4722 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2830 2.75 - 3.29: 26309 3.29 - 3.83: 42867 3.83 - 4.36: 49414 4.36 - 4.90: 85041 Nonbonded interactions: 206461 Sorted by model distance: nonbonded pdb=" OG SER D 91 " pdb=" OE1 GLN D 227 " model vdw 2.216 3.040 nonbonded pdb=" OE1 GLN A 52 " pdb=" OG1 THR A 274 " model vdw 2.217 3.040 nonbonded pdb=" O GLU C 661 " pdb=" OH TYR C 695 " model vdw 2.229 3.040 nonbonded pdb=" OE1 GLN B 52 " pdb=" OG1 THR B 274 " model vdw 2.236 3.040 nonbonded pdb=" OG1 THR B 719 " pdb=" O VAL B1068 " model vdw 2.236 3.040 ... (remaining 206456 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 1309)) selection = (chain 'B' and (resid 26 through 1147 or resid 1301 through 1309)) selection = (chain 'C' and (resid 26 through 243 or resid 262 through 1147 or resid 1301 thr \ ough 1309)) } 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: 1.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.910 Check model and map are aligned: 0.170 Set scattering table: 0.230 Process input model: 54.580 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 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 0.102 26904 Z= 0.199 Angle : 0.572 8.975 36699 Z= 0.322 Chirality : 0.046 0.680 4216 Planarity : 0.016 0.306 4697 Dihedral : 9.328 86.360 9998 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.75 % Favored : 91.94 % Rotamer: Outliers : 5.15 % Allowed : 8.37 % Favored : 86.49 % 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: -4.15 (0.12), residues: 3276 helix: -0.87 (0.19), residues: 639 sheet: -2.88 (0.18), residues: 595 loop : -3.56 (0.11), residues: 2042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 162 HIS 0.002 0.000 HIS C 519 PHE 0.010 0.001 PHE C 375 TYR 0.011 0.001 TYR C1067 ARG 0.001 0.000 ARG A1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00537 ( 28) link_NAG-ASN : angle 2.14630 ( 84) hydrogen bonds : bond 0.16242 ( 750) hydrogen bonds : angle 6.68850 ( 2004) SS BOND : bond 0.00151 ( 41) SS BOND : angle 0.59250 ( 82) covalent geometry : bond 0.00320 (26835) covalent geometry : angle 0.56280 (36533) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 884 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 737 time to evaluate : 2.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.7624 (p0) cc_final: 0.7316 (p0) REVERT: A 43 PHE cc_start: 0.8230 (t80) cc_final: 0.8005 (t80) REVERT: A 46 SER cc_start: 0.8974 (m) cc_final: 0.8726 (p) REVERT: A 118 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7278 (pp) REVERT: A 186 ASN cc_start: 0.7068 (p0) cc_final: 0.6674 (p0) REVERT: A 208 ILE cc_start: 0.8579 (pp) cc_final: 0.8376 (pt) REVERT: A 239 GLN cc_start: 0.7272 (tp40) cc_final: 0.6972 (tp40) REVERT: A 241 LEU cc_start: 0.7851 (pt) cc_final: 0.7389 (pp) REVERT: A 307 THR cc_start: 0.8400 (m) cc_final: 0.7929 (p) REVERT: A 528 LYS cc_start: 0.7364 (tptp) cc_final: 0.7158 (tptp) REVERT: A 558 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8273 (mmmm) REVERT: A 563 GLN cc_start: 0.6738 (mt0) cc_final: 0.6380 (mt0) REVERT: A 574 ASP cc_start: 0.6988 (t70) cc_final: 0.6608 (t0) REVERT: A 581 THR cc_start: 0.8154 (t) cc_final: 0.7950 (t) REVERT: A 602 THR cc_start: 0.8516 (m) cc_final: 0.8245 (p) REVERT: A 615 VAL cc_start: 0.8521 (t) cc_final: 0.8118 (m) REVERT: A 655 TYR cc_start: 0.8202 (t80) cc_final: 0.7935 (t80) REVERT: A 663 ASP cc_start: 0.7739 (t70) cc_final: 0.7354 (t0) REVERT: A 664 ILE cc_start: 0.8743 (mt) cc_final: 0.8256 (mm) REVERT: A 675 GLN cc_start: 0.7081 (mm-40) cc_final: 0.6750 (mm-40) REVERT: A 703 ASN cc_start: 0.7907 (t0) cc_final: 0.7623 (t0) REVERT: A 803 SER cc_start: 0.8156 (m) cc_final: 0.7936 (p) REVERT: A 819 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7390 (mt-10) REVERT: A 820 ASP cc_start: 0.7516 (m-30) cc_final: 0.7259 (m-30) REVERT: A 851 CYS cc_start: 0.8033 (t) cc_final: 0.7679 (t) REVERT: A 854 LYS cc_start: 0.8167 (ttpp) cc_final: 0.7966 (tttm) REVERT: A 868 GLU cc_start: 0.7530 (tp30) cc_final: 0.7242 (tp30) REVERT: A 933 LYS cc_start: 0.8452 (mtmt) cc_final: 0.8142 (mttp) REVERT: A 985 ASP cc_start: 0.7337 (p0) cc_final: 0.7031 (p0) REVERT: A 1017 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7572 (tm-30) REVERT: A 1048 HIS cc_start: 0.8225 (t70) cc_final: 0.7886 (t-170) REVERT: A 1050 MET cc_start: 0.7243 (mtm) cc_final: 0.6902 (mtm) REVERT: A 1072 GLU cc_start: 0.8390 (pm20) cc_final: 0.7927 (pm20) REVERT: A 1135 ASN cc_start: 0.8183 (t0) cc_final: 0.7936 (t0) REVERT: A 1144 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7617 (mp0) REVERT: B 129 LYS cc_start: 0.8448 (ttmt) cc_final: 0.7603 (tppt) REVERT: B 187 LEU cc_start: 0.7933 (tp) cc_final: 0.7598 (mt) REVERT: B 204 LYS cc_start: 0.7539 (tptp) cc_final: 0.7176 (tptp) REVERT: B 280 ASN cc_start: 0.8334 (t0) cc_final: 0.8122 (t0) REVERT: B 281 GLU cc_start: 0.7201 (pp20) cc_final: 0.6956 (pp20) REVERT: B 297 SER cc_start: 0.8216 (m) cc_final: 0.7926 (p) REVERT: B 307 THR cc_start: 0.8753 (m) cc_final: 0.8369 (p) REVERT: B 319 ARG cc_start: 0.7390 (ttm110) cc_final: 0.6871 (ptp-110) REVERT: B 362 VAL cc_start: 0.8287 (OUTLIER) cc_final: 0.7786 (m) REVERT: B 406 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7342 (mt-10) REVERT: B 542 ASN cc_start: 0.8120 (t0) cc_final: 0.7899 (t0) REVERT: B 557 LYS cc_start: 0.8340 (mttm) cc_final: 0.8105 (mttm) REVERT: B 580 GLN cc_start: 0.8198 (mm110) cc_final: 0.7947 (mm-40) REVERT: B 586 ASP cc_start: 0.7483 (t0) cc_final: 0.7266 (t0) REVERT: B 674 TYR cc_start: 0.8018 (t80) cc_final: 0.7639 (t80) REVERT: B 747 THR cc_start: 0.8276 (p) cc_final: 0.7566 (p) REVERT: B 754 LEU cc_start: 0.8895 (mt) cc_final: 0.8670 (mm) REVERT: B 773 GLU cc_start: 0.6990 (tm-30) cc_final: 0.6436 (tm-30) REVERT: B 776 LYS cc_start: 0.8679 (ttpp) cc_final: 0.8218 (tptm) REVERT: B 780 GLU cc_start: 0.7006 (pt0) cc_final: 0.6737 (pt0) REVERT: B 795 LYS cc_start: 0.8590 (mttt) cc_final: 0.8384 (mttm) REVERT: B 821 LEU cc_start: 0.8647 (tp) cc_final: 0.8204 (tp) REVERT: B 851 CYS cc_start: 0.7665 (t) cc_final: 0.7365 (t) REVERT: B 856 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8667 (mmtm) REVERT: B 914 ASN cc_start: 0.7937 (p0) cc_final: 0.7267 (p0) REVERT: B 949 GLN cc_start: 0.8216 (mm110) cc_final: 0.7673 (mm-40) REVERT: B 953 ASN cc_start: 0.8268 (m-40) cc_final: 0.7775 (m-40) REVERT: B 960 ASN cc_start: 0.7724 (m110) cc_final: 0.7434 (t0) REVERT: B 964 LYS cc_start: 0.8180 (mtmp) cc_final: 0.7836 (mtmm) REVERT: B 979 ASP cc_start: 0.7866 (m-30) cc_final: 0.7425 (m-30) REVERT: B 991 VAL cc_start: 0.8878 (t) cc_final: 0.8098 (p) REVERT: B 1097 SER cc_start: 0.9232 (t) cc_final: 0.9018 (p) REVERT: B 1123 SER cc_start: 0.7890 (t) cc_final: 0.7575 (p) REVERT: C 54 LEU cc_start: 0.8543 (mt) cc_final: 0.8076 (mt) REVERT: C 91 TYR cc_start: 0.7331 (t80) cc_final: 0.6335 (t80) REVERT: C 92 PHE cc_start: 0.7558 (t80) cc_final: 0.7011 (t80) REVERT: C 120 VAL cc_start: 0.8099 (m) cc_final: 0.7871 (p) REVERT: C 133 PHE cc_start: 0.7496 (p90) cc_final: 0.7159 (p90) REVERT: C 224 GLU cc_start: 0.8272 (pm20) cc_final: 0.7832 (pm20) REVERT: C 235 ILE cc_start: 0.8243 (mt) cc_final: 0.7853 (mm) REVERT: C 237 ARG cc_start: 0.7581 (mtm180) cc_final: 0.7268 (ptt180) REVERT: C 265 TYR cc_start: 0.7049 (p90) cc_final: 0.6826 (p90) REVERT: C 355 ARG cc_start: 0.8292 (ttt90) cc_final: 0.7842 (ttt-90) REVERT: C 378 LYS cc_start: 0.7449 (mmmm) cc_final: 0.7173 (mmmm) REVERT: C 546 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7508 (tp) REVERT: C 560 LEU cc_start: 0.8183 (mt) cc_final: 0.7506 (mp) REVERT: C 562 PHE cc_start: 0.7728 (p90) cc_final: 0.7390 (p90) REVERT: C 564 GLN cc_start: 0.6365 (mp-120) cc_final: 0.6093 (mp10) REVERT: C 574 ASP cc_start: 0.6799 (t70) cc_final: 0.6220 (t0) REVERT: C 615 VAL cc_start: 0.8413 (t) cc_final: 0.8178 (m) REVERT: C 663 ASP cc_start: 0.7719 (t70) cc_final: 0.7478 (t0) REVERT: C 693 ILE cc_start: 0.8725 (pt) cc_final: 0.8495 (pt) REVERT: C 732 THR cc_start: 0.8945 (OUTLIER) cc_final: 0.8527 (p) REVERT: C 772 VAL cc_start: 0.8603 (t) cc_final: 0.8287 (m) REVERT: C 773 GLU cc_start: 0.7246 (tt0) cc_final: 0.6777 (tt0) REVERT: C 776 LYS cc_start: 0.8440 (tmmt) cc_final: 0.8135 (ttmm) REVERT: C 777 ASN cc_start: 0.7871 (m-40) cc_final: 0.7574 (m110) REVERT: C 797 PHE cc_start: 0.8037 (m-10) cc_final: 0.7826 (m-80) REVERT: C 803 SER cc_start: 0.8725 (m) cc_final: 0.8392 (p) REVERT: C 821 LEU cc_start: 0.8418 (tp) cc_final: 0.7947 (tt) REVERT: C 949 GLN cc_start: 0.7888 (mm110) cc_final: 0.7438 (mm-40) REVERT: C 953 ASN cc_start: 0.7906 (m-40) cc_final: 0.7594 (m110) REVERT: C 964 LYS cc_start: 0.8404 (tmtm) cc_final: 0.8121 (ttmm) REVERT: C 965 GLN cc_start: 0.7809 (mt0) cc_final: 0.7586 (tt0) REVERT: C 970 PHE cc_start: 0.8406 (m-10) cc_final: 0.8185 (m-10) REVERT: C 976 VAL cc_start: 0.8791 (t) cc_final: 0.8462 (t) REVERT: C 979 ASP cc_start: 0.7692 (m-30) cc_final: 0.7408 (m-30) REVERT: C 1072 GLU cc_start: 0.8150 (pm20) cc_final: 0.7936 (pm20) REVERT: C 1111 GLU cc_start: 0.7411 (tt0) cc_final: 0.7168 (tt0) REVERT: C 1118 ASP cc_start: 0.7428 (t70) cc_final: 0.7012 (t0) REVERT: C 1136 THR cc_start: 0.8422 (OUTLIER) cc_final: 0.8140 (p) REVERT: C 1138 TYR cc_start: 0.7143 (t80) cc_final: 0.6899 (t80) outliers start: 147 outliers final: 60 residues processed: 855 average time/residue: 0.4034 time to fit residues: 525.3957 Evaluate side-chains 621 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 554 time to evaluate : 2.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 208 ILE 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 511 VAL Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 856 LYS Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 194 ASN Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 234 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 279 optimal weight: 4.9990 chunk 250 optimal weight: 0.9980 chunk 139 optimal weight: 9.9990 chunk 85 optimal weight: 1.9990 chunk 169 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 259 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 193 optimal weight: 4.9990 chunk 300 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 173 GLN A 181 GLN A 186 ASN A 245 HIS A 414 GLN ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 GLN ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A 784 GLN A 853 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN A1010 GLN A1011 GLN A1048 HIS ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN B 99 ASN B 164 ASN B 205 HIS B 334 ASN B 370 ASN B 409 GLN B 540 ASN B 580 GLN B 751 ASN B 784 GLN B 853 GLN B 872 GLN B 895 GLN B 907 ASN B 913 GLN B 914 ASN B 935 GLN B 957 GLN B 960 ASN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN C 81 ASN C 121 ASN ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN C 186 ASN C 360 ASN C 394 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 ASN C 540 ASN C 564 GLN C 690 GLN C 784 GLN C 853 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN C1002 GLN C1005 GLN C1010 GLN C1011 GLN ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN D 40 GLN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 GLN D 165 GLN D 202 ASN D 207 GLN Total number of N/Q/H flips: 60 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.158687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.116630 restraints weight = 45466.549| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 3.22 r_work: 0.3233 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.146 26904 Z= 0.332 Angle : 0.748 9.662 36699 Z= 0.378 Chirality : 0.050 0.337 4216 Planarity : 0.005 0.051 4697 Dihedral : 7.477 59.424 4312 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.07 % Favored : 89.93 % Rotamer: Outliers : 5.67 % Allowed : 14.70 % Favored : 79.63 % 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: -3.29 (0.13), residues: 3276 helix: 0.03 (0.20), residues: 663 sheet: -2.12 (0.20), residues: 595 loop : -3.17 (0.12), residues: 2018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 104 HIS 0.008 0.001 HIS C1048 PHE 0.026 0.002 PHE C 375 TYR 0.028 0.002 TYR C1067 ARG 0.010 0.001 ARG B 188 Details of bonding type rmsd link_NAG-ASN : bond 0.00505 ( 28) link_NAG-ASN : angle 2.79845 ( 84) hydrogen bonds : bond 0.04593 ( 750) hydrogen bonds : angle 5.20182 ( 2004) SS BOND : bond 0.00425 ( 41) SS BOND : angle 2.13945 ( 82) covalent geometry : bond 0.00713 (26835) covalent geometry : angle 0.73052 (36533) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 573 time to evaluate : 2.862 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: A 46 SER cc_start: 0.9217 (m) cc_final: 0.8997 (p) REVERT: A 64 TRP cc_start: 0.8386 (t60) cc_final: 0.7917 (t-100) REVERT: A 66 HIS cc_start: 0.8089 (OUTLIER) cc_final: 0.7616 (m90) REVERT: A 97 LYS cc_start: 0.8408 (tppt) cc_final: 0.8022 (tppt) REVERT: A 102 ARG cc_start: 0.8700 (mtm180) cc_final: 0.8300 (mtm-85) REVERT: A 104 TRP cc_start: 0.8729 (m-90) cc_final: 0.8170 (m-90) REVERT: A 109 THR cc_start: 0.8651 (p) cc_final: 0.8364 (t) REVERT: A 121 ASN cc_start: 0.7715 (m-40) cc_final: 0.7282 (p0) REVERT: A 132 GLU cc_start: 0.6812 (pm20) cc_final: 0.6064 (pm20) REVERT: A 215 ASP cc_start: 0.7992 (m-30) cc_final: 0.7712 (m-30) REVERT: A 224 GLU cc_start: 0.8122 (mp0) cc_final: 0.7865 (mp0) REVERT: A 269 TYR cc_start: 0.8629 (m-80) cc_final: 0.7928 (m-80) REVERT: A 297 SER cc_start: 0.8683 (m) cc_final: 0.8274 (p) REVERT: A 306 PHE cc_start: 0.8836 (m-10) cc_final: 0.8546 (m-80) REVERT: A 307 THR cc_start: 0.8746 (m) cc_final: 0.8465 (p) REVERT: A 386 LYS cc_start: 0.7769 (OUTLIER) cc_final: 0.7402 (mttp) REVERT: A 569 ILE cc_start: 0.8627 (pt) cc_final: 0.8277 (mp) REVERT: A 602 THR cc_start: 0.8691 (OUTLIER) cc_final: 0.8456 (p) REVERT: A 663 ASP cc_start: 0.8041 (t70) cc_final: 0.7554 (t0) REVERT: A 664 ILE cc_start: 0.8905 (mt) cc_final: 0.8459 (mm) REVERT: A 675 GLN cc_start: 0.7610 (mm-40) cc_final: 0.7222 (mm-40) REVERT: A 697 MET cc_start: 0.8220 (mtp) cc_final: 0.7783 (mtp) REVERT: A 779 GLN cc_start: 0.8704 (tt0) cc_final: 0.8419 (tt0) REVERT: A 790 LYS cc_start: 0.8194 (mppt) cc_final: 0.7796 (mppt) REVERT: A 803 SER cc_start: 0.8614 (m) cc_final: 0.8364 (p) REVERT: A 851 CYS cc_start: 0.8521 (t) cc_final: 0.8154 (t) REVERT: A 855 PHE cc_start: 0.8400 (m-80) cc_final: 0.7941 (m-80) REVERT: A 868 GLU cc_start: 0.8462 (tp30) cc_final: 0.8167 (tp30) REVERT: A 869 MET cc_start: 0.8796 (mtt) cc_final: 0.8586 (mtm) REVERT: A 933 LYS cc_start: 0.8622 (mtmt) cc_final: 0.8355 (mttp) REVERT: A 994 ASP cc_start: 0.7748 (t70) cc_final: 0.7455 (t70) REVERT: A 995 ARG cc_start: 0.8581 (mtm-85) cc_final: 0.8340 (ttp-110) REVERT: A 1001 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8864 (tp) REVERT: A 1002 GLN cc_start: 0.8307 (tp40) cc_final: 0.8096 (tp40) REVERT: A 1017 GLU cc_start: 0.8378 (tm-30) cc_final: 0.8100 (tm-30) REVERT: A 1050 MET cc_start: 0.8319 (mtm) cc_final: 0.7965 (mtp) REVERT: A 1107 ARG cc_start: 0.7971 (mtt90) cc_final: 0.7723 (mtt90) REVERT: A 1139 ASP cc_start: 0.7906 (p0) cc_final: 0.7659 (p0) REVERT: B 52 GLN cc_start: 0.8171 (tm-30) cc_final: 0.7693 (tm-30) REVERT: B 95 ILE cc_start: 0.8697 (mt) cc_final: 0.8001 (tt) REVERT: B 120 VAL cc_start: 0.8340 (t) cc_final: 0.8108 (p) REVERT: B 121 ASN cc_start: 0.7647 (p0) cc_final: 0.7376 (p0) REVERT: B 187 LEU cc_start: 0.8060 (tp) cc_final: 0.7689 (mp) REVERT: B 199 PHE cc_start: 0.8793 (t80) cc_final: 0.8377 (t80) REVERT: B 229 LEU cc_start: 0.8352 (pp) cc_final: 0.8110 (pp) REVERT: B 271 GLN cc_start: 0.8234 (mt0) cc_final: 0.7949 (mt0) REVERT: B 281 GLU cc_start: 0.7816 (pp20) cc_final: 0.7587 (pp20) REVERT: B 297 SER cc_start: 0.8595 (m) cc_final: 0.8363 (p) REVERT: B 307 THR cc_start: 0.8905 (m) cc_final: 0.8528 (p) REVERT: B 365 TYR cc_start: 0.8239 (m-80) cc_final: 0.7869 (m-10) REVERT: B 406 GLU cc_start: 0.8363 (mt-10) cc_final: 0.7996 (mt-10) REVERT: B 542 ASN cc_start: 0.8503 (t0) cc_final: 0.7981 (t0) REVERT: B 558 LYS cc_start: 0.8919 (mmmt) cc_final: 0.8569 (mmmt) REVERT: B 580 GLN cc_start: 0.8752 (mm-40) cc_final: 0.8285 (mm-40) REVERT: B 586 ASP cc_start: 0.7935 (t0) cc_final: 0.7556 (t0) REVERT: B 589 PRO cc_start: 0.8855 (Cg_exo) cc_final: 0.8325 (Cg_endo) REVERT: B 674 TYR cc_start: 0.8348 (t80) cc_final: 0.8147 (t80) REVERT: B 759 PHE cc_start: 0.7827 (m-80) cc_final: 0.7397 (m-80) REVERT: B 764 LYS cc_start: 0.8820 (ttmm) cc_final: 0.8602 (ttmm) REVERT: B 773 GLU cc_start: 0.7725 (tm-30) cc_final: 0.6987 (tm-30) REVERT: B 776 LYS cc_start: 0.8999 (ttpp) cc_final: 0.8570 (tptm) REVERT: B 795 LYS cc_start: 0.8972 (mttt) cc_final: 0.8720 (mttm) REVERT: B 825 LYS cc_start: 0.8722 (mtmm) cc_final: 0.8497 (mtpp) REVERT: B 850 ILE cc_start: 0.9077 (mm) cc_final: 0.8749 (tp) REVERT: B 851 CYS cc_start: 0.8465 (t) cc_final: 0.7836 (p) REVERT: B 856 LYS cc_start: 0.9220 (OUTLIER) cc_final: 0.9000 (tptt) REVERT: B 904 TYR cc_start: 0.8365 (m-10) cc_final: 0.8151 (m-10) REVERT: B 949 GLN cc_start: 0.8685 (mm110) cc_final: 0.8405 (mm-40) REVERT: B 950 ASP cc_start: 0.7981 (t70) cc_final: 0.7593 (t70) REVERT: B 955 ASN cc_start: 0.8418 (m110) cc_final: 0.8074 (m110) REVERT: B 964 LYS cc_start: 0.8620 (mtmp) cc_final: 0.8297 (ttmm) REVERT: B 979 ASP cc_start: 0.8199 (m-30) cc_final: 0.7958 (m-30) REVERT: B 1010 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.8115 (mp10) REVERT: B 1041 ASP cc_start: 0.8568 (m-30) cc_final: 0.8112 (t0) REVERT: B 1118 ASP cc_start: 0.7988 (t70) cc_final: 0.7481 (t0) REVERT: C 40 ASP cc_start: 0.8086 (t70) cc_final: 0.7786 (t0) REVERT: C 81 ASN cc_start: 0.7917 (p0) cc_final: 0.7564 (t0) REVERT: C 119 ILE cc_start: 0.8111 (OUTLIER) cc_final: 0.7862 (mm) REVERT: C 135 PHE cc_start: 0.7612 (p90) cc_final: 0.7210 (p90) REVERT: C 177 MET cc_start: 0.7158 (tpp) cc_final: 0.5873 (tpp) REVERT: C 188 ARG cc_start: 0.8160 (ptp-170) cc_final: 0.7728 (ptp-170) REVERT: C 235 ILE cc_start: 0.8609 (mt) cc_final: 0.8071 (mm) REVERT: C 237 ARG cc_start: 0.8487 (mtm180) cc_final: 0.8013 (mtp180) REVERT: C 265 TYR cc_start: 0.7926 (p90) cc_final: 0.7723 (p90) REVERT: C 280 ASN cc_start: 0.8444 (t0) cc_final: 0.8055 (t0) REVERT: C 281 GLU cc_start: 0.7711 (pp20) cc_final: 0.7290 (pp20) REVERT: C 357 ARG cc_start: 0.7579 (mtp180) cc_final: 0.7339 (ttm110) REVERT: C 378 LYS cc_start: 0.7854 (mmmm) cc_final: 0.7471 (mmmm) REVERT: C 386 LYS cc_start: 0.8264 (mttp) cc_final: 0.7797 (tttt) REVERT: C 392 PHE cc_start: 0.6753 (m-80) cc_final: 0.6350 (m-80) REVERT: C 420 ASP cc_start: 0.8432 (t0) cc_final: 0.8024 (t0) REVERT: C 462 LYS cc_start: 0.8096 (tptt) cc_final: 0.7644 (ttmm) REVERT: C 537 LYS cc_start: 0.8825 (tttp) cc_final: 0.8552 (mtpp) REVERT: C 551 VAL cc_start: 0.8757 (OUTLIER) cc_final: 0.8513 (p) REVERT: C 562 PHE cc_start: 0.8021 (p90) cc_final: 0.7672 (p90) REVERT: C 655 TYR cc_start: 0.8270 (t80) cc_final: 0.7884 (t80) REVERT: C 693 ILE cc_start: 0.8934 (pt) cc_final: 0.8643 (pt) REVERT: C 725 GLU cc_start: 0.8289 (tt0) cc_final: 0.7978 (tm-30) REVERT: C 759 PHE cc_start: 0.7664 (t80) cc_final: 0.7062 (t80) REVERT: C 763 LEU cc_start: 0.8664 (mp) cc_final: 0.8250 (mp) REVERT: C 773 GLU cc_start: 0.8189 (tt0) cc_final: 0.7749 (tp30) REVERT: C 776 LYS cc_start: 0.8673 (tmmt) cc_final: 0.8415 (ttmm) REVERT: C 779 GLN cc_start: 0.8523 (tm-30) cc_final: 0.8241 (tm-30) REVERT: C 792 PRO cc_start: 0.8480 (Cg_exo) cc_final: 0.8261 (Cg_endo) REVERT: C 796 TYR cc_start: 0.8503 (t80) cc_final: 0.8188 (t80) REVERT: C 803 SER cc_start: 0.9101 (m) cc_final: 0.8859 (p) REVERT: C 808 ASP cc_start: 0.8194 (t70) cc_final: 0.7601 (p0) REVERT: C 851 CYS cc_start: 0.8195 (t) cc_final: 0.7590 (t) REVERT: C 868 GLU cc_start: 0.8495 (mp0) cc_final: 0.8200 (mp0) REVERT: C 900 MET cc_start: 0.8513 (mtp) cc_final: 0.8193 (mtp) REVERT: C 949 GLN cc_start: 0.8639 (mm110) cc_final: 0.8232 (mm-40) REVERT: C 953 ASN cc_start: 0.8395 (m-40) cc_final: 0.8151 (m-40) REVERT: C 964 LYS cc_start: 0.8827 (tmtm) cc_final: 0.8548 (ttmm) REVERT: C 990 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8074 (tm-30) REVERT: C 1002 GLN cc_start: 0.8376 (tp40) cc_final: 0.7752 (tp-100) REVERT: C 1005 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.8638 (tp40) REVERT: C 1010 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8180 (mp10) REVERT: C 1038 LYS cc_start: 0.8898 (mtpt) cc_final: 0.8503 (mtmm) REVERT: C 1072 GLU cc_start: 0.8605 (pm20) cc_final: 0.8299 (pm20) REVERT: C 1107 ARG cc_start: 0.8019 (mtt180) cc_final: 0.7671 (mpt-90) REVERT: C 1118 ASP cc_start: 0.8218 (t70) cc_final: 0.7827 (t0) REVERT: C 1138 TYR cc_start: 0.8003 (t80) cc_final: 0.7680 (t80) REVERT: D 129 GLN cc_start: 0.5588 (OUTLIER) cc_final: 0.5289 (pp30) outliers start: 162 outliers final: 93 residues processed: 703 average time/residue: 0.3995 time to fit residues: 434.9946 Evaluate side-chains 614 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 510 time to evaluate : 2.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 388 ASN 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 511 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 856 LYS Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 129 GLN Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 226 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 145 optimal weight: 10.0000 chunk 308 optimal weight: 30.0000 chunk 183 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 320 optimal weight: 0.1980 chunk 109 optimal weight: 3.9990 chunk 244 optimal weight: 10.0000 chunk 150 optimal weight: 0.7980 chunk 196 optimal weight: 0.9980 chunk 288 optimal weight: 2.9990 chunk 251 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 122 ASN A 205 HIS A 239 GLN ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 804 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 HIS B 218 GLN B 542 ASN B 913 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 563 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.162410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.120446 restraints weight = 44910.077| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 3.27 r_work: 0.3250 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 26904 Z= 0.186 Angle : 0.658 13.898 36699 Z= 0.329 Chirality : 0.047 0.345 4216 Planarity : 0.004 0.048 4697 Dihedral : 7.078 59.935 4287 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.55 % Favored : 90.45 % Rotamer: Outliers : 5.22 % Allowed : 17.22 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.84 (0.14), residues: 3276 helix: 0.57 (0.21), residues: 654 sheet: -1.80 (0.20), residues: 611 loop : -2.94 (0.12), residues: 2011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 104 HIS 0.006 0.001 HIS A1048 PHE 0.026 0.001 PHE B 759 TYR 0.020 0.001 TYR C1067 ARG 0.008 0.001 ARG A 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00414 ( 28) link_NAG-ASN : angle 2.50257 ( 84) hydrogen bonds : bond 0.03834 ( 750) hydrogen bonds : angle 4.99662 ( 2004) SS BOND : bond 0.00431 ( 41) SS BOND : angle 2.48985 ( 82) covalent geometry : bond 0.00411 (26835) covalent geometry : angle 0.63798 (36533) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 539 time to evaluate : 5.026 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 45 SER cc_start: 0.8874 (t) cc_final: 0.8671 (t) REVERT: A 46 SER cc_start: 0.9187 (m) cc_final: 0.8971 (p) REVERT: A 64 TRP cc_start: 0.8089 (t60) cc_final: 0.7860 (t-100) REVERT: A 66 HIS cc_start: 0.8139 (OUTLIER) cc_final: 0.7827 (m90) REVERT: A 97 LYS cc_start: 0.8436 (tppt) cc_final: 0.8023 (tppt) REVERT: A 109 THR cc_start: 0.8666 (p) cc_final: 0.8394 (t) REVERT: A 132 GLU cc_start: 0.6444 (pm20) cc_final: 0.5753 (pm20) REVERT: A 164 ASN cc_start: 0.7606 (p0) cc_final: 0.6959 (p0) REVERT: A 198 TYR cc_start: 0.8162 (m-80) cc_final: 0.7897 (m-80) REVERT: A 215 ASP cc_start: 0.7993 (m-30) cc_final: 0.7647 (m-30) REVERT: A 224 GLU cc_start: 0.8140 (mp0) cc_final: 0.7881 (mp0) REVERT: A 269 TYR cc_start: 0.8642 (m-80) cc_final: 0.7746 (m-80) REVERT: A 297 SER cc_start: 0.8669 (m) cc_final: 0.8254 (p) REVERT: A 298 GLU cc_start: 0.8215 (tt0) cc_final: 0.7914 (tp30) REVERT: A 307 THR cc_start: 0.8715 (m) cc_final: 0.8477 (p) REVERT: A 356 LYS cc_start: 0.7496 (OUTLIER) cc_final: 0.7053 (tmmm) REVERT: A 542 ASN cc_start: 0.8664 (t0) cc_final: 0.8417 (t0) REVERT: A 569 ILE cc_start: 0.8617 (pt) cc_final: 0.8286 (mp) REVERT: A 580 GLN cc_start: 0.8067 (pt0) cc_final: 0.7650 (pt0) REVERT: A 602 THR cc_start: 0.8609 (OUTLIER) cc_final: 0.8383 (p) REVERT: A 663 ASP cc_start: 0.7959 (t70) cc_final: 0.7582 (t0) REVERT: A 664 ILE cc_start: 0.8887 (mt) cc_final: 0.8473 (mm) REVERT: A 675 GLN cc_start: 0.7609 (mm-40) cc_final: 0.7119 (mm-40) REVERT: A 703 ASN cc_start: 0.8261 (t0) cc_final: 0.8028 (t0) REVERT: A 708 SER cc_start: 0.8689 (t) cc_final: 0.8357 (m) REVERT: A 725 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7503 (tm-30) REVERT: A 773 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7192 (tm-30) REVERT: A 780 GLU cc_start: 0.8121 (pt0) cc_final: 0.7588 (tm-30) REVERT: A 790 LYS cc_start: 0.8181 (mppt) cc_final: 0.7775 (mppt) REVERT: A 803 SER cc_start: 0.8588 (m) cc_final: 0.8334 (p) REVERT: A 851 CYS cc_start: 0.8502 (t) cc_final: 0.8099 (t) REVERT: A 855 PHE cc_start: 0.8451 (m-80) cc_final: 0.8071 (m-80) REVERT: A 868 GLU cc_start: 0.8308 (tp30) cc_final: 0.8003 (tm-30) REVERT: A 869 MET cc_start: 0.8748 (mtt) cc_final: 0.8450 (mtm) REVERT: A 933 LYS cc_start: 0.8522 (mtmt) cc_final: 0.8228 (mttp) REVERT: A 994 ASP cc_start: 0.7687 (t70) cc_final: 0.7416 (t70) REVERT: A 995 ARG cc_start: 0.8518 (mtm-85) cc_final: 0.8285 (ttp-110) REVERT: A 1017 GLU cc_start: 0.8364 (tm-30) cc_final: 0.7875 (tp30) REVERT: A 1050 MET cc_start: 0.8084 (mtm) cc_final: 0.7862 (mtp) REVERT: A 1107 ARG cc_start: 0.7944 (mtt90) cc_final: 0.7649 (mtt90) REVERT: B 95 ILE cc_start: 0.8764 (mt) cc_final: 0.8296 (tt) REVERT: B 120 VAL cc_start: 0.8422 (t) cc_final: 0.8199 (p) REVERT: B 121 ASN cc_start: 0.7730 (p0) cc_final: 0.6594 (t0) REVERT: B 271 GLN cc_start: 0.8259 (mt0) cc_final: 0.7994 (mt0) REVERT: B 297 SER cc_start: 0.8586 (m) cc_final: 0.8356 (p) REVERT: B 307 THR cc_start: 0.8882 (m) cc_final: 0.8492 (p) REVERT: B 347 PHE cc_start: 0.4124 (OUTLIER) cc_final: 0.3359 (t80) REVERT: B 406 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8003 (mt-10) REVERT: B 542 ASN cc_start: 0.8379 (t160) cc_final: 0.7969 (t0) REVERT: B 558 LYS cc_start: 0.8911 (mmmt) cc_final: 0.8447 (mmmt) REVERT: B 580 GLN cc_start: 0.8761 (mm-40) cc_final: 0.8311 (mm-40) REVERT: B 589 PRO cc_start: 0.9009 (Cg_exo) cc_final: 0.8743 (Cg_endo) REVERT: B 674 TYR cc_start: 0.8389 (t80) cc_final: 0.8180 (t80) REVERT: B 725 GLU cc_start: 0.8139 (pt0) cc_final: 0.7788 (pt0) REVERT: B 762 GLN cc_start: 0.8095 (pt0) cc_final: 0.7814 (pt0) REVERT: B 764 LYS cc_start: 0.8754 (ttmm) cc_final: 0.8469 (ttpp) REVERT: B 773 GLU cc_start: 0.7676 (tm-30) cc_final: 0.6880 (tm-30) REVERT: B 776 LYS cc_start: 0.8941 (ttpp) cc_final: 0.8672 (tptm) REVERT: B 795 LYS cc_start: 0.8933 (mttt) cc_final: 0.8725 (mttm) REVERT: B 796 TYR cc_start: 0.9019 (t80) cc_final: 0.8698 (t80) REVERT: B 816 SER cc_start: 0.8952 (m) cc_final: 0.8554 (p) REVERT: B 820 ASP cc_start: 0.8155 (m-30) cc_final: 0.7921 (t0) REVERT: B 825 LYS cc_start: 0.8720 (mtmm) cc_final: 0.8469 (mtpp) REVERT: B 850 ILE cc_start: 0.9048 (mm) cc_final: 0.8708 (tp) REVERT: B 851 CYS cc_start: 0.8491 (t) cc_final: 0.7710 (p) REVERT: B 904 TYR cc_start: 0.8280 (m-10) cc_final: 0.7021 (m-10) REVERT: B 949 GLN cc_start: 0.8697 (mm110) cc_final: 0.8425 (mm-40) REVERT: B 950 ASP cc_start: 0.7948 (t70) cc_final: 0.7615 (t70) REVERT: B 955 ASN cc_start: 0.8390 (m110) cc_final: 0.8148 (m-40) REVERT: B 964 LYS cc_start: 0.8601 (mtmp) cc_final: 0.8281 (ttmm) REVERT: B 979 ASP cc_start: 0.8094 (m-30) cc_final: 0.7738 (m-30) REVERT: B 1010 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.8023 (mp10) REVERT: B 1017 GLU cc_start: 0.8389 (tm-30) cc_final: 0.7876 (tm-30) REVERT: B 1031 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7893 (mt-10) REVERT: B 1041 ASP cc_start: 0.8522 (m-30) cc_final: 0.8061 (t0) REVERT: B 1118 ASP cc_start: 0.8005 (t70) cc_final: 0.7459 (t0) REVERT: C 40 ASP cc_start: 0.8087 (t70) cc_final: 0.7729 (t0) REVERT: C 81 ASN cc_start: 0.7728 (p0) cc_final: 0.7495 (t0) REVERT: C 133 PHE cc_start: 0.7191 (p90) cc_final: 0.6708 (p90) REVERT: C 135 PHE cc_start: 0.7184 (p90) cc_final: 0.6626 (p90) REVERT: C 177 MET cc_start: 0.7146 (tpp) cc_final: 0.6094 (tpp) REVERT: C 188 ARG cc_start: 0.8208 (ptp-170) cc_final: 0.7880 (ptp-170) REVERT: C 226 LEU cc_start: 0.8559 (mt) cc_final: 0.8350 (mp) REVERT: C 235 ILE cc_start: 0.8458 (mt) cc_final: 0.8208 (mm) REVERT: C 237 ARG cc_start: 0.8388 (mtm180) cc_final: 0.7794 (mtm180) REVERT: C 242 LEU cc_start: 0.6887 (OUTLIER) cc_final: 0.6563 (pp) REVERT: C 280 ASN cc_start: 0.8370 (t0) cc_final: 0.7964 (t0) REVERT: C 281 GLU cc_start: 0.7746 (pp20) cc_final: 0.7370 (pp20) REVERT: C 323 THR cc_start: 0.8064 (p) cc_final: 0.7818 (p) REVERT: C 378 LYS cc_start: 0.7791 (mmmm) cc_final: 0.7422 (mmmm) REVERT: C 386 LYS cc_start: 0.8265 (mttp) cc_final: 0.7730 (tttt) REVERT: C 392 PHE cc_start: 0.6982 (m-80) cc_final: 0.6615 (m-80) REVERT: C 420 ASP cc_start: 0.8433 (t0) cc_final: 0.7989 (t0) REVERT: C 462 LYS cc_start: 0.8093 (tptt) cc_final: 0.7641 (ttmm) REVERT: C 511 VAL cc_start: 0.7606 (t) cc_final: 0.7307 (p) REVERT: C 533 LEU cc_start: 0.7963 (tp) cc_final: 0.7658 (pt) REVERT: C 537 LYS cc_start: 0.8766 (tttp) cc_final: 0.8282 (mtpp) REVERT: C 551 VAL cc_start: 0.8739 (OUTLIER) cc_final: 0.8486 (p) REVERT: C 558 LYS cc_start: 0.8574 (mptt) cc_final: 0.8060 (mppt) REVERT: C 569 ILE cc_start: 0.7889 (mm) cc_final: 0.7609 (mm) REVERT: C 574 ASP cc_start: 0.8061 (t70) cc_final: 0.7709 (t0) REVERT: C 655 TYR cc_start: 0.8293 (t80) cc_final: 0.8056 (t80) REVERT: C 671 CYS cc_start: 0.6873 (m) cc_final: 0.6490 (m) REVERT: C 693 ILE cc_start: 0.8889 (pt) cc_final: 0.8685 (pt) REVERT: C 725 GLU cc_start: 0.8242 (tt0) cc_final: 0.7957 (tm-30) REVERT: C 773 GLU cc_start: 0.8091 (tt0) cc_final: 0.7265 (tp30) REVERT: C 776 LYS cc_start: 0.8686 (tmmt) cc_final: 0.8440 (ttmm) REVERT: C 777 ASN cc_start: 0.8410 (m-40) cc_final: 0.7406 (m110) REVERT: C 779 GLN cc_start: 0.8578 (tm-30) cc_final: 0.8213 (tm-30) REVERT: C 808 ASP cc_start: 0.8244 (t70) cc_final: 0.7565 (p0) REVERT: C 821 LEU cc_start: 0.8591 (tp) cc_final: 0.8321 (tt) REVERT: C 851 CYS cc_start: 0.8200 (t) cc_final: 0.7581 (t) REVERT: C 949 GLN cc_start: 0.8575 (mm110) cc_final: 0.8201 (mm-40) REVERT: C 964 LYS cc_start: 0.8769 (tmtm) cc_final: 0.8380 (ttmm) REVERT: C 990 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8002 (tm-30) REVERT: C 1002 GLN cc_start: 0.8249 (tp40) cc_final: 0.7970 (tp40) REVERT: C 1010 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8117 (mp10) REVERT: C 1072 GLU cc_start: 0.8574 (pm20) cc_final: 0.8242 (pm20) REVERT: C 1107 ARG cc_start: 0.7913 (mtt180) cc_final: 0.7486 (mtt180) REVERT: C 1118 ASP cc_start: 0.8188 (t70) cc_final: 0.7754 (t0) REVERT: C 1138 TYR cc_start: 0.7944 (t80) cc_final: 0.7644 (t80) REVERT: C 1139 ASP cc_start: 0.8059 (t70) cc_final: 0.7858 (t0) outliers start: 149 outliers final: 101 residues processed: 653 average time/residue: 0.5069 time to fit residues: 513.3283 Evaluate side-chains 637 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 528 time to evaluate : 3.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 388 ASN 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 511 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 234 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 65 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 184 optimal weight: 5.9990 chunk 172 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 266 optimal weight: 2.9990 chunk 147 optimal weight: 9.9990 chunk 283 optimal weight: 0.5980 chunk 195 optimal weight: 2.9990 chunk 144 optimal weight: 50.0000 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A1083 HIS A1125 ASN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN B 957 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 563 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 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 = 0.4392 r_free = 0.4392 target = 0.194382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.166361 restraints weight = 56503.825| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.43 r_work: 0.3356 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 26904 Z= 0.213 Angle : 0.663 12.899 36699 Z= 0.332 Chirality : 0.047 0.335 4216 Planarity : 0.004 0.049 4697 Dihedral : 7.031 59.596 4278 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.07 % Favored : 89.93 % Rotamer: Outliers : 5.67 % Allowed : 17.12 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.66 (0.14), residues: 3276 helix: 0.69 (0.21), residues: 658 sheet: -1.81 (0.20), residues: 621 loop : -2.77 (0.12), residues: 1997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 64 HIS 0.012 0.001 HIS A 205 PHE 0.021 0.002 PHE C 970 TYR 0.022 0.001 TYR C1067 ARG 0.008 0.001 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00424 ( 28) link_NAG-ASN : angle 2.42024 ( 84) hydrogen bonds : bond 0.03866 ( 750) hydrogen bonds : angle 4.98885 ( 2004) SS BOND : bond 0.00338 ( 41) SS BOND : angle 2.12655 ( 82) covalent geometry : bond 0.00463 (26835) covalent geometry : angle 0.64632 (36533) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 540 time to evaluate : 2.615 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 46 SER cc_start: 0.9215 (m) cc_final: 0.8963 (p) REVERT: A 64 TRP cc_start: 0.8217 (t60) cc_final: 0.7905 (t-100) REVERT: A 66 HIS cc_start: 0.8239 (OUTLIER) cc_final: 0.7706 (m90) REVERT: A 97 LYS cc_start: 0.8650 (tppt) cc_final: 0.8297 (tppt) REVERT: A 109 THR cc_start: 0.8697 (p) cc_final: 0.8431 (t) REVERT: A 132 GLU cc_start: 0.6743 (pm20) cc_final: 0.5968 (pm20) REVERT: A 164 ASN cc_start: 0.7723 (p0) cc_final: 0.7194 (p0) REVERT: A 186 ASN cc_start: 0.7896 (p0) cc_final: 0.7484 (p0) REVERT: A 215 ASP cc_start: 0.7989 (m-30) cc_final: 0.7703 (m-30) REVERT: A 224 GLU cc_start: 0.8263 (mp0) cc_final: 0.8062 (mp0) REVERT: A 282 ASN cc_start: 0.8888 (OUTLIER) cc_final: 0.8331 (m-40) REVERT: A 297 SER cc_start: 0.8660 (m) cc_final: 0.8236 (p) REVERT: A 298 GLU cc_start: 0.8319 (tt0) cc_final: 0.7998 (tp30) REVERT: A 307 THR cc_start: 0.8791 (m) cc_final: 0.8476 (p) REVERT: A 324 GLU cc_start: 0.7514 (mp0) cc_final: 0.7312 (pm20) REVERT: A 356 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7196 (tmmm) REVERT: A 390 LEU cc_start: 0.7504 (OUTLIER) cc_final: 0.7064 (tt) REVERT: A 542 ASN cc_start: 0.8643 (t0) cc_final: 0.8381 (t0) REVERT: A 569 ILE cc_start: 0.8641 (pt) cc_final: 0.8402 (mp) REVERT: A 580 GLN cc_start: 0.8271 (pt0) cc_final: 0.7835 (pt0) REVERT: A 602 THR cc_start: 0.8633 (m) cc_final: 0.8402 (p) REVERT: A 675 GLN cc_start: 0.7690 (mm-40) cc_final: 0.7198 (mm-40) REVERT: A 708 SER cc_start: 0.8631 (t) cc_final: 0.8307 (m) REVERT: A 725 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7447 (tm-30) REVERT: A 773 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7254 (tm-30) REVERT: A 780 GLU cc_start: 0.8171 (pt0) cc_final: 0.7616 (tm-30) REVERT: A 788 ILE cc_start: 0.8959 (mm) cc_final: 0.8690 (mm) REVERT: A 790 LYS cc_start: 0.8247 (mppt) cc_final: 0.7834 (mppt) REVERT: A 803 SER cc_start: 0.8690 (m) cc_final: 0.8403 (p) REVERT: A 851 CYS cc_start: 0.8566 (t) cc_final: 0.8282 (t) REVERT: A 868 GLU cc_start: 0.8418 (tp30) cc_final: 0.8105 (tm-30) REVERT: A 933 LYS cc_start: 0.8525 (mtmt) cc_final: 0.8236 (mttp) REVERT: A 994 ASP cc_start: 0.7735 (t70) cc_final: 0.7472 (t70) REVERT: A 995 ARG cc_start: 0.8613 (mtm-85) cc_final: 0.8368 (ttp-110) REVERT: A 1017 GLU cc_start: 0.8443 (tm-30) cc_final: 0.7981 (tp30) REVERT: A 1050 MET cc_start: 0.8125 (mtm) cc_final: 0.7911 (mtp) REVERT: B 52 GLN cc_start: 0.8288 (tm-30) cc_final: 0.7706 (tm-30) REVERT: B 95 ILE cc_start: 0.8824 (mt) cc_final: 0.8171 (tt) REVERT: B 120 VAL cc_start: 0.8674 (t) cc_final: 0.8418 (p) REVERT: B 121 ASN cc_start: 0.7775 (p0) cc_final: 0.6758 (t0) REVERT: B 187 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7899 (mp) REVERT: B 190 PHE cc_start: 0.8751 (m-10) cc_final: 0.8398 (m-10) REVERT: B 199 PHE cc_start: 0.8918 (t80) cc_final: 0.8508 (t80) REVERT: B 224 GLU cc_start: 0.8056 (pm20) cc_final: 0.7826 (mp0) REVERT: B 271 GLN cc_start: 0.8327 (mt0) cc_final: 0.8101 (mt0) REVERT: B 297 SER cc_start: 0.8630 (m) cc_final: 0.8338 (p) REVERT: B 299 THR cc_start: 0.8834 (m) cc_final: 0.8528 (p) REVERT: B 307 THR cc_start: 0.8899 (m) cc_final: 0.8509 (p) REVERT: B 319 ARG cc_start: 0.8173 (ttm110) cc_final: 0.7877 (ttm110) REVERT: B 347 PHE cc_start: 0.4377 (OUTLIER) cc_final: 0.3512 (t80) REVERT: B 361 CYS cc_start: 0.7092 (OUTLIER) cc_final: 0.6807 (t) REVERT: B 406 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8020 (mt-10) REVERT: B 558 LYS cc_start: 0.8936 (mmmt) cc_final: 0.8477 (mmmt) REVERT: B 568 ASP cc_start: 0.8087 (p0) cc_final: 0.7737 (p0) REVERT: B 580 GLN cc_start: 0.8802 (mm-40) cc_final: 0.8364 (mm-40) REVERT: B 674 TYR cc_start: 0.8517 (t80) cc_final: 0.8288 (t80) REVERT: B 725 GLU cc_start: 0.8107 (pt0) cc_final: 0.7753 (pt0) REVERT: B 762 GLN cc_start: 0.8050 (pt0) cc_final: 0.7757 (pt0) REVERT: B 764 LYS cc_start: 0.8805 (ttmm) cc_final: 0.8520 (ttpp) REVERT: B 773 GLU cc_start: 0.7795 (tm-30) cc_final: 0.6991 (tm-30) REVERT: B 776 LYS cc_start: 0.8946 (ttpp) cc_final: 0.8703 (tptm) REVERT: B 795 LYS cc_start: 0.8984 (mttt) cc_final: 0.8767 (mttm) REVERT: B 796 TYR cc_start: 0.9055 (t80) cc_final: 0.8735 (t80) REVERT: B 816 SER cc_start: 0.8900 (m) cc_final: 0.8493 (p) REVERT: B 825 LYS cc_start: 0.8808 (mtmm) cc_final: 0.8578 (mtpp) REVERT: B 850 ILE cc_start: 0.9039 (mm) cc_final: 0.8710 (tp) REVERT: B 851 CYS cc_start: 0.8550 (t) cc_final: 0.7740 (p) REVERT: B 904 TYR cc_start: 0.8241 (m-10) cc_final: 0.7163 (m-10) REVERT: B 914 ASN cc_start: 0.8558 (p0) cc_final: 0.8338 (p0) REVERT: B 918 GLU cc_start: 0.7931 (mp0) cc_final: 0.7715 (mp0) REVERT: B 949 GLN cc_start: 0.8825 (mm-40) cc_final: 0.8525 (mm-40) REVERT: B 950 ASP cc_start: 0.8088 (t70) cc_final: 0.7764 (t70) REVERT: B 955 ASN cc_start: 0.8444 (m110) cc_final: 0.8222 (m-40) REVERT: B 964 LYS cc_start: 0.8641 (mtmp) cc_final: 0.8326 (ttmm) REVERT: B 979 ASP cc_start: 0.8198 (m-30) cc_final: 0.7851 (m-30) REVERT: B 1010 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8001 (mp10) REVERT: B 1017 GLU cc_start: 0.8439 (tm-30) cc_final: 0.7943 (tm-30) REVERT: B 1031 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7888 (mt-10) REVERT: B 1041 ASP cc_start: 0.8604 (m-30) cc_final: 0.8128 (t0) REVERT: B 1118 ASP cc_start: 0.8091 (t70) cc_final: 0.7659 (t0) REVERT: C 40 ASP cc_start: 0.8138 (OUTLIER) cc_final: 0.7894 (t0) REVERT: C 177 MET cc_start: 0.7395 (tpp) cc_final: 0.6199 (tpp) REVERT: C 188 ARG cc_start: 0.8411 (ptp-170) cc_final: 0.7898 (ptp-170) REVERT: C 198 TYR cc_start: 0.7725 (m-80) cc_final: 0.6516 (m-80) REVERT: C 199 PHE cc_start: 0.8103 (t80) cc_final: 0.7464 (t80) REVERT: C 200 LYS cc_start: 0.8488 (mmtm) cc_final: 0.7852 (mmtm) REVERT: C 235 ILE cc_start: 0.8598 (mt) cc_final: 0.8289 (mm) REVERT: C 237 ARG cc_start: 0.8437 (mtm180) cc_final: 0.7871 (mtm180) REVERT: C 242 LEU cc_start: 0.6978 (OUTLIER) cc_final: 0.6559 (pp) REVERT: C 280 ASN cc_start: 0.8476 (t0) cc_final: 0.8049 (t0) REVERT: C 281 GLU cc_start: 0.7871 (pp20) cc_final: 0.7498 (pp20) REVERT: C 319 ARG cc_start: 0.8577 (ttm-80) cc_final: 0.8376 (ttm-80) REVERT: C 378 LYS cc_start: 0.7814 (mmmm) cc_final: 0.7432 (mmmm) REVERT: C 386 LYS cc_start: 0.8282 (mttp) cc_final: 0.7848 (mtpt) REVERT: C 392 PHE cc_start: 0.7058 (m-80) cc_final: 0.6598 (m-80) REVERT: C 420 ASP cc_start: 0.8398 (t0) cc_final: 0.7966 (t0) REVERT: C 462 LYS cc_start: 0.7991 (tptt) cc_final: 0.7582 (ttmm) REVERT: C 501 TYR cc_start: 0.6447 (OUTLIER) cc_final: 0.6092 (m-10) REVERT: C 511 VAL cc_start: 0.7741 (t) cc_final: 0.7524 (p) REVERT: C 528 LYS cc_start: 0.8793 (mmmm) cc_final: 0.8450 (mmmt) REVERT: C 551 VAL cc_start: 0.8769 (OUTLIER) cc_final: 0.8479 (p) REVERT: C 557 LYS cc_start: 0.7721 (mttm) cc_final: 0.7462 (mttt) REVERT: C 558 LYS cc_start: 0.8582 (mptt) cc_final: 0.8011 (mppt) REVERT: C 569 ILE cc_start: 0.7858 (mm) cc_final: 0.7599 (mm) REVERT: C 602 THR cc_start: 0.8748 (m) cc_final: 0.8353 (p) REVERT: C 655 TYR cc_start: 0.8382 (t80) cc_final: 0.8140 (t80) REVERT: C 671 CYS cc_start: 0.7060 (m) cc_final: 0.6712 (m) REVERT: C 725 GLU cc_start: 0.8335 (tt0) cc_final: 0.8040 (tm-30) REVERT: C 726 ILE cc_start: 0.9338 (OUTLIER) cc_final: 0.8920 (mm) REVERT: C 739 THR cc_start: 0.8702 (m) cc_final: 0.8286 (t) REVERT: C 773 GLU cc_start: 0.8118 (tt0) cc_final: 0.7255 (tp30) REVERT: C 776 LYS cc_start: 0.8679 (tmmt) cc_final: 0.8383 (ttmm) REVERT: C 777 ASN cc_start: 0.8438 (m-40) cc_final: 0.7361 (m110) REVERT: C 779 GLN cc_start: 0.8570 (tm-30) cc_final: 0.8255 (tm-30) REVERT: C 808 ASP cc_start: 0.8209 (t70) cc_final: 0.7541 (p0) REVERT: C 821 LEU cc_start: 0.8695 (tp) cc_final: 0.8359 (tt) REVERT: C 851 CYS cc_start: 0.8197 (t) cc_final: 0.7592 (t) REVERT: C 868 GLU cc_start: 0.8539 (mp0) cc_final: 0.8297 (mp0) REVERT: C 933 LYS cc_start: 0.8646 (mtpp) cc_final: 0.8405 (mtmm) REVERT: C 949 GLN cc_start: 0.8658 (mm110) cc_final: 0.8349 (mm-40) REVERT: C 964 LYS cc_start: 0.8864 (tmtm) cc_final: 0.8439 (ttmm) REVERT: C 988 GLU cc_start: 0.8531 (tp30) cc_final: 0.7691 (tp30) REVERT: C 990 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8082 (tm-30) REVERT: C 1002 GLN cc_start: 0.8423 (tp40) cc_final: 0.8114 (tp40) REVERT: C 1010 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8218 (mp10) REVERT: C 1072 GLU cc_start: 0.8604 (pm20) cc_final: 0.8280 (pm20) REVERT: C 1107 ARG cc_start: 0.7985 (mtt180) cc_final: 0.7632 (mtt180) REVERT: C 1138 TYR cc_start: 0.7998 (t80) cc_final: 0.7676 (t80) outliers start: 162 outliers final: 105 residues processed: 664 average time/residue: 0.4225 time to fit residues: 432.1464 Evaluate side-chains 635 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 516 time to evaluate : 2.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 388 ASN 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 511 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 205 HIS Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 226 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 177 optimal weight: 0.0270 chunk 137 optimal weight: 0.0010 chunk 39 optimal weight: 6.9990 chunk 249 optimal weight: 9.9990 chunk 30 optimal weight: 20.0000 chunk 34 optimal weight: 0.8980 chunk 127 optimal weight: 0.8980 chunk 298 optimal weight: 0.9990 chunk 187 optimal weight: 1.9990 chunk 264 optimal weight: 0.9980 chunk 216 optimal weight: 0.8980 overall best weight: 0.5444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 437 ASN ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN B 81 ASN B 317 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN C 81 ASN C 317 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C1058 HIS ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.196509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.169880 restraints weight = 56621.204| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.17 r_work: 0.3382 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 26904 Z= 0.117 Angle : 0.614 12.549 36699 Z= 0.304 Chirality : 0.045 0.319 4216 Planarity : 0.004 0.060 4697 Dihedral : 6.688 59.292 4274 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 4.97 % Allowed : 18.80 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.42 (0.14), residues: 3276 helix: 0.95 (0.21), residues: 656 sheet: -1.62 (0.20), residues: 613 loop : -2.64 (0.13), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 104 HIS 0.007 0.001 HIS A1083 PHE 0.023 0.001 PHE B 168 TYR 0.020 0.001 TYR B 707 ARG 0.004 0.000 ARG A 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00382 ( 28) link_NAG-ASN : angle 2.24314 ( 84) hydrogen bonds : bond 0.03286 ( 750) hydrogen bonds : angle 4.81887 ( 2004) SS BOND : bond 0.00241 ( 41) SS BOND : angle 1.54869 ( 82) covalent geometry : bond 0.00261 (26835) covalent geometry : angle 0.60144 (36533) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 529 time to evaluate : 2.608 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 66 HIS cc_start: 0.8251 (OUTLIER) cc_final: 0.7875 (m90) REVERT: A 97 LYS cc_start: 0.8652 (tppt) cc_final: 0.8367 (tppt) REVERT: A 102 ARG cc_start: 0.8734 (ptp-170) cc_final: 0.8513 (ptp-170) REVERT: A 109 THR cc_start: 0.8685 (p) cc_final: 0.8417 (t) REVERT: A 186 ASN cc_start: 0.7896 (p0) cc_final: 0.7459 (p0) REVERT: A 198 TYR cc_start: 0.8119 (m-10) cc_final: 0.7891 (m-80) REVERT: A 224 GLU cc_start: 0.8298 (mp0) cc_final: 0.8063 (mp0) REVERT: A 239 GLN cc_start: 0.8080 (tp40) cc_final: 0.7643 (tp40) REVERT: A 269 TYR cc_start: 0.8542 (m-80) cc_final: 0.7578 (m-80) REVERT: A 282 ASN cc_start: 0.8836 (OUTLIER) cc_final: 0.8372 (m-40) REVERT: A 297 SER cc_start: 0.8636 (m) cc_final: 0.8214 (p) REVERT: A 298 GLU cc_start: 0.8256 (tt0) cc_final: 0.7999 (tp30) REVERT: A 307 THR cc_start: 0.8758 (m) cc_final: 0.8450 (p) REVERT: A 356 LYS cc_start: 0.7580 (OUTLIER) cc_final: 0.7145 (tmmm) REVERT: A 390 LEU cc_start: 0.7314 (OUTLIER) cc_final: 0.6861 (tt) REVERT: A 542 ASN cc_start: 0.8650 (t0) cc_final: 0.8344 (t0) REVERT: A 569 ILE cc_start: 0.8615 (pt) cc_final: 0.8309 (mp) REVERT: A 580 GLN cc_start: 0.8180 (pt0) cc_final: 0.7708 (pt0) REVERT: A 602 THR cc_start: 0.8614 (OUTLIER) cc_final: 0.8397 (p) REVERT: A 675 GLN cc_start: 0.7604 (mm-40) cc_final: 0.7148 (mm-40) REVERT: A 702 GLU cc_start: 0.7966 (mp0) cc_final: 0.7704 (mp0) REVERT: A 703 ASN cc_start: 0.8263 (t0) cc_final: 0.8009 (t0) REVERT: A 708 SER cc_start: 0.8496 (t) cc_final: 0.8203 (m) REVERT: A 725 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7514 (tm-30) REVERT: A 773 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7205 (tm-30) REVERT: A 780 GLU cc_start: 0.8190 (pt0) cc_final: 0.7657 (tm-30) REVERT: A 788 ILE cc_start: 0.8940 (mm) cc_final: 0.8677 (mm) REVERT: A 790 LYS cc_start: 0.8248 (mppt) cc_final: 0.7891 (mppt) REVERT: A 796 TYR cc_start: 0.8656 (t80) cc_final: 0.8363 (t80) REVERT: A 803 SER cc_start: 0.8523 (m) cc_final: 0.8278 (p) REVERT: A 851 CYS cc_start: 0.8622 (t) cc_final: 0.8012 (t) REVERT: A 855 PHE cc_start: 0.8366 (m-10) cc_final: 0.8095 (m-80) REVERT: A 868 GLU cc_start: 0.8319 (tp30) cc_final: 0.8039 (tm-30) REVERT: A 869 MET cc_start: 0.8672 (mtt) cc_final: 0.8460 (mtm) REVERT: A 933 LYS cc_start: 0.8376 (mtmt) cc_final: 0.8089 (mttp) REVERT: A 990 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7865 (tm-30) REVERT: A 994 ASP cc_start: 0.7641 (t70) cc_final: 0.7367 (t70) REVERT: A 995 ARG cc_start: 0.8420 (mtm-85) cc_final: 0.8190 (ttp-110) REVERT: A 1017 GLU cc_start: 0.8360 (tm-30) cc_final: 0.7783 (tp30) REVERT: A 1050 MET cc_start: 0.8114 (mtm) cc_final: 0.7892 (mtp) REVERT: A 1107 ARG cc_start: 0.7920 (mtt90) cc_final: 0.7597 (mtt90) REVERT: B 52 GLN cc_start: 0.8207 (tm-30) cc_final: 0.7850 (tm-30) REVERT: B 95 ILE cc_start: 0.8674 (mt) cc_final: 0.8100 (tt) REVERT: B 121 ASN cc_start: 0.7742 (p0) cc_final: 0.6739 (t0) REVERT: B 127 VAL cc_start: 0.7872 (OUTLIER) cc_final: 0.7669 (t) REVERT: B 187 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7957 (mp) REVERT: B 297 SER cc_start: 0.8548 (m) cc_final: 0.8287 (p) REVERT: B 307 THR cc_start: 0.8860 (m) cc_final: 0.8460 (p) REVERT: B 319 ARG cc_start: 0.8199 (ttm110) cc_final: 0.7923 (ttm110) REVERT: B 327 VAL cc_start: 0.8846 (t) cc_final: 0.8528 (m) REVERT: B 347 PHE cc_start: 0.3891 (OUTLIER) cc_final: 0.3156 (t80) REVERT: B 361 CYS cc_start: 0.7220 (OUTLIER) cc_final: 0.6917 (t) REVERT: B 406 GLU cc_start: 0.8377 (mt-10) cc_final: 0.7933 (mt-10) REVERT: B 558 LYS cc_start: 0.8863 (mmmt) cc_final: 0.8311 (mmmt) REVERT: B 568 ASP cc_start: 0.7976 (p0) cc_final: 0.7538 (p0) REVERT: B 580 GLN cc_start: 0.8727 (mm-40) cc_final: 0.8317 (mm-40) REVERT: B 674 TYR cc_start: 0.8431 (t80) cc_final: 0.8212 (t80) REVERT: B 707 TYR cc_start: 0.8547 (t80) cc_final: 0.8261 (t80) REVERT: B 725 GLU cc_start: 0.8125 (pt0) cc_final: 0.7767 (pt0) REVERT: B 764 LYS cc_start: 0.8720 (ttmm) cc_final: 0.8391 (ttpp) REVERT: B 773 GLU cc_start: 0.7689 (tm-30) cc_final: 0.6963 (tm-30) REVERT: B 776 LYS cc_start: 0.8888 (ttpp) cc_final: 0.8650 (tptm) REVERT: B 795 LYS cc_start: 0.8953 (mttt) cc_final: 0.8745 (mttm) REVERT: B 816 SER cc_start: 0.8847 (m) cc_final: 0.8458 (p) REVERT: B 825 LYS cc_start: 0.8792 (mtmm) cc_final: 0.8552 (mtpp) REVERT: B 851 CYS cc_start: 0.8538 (t) cc_final: 0.8122 (t) REVERT: B 904 TYR cc_start: 0.8105 (m-10) cc_final: 0.6936 (m-10) REVERT: B 914 ASN cc_start: 0.8511 (p0) cc_final: 0.8206 (p0) REVERT: B 918 GLU cc_start: 0.7980 (mp0) cc_final: 0.7675 (mp0) REVERT: B 949 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8442 (mm-40) REVERT: B 950 ASP cc_start: 0.8023 (t70) cc_final: 0.7720 (t70) REVERT: B 964 LYS cc_start: 0.8599 (mtmp) cc_final: 0.8312 (ttmm) REVERT: B 977 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8783 (mt) REVERT: B 979 ASP cc_start: 0.8173 (m-30) cc_final: 0.7854 (m-30) REVERT: B 990 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7861 (tp30) REVERT: B 1010 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8424 (mm-40) REVERT: B 1017 GLU cc_start: 0.8472 (tm-30) cc_final: 0.7995 (tm-30) REVERT: B 1019 ARG cc_start: 0.8158 (ttp80) cc_final: 0.7379 (ttp80) REVERT: B 1031 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7756 (mt-10) REVERT: B 1041 ASP cc_start: 0.8604 (m-30) cc_final: 0.8115 (t0) REVERT: B 1118 ASP cc_start: 0.7945 (t70) cc_final: 0.7481 (t0) REVERT: B 1125 ASN cc_start: 0.8333 (t0) cc_final: 0.7976 (t0) REVERT: C 81 ASN cc_start: 0.7944 (p0) cc_final: 0.7611 (p0) REVERT: C 135 PHE cc_start: 0.6354 (p90) cc_final: 0.6084 (p90) REVERT: C 177 MET cc_start: 0.7138 (tpp) cc_final: 0.5873 (tpp) REVERT: C 188 ARG cc_start: 0.8367 (ptp-170) cc_final: 0.7843 (ptp-110) REVERT: C 199 PHE cc_start: 0.7990 (t80) cc_final: 0.7581 (t80) REVERT: C 235 ILE cc_start: 0.8568 (mt) cc_final: 0.8332 (mm) REVERT: C 237 ARG cc_start: 0.8341 (mtm180) cc_final: 0.7811 (mtm180) REVERT: C 269 TYR cc_start: 0.8529 (m-80) cc_final: 0.8195 (m-80) REVERT: C 280 ASN cc_start: 0.8500 (t0) cc_final: 0.8158 (t0) REVERT: C 281 GLU cc_start: 0.7886 (pp20) cc_final: 0.7504 (pp20) REVERT: C 328 ARG cc_start: 0.7247 (mtm-85) cc_final: 0.6806 (mtm-85) REVERT: C 347 PHE cc_start: 0.8814 (t80) cc_final: 0.7799 (t80) REVERT: C 355 ARG cc_start: 0.8326 (ttm-80) cc_final: 0.7800 (tpt90) REVERT: C 357 ARG cc_start: 0.7658 (mtm180) cc_final: 0.6578 (mtp85) REVERT: C 378 LYS cc_start: 0.7800 (mmmm) cc_final: 0.7406 (mmmm) REVERT: C 386 LYS cc_start: 0.8233 (mttp) cc_final: 0.7785 (mtpt) REVERT: C 392 PHE cc_start: 0.7041 (m-80) cc_final: 0.6788 (m-80) REVERT: C 420 ASP cc_start: 0.8385 (t0) cc_final: 0.7919 (t0) REVERT: C 462 LYS cc_start: 0.8002 (tptt) cc_final: 0.7596 (ttmm) REVERT: C 528 LYS cc_start: 0.8689 (mmmm) cc_final: 0.8378 (mmmt) REVERT: C 537 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8513 (ptmm) REVERT: C 558 LYS cc_start: 0.8513 (mptt) cc_final: 0.8034 (mppt) REVERT: C 562 PHE cc_start: 0.8147 (p90) cc_final: 0.7844 (p90) REVERT: C 569 ILE cc_start: 0.7891 (mm) cc_final: 0.7576 (mm) REVERT: C 574 ASP cc_start: 0.8027 (t70) cc_final: 0.7607 (t0) REVERT: C 602 THR cc_start: 0.8684 (m) cc_final: 0.8244 (p) REVERT: C 671 CYS cc_start: 0.6890 (m) cc_final: 0.6521 (m) REVERT: C 725 GLU cc_start: 0.8335 (tt0) cc_final: 0.8017 (tm-30) REVERT: C 726 ILE cc_start: 0.9344 (OUTLIER) cc_final: 0.8966 (mm) REVERT: C 739 THR cc_start: 0.8528 (m) cc_final: 0.8182 (t) REVERT: C 773 GLU cc_start: 0.8095 (tt0) cc_final: 0.6859 (tp30) REVERT: C 774 GLN cc_start: 0.7980 (mm-40) cc_final: 0.7500 (mp10) REVERT: C 776 LYS cc_start: 0.8700 (tmmt) cc_final: 0.8404 (ttmm) REVERT: C 777 ASN cc_start: 0.8411 (m-40) cc_final: 0.7402 (m110) REVERT: C 779 GLN cc_start: 0.8527 (tm-30) cc_final: 0.8145 (tm-30) REVERT: C 808 ASP cc_start: 0.8142 (t70) cc_final: 0.7868 (t0) REVERT: C 851 CYS cc_start: 0.8222 (t) cc_final: 0.7598 (t) REVERT: C 868 GLU cc_start: 0.8519 (mp0) cc_final: 0.8262 (mp0) REVERT: C 933 LYS cc_start: 0.8613 (mtpp) cc_final: 0.8392 (mtmm) REVERT: C 949 GLN cc_start: 0.8688 (mm110) cc_final: 0.8357 (mm-40) REVERT: C 964 LYS cc_start: 0.8754 (tmtm) cc_final: 0.8368 (ttmm) REVERT: C 988 GLU cc_start: 0.8410 (tp30) cc_final: 0.7535 (tp30) REVERT: C 1002 GLN cc_start: 0.8316 (tp40) cc_final: 0.7960 (tp40) REVERT: C 1010 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8145 (mp10) REVERT: C 1017 GLU cc_start: 0.8292 (tp30) cc_final: 0.7841 (tp30) REVERT: C 1019 ARG cc_start: 0.7905 (ttp80) cc_final: 0.7525 (ttp80) REVERT: C 1072 GLU cc_start: 0.8584 (pm20) cc_final: 0.8252 (pm20) REVERT: C 1107 ARG cc_start: 0.7894 (mtt180) cc_final: 0.7459 (mtt180) REVERT: C 1118 ASP cc_start: 0.8167 (t0) cc_final: 0.7852 (t0) REVERT: C 1138 TYR cc_start: 0.7895 (t80) cc_final: 0.7554 (t80) outliers start: 142 outliers final: 96 residues processed: 635 average time/residue: 0.4112 time to fit residues: 401.8096 Evaluate side-chains 609 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 497 time to evaluate : 2.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 388 ASN 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 511 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 949 GLN Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 537 LYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 245 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 311 optimal weight: 5.9990 chunk 188 optimal weight: 0.9980 chunk 196 optimal weight: 0.0370 chunk 85 optimal weight: 4.9990 chunk 141 optimal weight: 8.9990 chunk 303 optimal weight: 0.0980 chunk 162 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 231 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 296 optimal weight: 3.9990 overall best weight: 1.4262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS A 394 ASN ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN B 183 ASN B 317 ASN B 448 ASN B 955 ASN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 563 GLN C 675 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1064 HIS ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.158323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.116853 restraints weight = 45696.534| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 3.13 r_work: 0.3240 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 26904 Z= 0.207 Angle : 0.658 13.291 36699 Z= 0.329 Chirality : 0.047 0.332 4216 Planarity : 0.004 0.049 4697 Dihedral : 6.696 58.842 4271 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.10 % Favored : 89.90 % Rotamer: Outliers : 5.29 % Allowed : 19.39 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.33 (0.14), residues: 3276 helix: 0.99 (0.21), residues: 658 sheet: -1.56 (0.21), residues: 581 loop : -2.58 (0.13), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 104 HIS 0.006 0.001 HIS A 205 PHE 0.023 0.002 PHE A 168 TYR 0.020 0.001 TYR C1067 ARG 0.005 0.000 ARG A1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00380 ( 28) link_NAG-ASN : angle 2.30159 ( 84) hydrogen bonds : bond 0.03740 ( 750) hydrogen bonds : angle 4.89081 ( 2004) SS BOND : bond 0.00289 ( 41) SS BOND : angle 1.79651 ( 82) covalent geometry : bond 0.00451 (26835) covalent geometry : angle 0.64483 (36533) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 524 time to evaluate : 2.630 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 64 TRP cc_start: 0.7964 (t60) cc_final: 0.7622 (t-100) REVERT: A 66 HIS cc_start: 0.8328 (OUTLIER) cc_final: 0.7669 (m90) REVERT: A 97 LYS cc_start: 0.8666 (tppt) cc_final: 0.8403 (tppt) REVERT: A 109 THR cc_start: 0.8699 (p) cc_final: 0.8405 (t) REVERT: A 132 GLU cc_start: 0.6771 (pm20) cc_final: 0.5984 (pm20) REVERT: A 164 ASN cc_start: 0.8031 (p0) cc_final: 0.7631 (p0) REVERT: A 186 ASN cc_start: 0.7828 (OUTLIER) cc_final: 0.7319 (p0) REVERT: A 224 GLU cc_start: 0.8255 (mp0) cc_final: 0.7740 (mp0) REVERT: A 239 GLN cc_start: 0.7993 (tp40) cc_final: 0.7697 (tp40) REVERT: A 269 TYR cc_start: 0.8647 (m-80) cc_final: 0.7702 (m-80) REVERT: A 282 ASN cc_start: 0.8876 (OUTLIER) cc_final: 0.8402 (m-40) REVERT: A 297 SER cc_start: 0.8619 (m) cc_final: 0.8228 (p) REVERT: A 307 THR cc_start: 0.8798 (m) cc_final: 0.8486 (p) REVERT: A 356 LYS cc_start: 0.7769 (OUTLIER) cc_final: 0.7288 (tmmm) REVERT: A 390 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.6925 (tt) REVERT: A 392 PHE cc_start: 0.7483 (m-80) cc_final: 0.7187 (m-80) REVERT: A 542 ASN cc_start: 0.8665 (t0) cc_final: 0.8321 (t0) REVERT: A 544 ASN cc_start: 0.8558 (m-40) cc_final: 0.8231 (t0) REVERT: A 562 PHE cc_start: 0.7956 (p90) cc_final: 0.7619 (p90) REVERT: A 569 ILE cc_start: 0.8616 (pt) cc_final: 0.8385 (mp) REVERT: A 580 GLN cc_start: 0.8315 (pt0) cc_final: 0.7878 (pt0) REVERT: A 602 THR cc_start: 0.8575 (OUTLIER) cc_final: 0.8353 (p) REVERT: A 664 ILE cc_start: 0.8940 (mt) cc_final: 0.8645 (mm) REVERT: A 675 GLN cc_start: 0.7543 (mm-40) cc_final: 0.7079 (mm-40) REVERT: A 702 GLU cc_start: 0.7888 (mp0) cc_final: 0.7684 (mp0) REVERT: A 708 SER cc_start: 0.8548 (t) cc_final: 0.8224 (m) REVERT: A 725 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7514 (tm-30) REVERT: A 773 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7180 (tm-30) REVERT: A 780 GLU cc_start: 0.8120 (pt0) cc_final: 0.7660 (tm-30) REVERT: A 788 ILE cc_start: 0.8927 (mm) cc_final: 0.8674 (mm) REVERT: A 790 LYS cc_start: 0.8270 (mppt) cc_final: 0.7963 (mppt) REVERT: A 803 SER cc_start: 0.8733 (m) cc_final: 0.8456 (p) REVERT: A 851 CYS cc_start: 0.8635 (t) cc_final: 0.7977 (t) REVERT: A 855 PHE cc_start: 0.8349 (m-10) cc_final: 0.8139 (m-80) REVERT: A 868 GLU cc_start: 0.8356 (tp30) cc_final: 0.8061 (tm-30) REVERT: A 869 MET cc_start: 0.8678 (mtt) cc_final: 0.8420 (mtm) REVERT: A 933 LYS cc_start: 0.8414 (mtmt) cc_final: 0.8108 (mttp) REVERT: A 994 ASP cc_start: 0.7688 (t70) cc_final: 0.7427 (t70) REVERT: A 995 ARG cc_start: 0.8494 (mtm-85) cc_final: 0.8270 (ttp-110) REVERT: A 1017 GLU cc_start: 0.8328 (tm-30) cc_final: 0.7830 (tp30) REVERT: A 1050 MET cc_start: 0.8140 (mtm) cc_final: 0.7938 (mtp) REVERT: B 52 GLN cc_start: 0.8328 (tm-30) cc_final: 0.7966 (tm-30) REVERT: B 121 ASN cc_start: 0.7926 (p0) cc_final: 0.7055 (t0) REVERT: B 205 HIS cc_start: 0.8181 (t70) cc_final: 0.7975 (t-90) REVERT: B 208 ILE cc_start: 0.7914 (OUTLIER) cc_final: 0.7606 (pt) REVERT: B 297 SER cc_start: 0.8473 (m) cc_final: 0.8246 (p) REVERT: B 307 THR cc_start: 0.8870 (m) cc_final: 0.8462 (p) REVERT: B 327 VAL cc_start: 0.8908 (t) cc_final: 0.8609 (m) REVERT: B 347 PHE cc_start: 0.4275 (OUTLIER) cc_final: 0.3588 (t80) REVERT: B 359 SER cc_start: 0.8010 (p) cc_final: 0.7778 (t) REVERT: B 361 CYS cc_start: 0.7237 (OUTLIER) cc_final: 0.7036 (t) REVERT: B 380 TYR cc_start: 0.7514 (m-80) cc_final: 0.7030 (m-80) REVERT: B 406 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8138 (mt-10) REVERT: B 547 LYS cc_start: 0.8666 (mmtm) cc_final: 0.8447 (mmtm) REVERT: B 558 LYS cc_start: 0.8820 (mmmt) cc_final: 0.8351 (mmmt) REVERT: B 580 GLN cc_start: 0.8725 (mm-40) cc_final: 0.8292 (mm-40) REVERT: B 674 TYR cc_start: 0.8513 (t80) cc_final: 0.8291 (t80) REVERT: B 725 GLU cc_start: 0.8105 (pt0) cc_final: 0.7761 (pt0) REVERT: B 762 GLN cc_start: 0.7988 (pt0) cc_final: 0.7763 (pt0) REVERT: B 764 LYS cc_start: 0.8790 (ttmm) cc_final: 0.8475 (ttpp) REVERT: B 773 GLU cc_start: 0.7709 (tm-30) cc_final: 0.7018 (tm-30) REVERT: B 795 LYS cc_start: 0.8935 (mttt) cc_final: 0.8732 (mttm) REVERT: B 816 SER cc_start: 0.8867 (m) cc_final: 0.8535 (p) REVERT: B 851 CYS cc_start: 0.8667 (t) cc_final: 0.8247 (t) REVERT: B 904 TYR cc_start: 0.8022 (m-10) cc_final: 0.7180 (m-10) REVERT: B 918 GLU cc_start: 0.7918 (mp0) cc_final: 0.7628 (mp0) REVERT: B 949 GLN cc_start: 0.8872 (mm-40) cc_final: 0.8423 (mm-40) REVERT: B 950 ASP cc_start: 0.8032 (t70) cc_final: 0.7680 (t70) REVERT: B 964 LYS cc_start: 0.8650 (mtmp) cc_final: 0.8330 (ttmm) REVERT: B 979 ASP cc_start: 0.8128 (m-30) cc_final: 0.7804 (m-30) REVERT: B 990 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7842 (tp30) REVERT: B 1010 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.7922 (mp10) REVERT: B 1017 GLU cc_start: 0.8373 (tm-30) cc_final: 0.7917 (tm-30) REVERT: B 1019 ARG cc_start: 0.8158 (ttp80) cc_final: 0.7496 (ttp80) REVERT: B 1031 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7807 (mt-10) REVERT: B 1041 ASP cc_start: 0.8437 (m-30) cc_final: 0.8031 (t0) REVERT: B 1118 ASP cc_start: 0.8010 (t70) cc_final: 0.7541 (t0) REVERT: B 1125 ASN cc_start: 0.8399 (t0) cc_final: 0.8088 (t0) REVERT: C 81 ASN cc_start: 0.8027 (p0) cc_final: 0.7629 (p0) REVERT: C 135 PHE cc_start: 0.6734 (p90) cc_final: 0.6481 (p90) REVERT: C 177 MET cc_start: 0.7166 (tpp) cc_final: 0.6256 (tpp) REVERT: C 188 ARG cc_start: 0.8444 (ptp-170) cc_final: 0.7958 (ptp-170) REVERT: C 199 PHE cc_start: 0.8144 (t80) cc_final: 0.7736 (t80) REVERT: C 235 ILE cc_start: 0.8678 (mt) cc_final: 0.8385 (mm) REVERT: C 237 ARG cc_start: 0.8282 (mtm180) cc_final: 0.7665 (mtm180) REVERT: C 280 ASN cc_start: 0.8494 (t0) cc_final: 0.8188 (t0) REVERT: C 281 GLU cc_start: 0.7927 (pp20) cc_final: 0.7589 (pp20) REVERT: C 335 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.7251 (tt) REVERT: C 355 ARG cc_start: 0.8255 (ttm-80) cc_final: 0.8001 (tpt90) REVERT: C 378 LYS cc_start: 0.7763 (mmmm) cc_final: 0.7334 (mmmm) REVERT: C 386 LYS cc_start: 0.8255 (mttp) cc_final: 0.7653 (ttmt) REVERT: C 392 PHE cc_start: 0.7238 (m-80) cc_final: 0.6851 (m-80) REVERT: C 462 LYS cc_start: 0.8060 (tptt) cc_final: 0.7687 (ttmm) REVERT: C 501 TYR cc_start: 0.6486 (OUTLIER) cc_final: 0.6110 (m-10) REVERT: C 528 LYS cc_start: 0.8856 (mmmm) cc_final: 0.8582 (mmmt) REVERT: C 558 LYS cc_start: 0.8561 (mptt) cc_final: 0.8080 (mppt) REVERT: C 569 ILE cc_start: 0.8054 (mm) cc_final: 0.7812 (mm) REVERT: C 574 ASP cc_start: 0.8036 (t70) cc_final: 0.7641 (t0) REVERT: C 602 THR cc_start: 0.8693 (m) cc_final: 0.8307 (p) REVERT: C 671 CYS cc_start: 0.6815 (m) cc_final: 0.6436 (m) REVERT: C 725 GLU cc_start: 0.8336 (tt0) cc_final: 0.8036 (tm-30) REVERT: C 726 ILE cc_start: 0.9343 (OUTLIER) cc_final: 0.8944 (mm) REVERT: C 739 THR cc_start: 0.8537 (m) cc_final: 0.8214 (t) REVERT: C 773 GLU cc_start: 0.8061 (tt0) cc_final: 0.7083 (tp30) REVERT: C 776 LYS cc_start: 0.8699 (tmmt) cc_final: 0.8422 (ttmm) REVERT: C 777 ASN cc_start: 0.8439 (m-40) cc_final: 0.7472 (m110) REVERT: C 779 GLN cc_start: 0.8600 (tm-30) cc_final: 0.8235 (tm-30) REVERT: C 808 ASP cc_start: 0.8159 (t70) cc_final: 0.7906 (t0) REVERT: C 851 CYS cc_start: 0.8213 (t) cc_final: 0.7613 (t) REVERT: C 868 GLU cc_start: 0.8490 (mp0) cc_final: 0.8232 (mp0) REVERT: C 933 LYS cc_start: 0.8629 (mtpp) cc_final: 0.8413 (mtmm) REVERT: C 949 GLN cc_start: 0.8716 (mm110) cc_final: 0.8366 (mm-40) REVERT: C 964 LYS cc_start: 0.8837 (tmtm) cc_final: 0.8448 (ttmm) REVERT: C 988 GLU cc_start: 0.8326 (tp30) cc_final: 0.7492 (tp30) REVERT: C 1002 GLN cc_start: 0.8397 (tp40) cc_final: 0.8093 (tp40) REVERT: C 1010 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.8071 (mp10) REVERT: C 1017 GLU cc_start: 0.8161 (tp30) cc_final: 0.7741 (tp30) REVERT: C 1072 GLU cc_start: 0.8481 (pm20) cc_final: 0.8198 (pm20) REVERT: C 1107 ARG cc_start: 0.7887 (mtt180) cc_final: 0.7454 (mtt180) REVERT: C 1138 TYR cc_start: 0.7881 (t80) cc_final: 0.7606 (t80) outliers start: 151 outliers final: 109 residues processed: 637 average time/residue: 0.4074 time to fit residues: 400.0307 Evaluate side-chains 634 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 510 time to evaluate : 3.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 361 CYS 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 511 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 205 HIS Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 226 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 77 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 215 optimal weight: 9.9990 chunk 295 optimal weight: 4.9990 chunk 227 optimal weight: 0.9980 chunk 223 optimal weight: 3.9990 chunk 255 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 308 optimal weight: 50.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 HIS ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.194930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.168333 restraints weight = 56343.898| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.19 r_work: 0.3392 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.4375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26904 Z= 0.147 Angle : 0.645 16.440 36699 Z= 0.319 Chirality : 0.046 0.331 4216 Planarity : 0.004 0.049 4697 Dihedral : 6.607 59.892 4269 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.46 % Favored : 90.54 % Rotamer: Outliers : 4.87 % Allowed : 20.02 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.20 (0.14), residues: 3276 helix: 1.13 (0.21), residues: 657 sheet: -1.55 (0.20), residues: 596 loop : -2.48 (0.13), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP B 104 HIS 0.011 0.001 HIS A 205 PHE 0.026 0.001 PHE A 190 TYR 0.021 0.001 TYR B 707 ARG 0.005 0.000 ARG C 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00355 ( 28) link_NAG-ASN : angle 2.20414 ( 84) hydrogen bonds : bond 0.03441 ( 750) hydrogen bonds : angle 4.84074 ( 2004) SS BOND : bond 0.00277 ( 41) SS BOND : angle 1.65633 ( 82) covalent geometry : bond 0.00326 (26835) covalent geometry : angle 0.63250 (36533) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 525 time to evaluate : 2.944 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 109 THR cc_start: 0.8574 (p) cc_final: 0.8303 (t) REVERT: A 132 GLU cc_start: 0.6932 (pm20) cc_final: 0.6136 (pm20) REVERT: A 186 ASN cc_start: 0.7799 (p0) cc_final: 0.7357 (p0) REVERT: A 224 GLU cc_start: 0.8332 (mp0) cc_final: 0.8044 (mp0) REVERT: A 239 GLN cc_start: 0.8053 (tp40) cc_final: 0.7696 (tp40) REVERT: A 269 TYR cc_start: 0.8578 (m-80) cc_final: 0.7660 (m-80) REVERT: A 282 ASN cc_start: 0.8901 (OUTLIER) cc_final: 0.8430 (m-40) REVERT: A 297 SER cc_start: 0.8544 (m) cc_final: 0.8162 (p) REVERT: A 307 THR cc_start: 0.8817 (m) cc_final: 0.8525 (p) REVERT: A 356 LYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7321 (tmmm) REVERT: A 390 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.6964 (tt) REVERT: A 392 PHE cc_start: 0.7684 (m-80) cc_final: 0.7337 (m-80) REVERT: A 542 ASN cc_start: 0.8636 (t0) cc_final: 0.8296 (t0) REVERT: A 544 ASN cc_start: 0.8545 (m-40) cc_final: 0.8214 (t0) REVERT: A 546 LEU cc_start: 0.8229 (tp) cc_final: 0.7992 (tt) REVERT: A 562 PHE cc_start: 0.7968 (p90) cc_final: 0.7511 (p90) REVERT: A 569 ILE cc_start: 0.8614 (pt) cc_final: 0.8371 (mp) REVERT: A 580 GLN cc_start: 0.8415 (pt0) cc_final: 0.7958 (pt0) REVERT: A 602 THR cc_start: 0.8584 (OUTLIER) cc_final: 0.8353 (p) REVERT: A 664 ILE cc_start: 0.8945 (mt) cc_final: 0.8666 (mm) REVERT: A 675 GLN cc_start: 0.7576 (mm-40) cc_final: 0.7136 (mm-40) REVERT: A 708 SER cc_start: 0.8537 (t) cc_final: 0.8226 (m) REVERT: A 725 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7527 (tm-30) REVERT: A 773 GLU cc_start: 0.7946 (tm-30) cc_final: 0.7194 (tm-30) REVERT: A 780 GLU cc_start: 0.8192 (pt0) cc_final: 0.7693 (tm-30) REVERT: A 788 ILE cc_start: 0.8968 (mm) cc_final: 0.8728 (mm) REVERT: A 790 LYS cc_start: 0.8246 (mppt) cc_final: 0.7944 (mppt) REVERT: A 803 SER cc_start: 0.8684 (m) cc_final: 0.8388 (p) REVERT: A 851 CYS cc_start: 0.8567 (t) cc_final: 0.7846 (t) REVERT: A 855 PHE cc_start: 0.8287 (m-10) cc_final: 0.8047 (m-80) REVERT: A 868 GLU cc_start: 0.8295 (tp30) cc_final: 0.8026 (tm-30) REVERT: A 869 MET cc_start: 0.8677 (mtt) cc_final: 0.8409 (mtm) REVERT: A 933 LYS cc_start: 0.8327 (mtmt) cc_final: 0.8042 (mttp) REVERT: A 955 ASN cc_start: 0.8239 (t0) cc_final: 0.8009 (t0) REVERT: A 964 LYS cc_start: 0.8752 (ttpp) cc_final: 0.8517 (ttpp) REVERT: A 990 GLU cc_start: 0.8297 (tm-30) cc_final: 0.7925 (tm-30) REVERT: A 994 ASP cc_start: 0.7681 (t70) cc_final: 0.7419 (t70) REVERT: A 996 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8412 (tp) REVERT: A 1017 GLU cc_start: 0.8342 (tm-30) cc_final: 0.7823 (tp30) REVERT: A 1050 MET cc_start: 0.8081 (mtm) cc_final: 0.7841 (mtp) REVERT: B 52 GLN cc_start: 0.8297 (tm-30) cc_final: 0.7908 (tm-30) REVERT: B 92 PHE cc_start: 0.8119 (t80) cc_final: 0.7526 (t80) REVERT: B 121 ASN cc_start: 0.7772 (p0) cc_final: 0.6866 (t0) REVERT: B 187 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7752 (mt) REVERT: B 190 PHE cc_start: 0.8375 (m-10) cc_final: 0.8118 (m-10) REVERT: B 297 SER cc_start: 0.8473 (m) cc_final: 0.8273 (p) REVERT: B 298 GLU cc_start: 0.8285 (tt0) cc_final: 0.8081 (tt0) REVERT: B 327 VAL cc_start: 0.8844 (t) cc_final: 0.8551 (m) REVERT: B 347 PHE cc_start: 0.4053 (OUTLIER) cc_final: 0.3328 (t80) REVERT: B 359 SER cc_start: 0.7863 (p) cc_final: 0.7617 (t) REVERT: B 361 CYS cc_start: 0.7089 (OUTLIER) cc_final: 0.6872 (t) REVERT: B 380 TYR cc_start: 0.7594 (m-80) cc_final: 0.7046 (m-80) REVERT: B 558 LYS cc_start: 0.8913 (mmmt) cc_final: 0.8479 (mmmt) REVERT: B 580 GLN cc_start: 0.8797 (mm-40) cc_final: 0.8391 (mm-40) REVERT: B 674 TYR cc_start: 0.8434 (t80) cc_final: 0.8205 (t80) REVERT: B 707 TYR cc_start: 0.8636 (t80) cc_final: 0.8310 (t80) REVERT: B 725 GLU cc_start: 0.8022 (pt0) cc_final: 0.7637 (pt0) REVERT: B 762 GLN cc_start: 0.7938 (pt0) cc_final: 0.7728 (pt0) REVERT: B 764 LYS cc_start: 0.8748 (ttmm) cc_final: 0.8443 (ttpp) REVERT: B 773 GLU cc_start: 0.7654 (tm-30) cc_final: 0.6966 (tm-30) REVERT: B 776 LYS cc_start: 0.8904 (tptm) cc_final: 0.8686 (tptm) REVERT: B 795 LYS cc_start: 0.8923 (mttt) cc_final: 0.8715 (mttm) REVERT: B 796 TYR cc_start: 0.8831 (t80) cc_final: 0.8585 (t80) REVERT: B 816 SER cc_start: 0.8845 (m) cc_final: 0.8481 (p) REVERT: B 825 LYS cc_start: 0.8702 (mtmm) cc_final: 0.8424 (mtmm) REVERT: B 851 CYS cc_start: 0.8639 (t) cc_final: 0.8202 (t) REVERT: B 904 TYR cc_start: 0.7964 (m-10) cc_final: 0.7065 (m-10) REVERT: B 949 GLN cc_start: 0.8842 (mm-40) cc_final: 0.8494 (mm-40) REVERT: B 950 ASP cc_start: 0.8103 (t70) cc_final: 0.7738 (t70) REVERT: B 957 GLN cc_start: 0.8446 (pt0) cc_final: 0.8224 (pt0) REVERT: B 964 LYS cc_start: 0.8602 (mtmp) cc_final: 0.8298 (ttmm) REVERT: B 979 ASP cc_start: 0.8109 (m-30) cc_final: 0.7745 (m-30) REVERT: B 990 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7937 (tp30) REVERT: B 1010 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.7955 (mp10) REVERT: B 1017 GLU cc_start: 0.8478 (tm-30) cc_final: 0.8011 (tm-30) REVERT: B 1019 ARG cc_start: 0.8100 (ttp80) cc_final: 0.7475 (ttp80) REVERT: B 1031 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7614 (mt-10) REVERT: B 1041 ASP cc_start: 0.8555 (m-30) cc_final: 0.8069 (t0) REVERT: B 1118 ASP cc_start: 0.7975 (t70) cc_final: 0.7503 (t0) REVERT: C 41 LYS cc_start: 0.8577 (mtpt) cc_final: 0.8110 (ptpp) REVERT: C 81 ASN cc_start: 0.7939 (p0) cc_final: 0.7730 (p0) REVERT: C 86 PHE cc_start: 0.8117 (t80) cc_final: 0.7671 (t80) REVERT: C 135 PHE cc_start: 0.6775 (p90) cc_final: 0.6522 (p90) REVERT: C 177 MET cc_start: 0.7092 (tpp) cc_final: 0.6032 (tpp) REVERT: C 188 ARG cc_start: 0.8443 (ptp-170) cc_final: 0.7909 (ptp-170) REVERT: C 199 PHE cc_start: 0.8117 (t80) cc_final: 0.7736 (t80) REVERT: C 235 ILE cc_start: 0.8670 (mt) cc_final: 0.8372 (mm) REVERT: C 237 ARG cc_start: 0.8407 (mtm180) cc_final: 0.7934 (mtm180) REVERT: C 269 TYR cc_start: 0.8554 (m-80) cc_final: 0.8222 (m-80) REVERT: C 280 ASN cc_start: 0.8541 (t0) cc_final: 0.8261 (t0) REVERT: C 281 GLU cc_start: 0.7967 (pp20) cc_final: 0.7644 (pp20) REVERT: C 308 VAL cc_start: 0.8824 (OUTLIER) cc_final: 0.8527 (m) REVERT: C 335 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7248 (tt) REVERT: C 347 PHE cc_start: 0.8778 (t80) cc_final: 0.7734 (t80) REVERT: C 355 ARG cc_start: 0.8241 (ttm-80) cc_final: 0.7777 (tpt90) REVERT: C 378 LYS cc_start: 0.7705 (mmmm) cc_final: 0.7309 (mmmm) REVERT: C 386 LYS cc_start: 0.8257 (mttp) cc_final: 0.7808 (mtpt) REVERT: C 462 LYS cc_start: 0.8229 (tptt) cc_final: 0.7824 (ttmm) REVERT: C 501 TYR cc_start: 0.6636 (OUTLIER) cc_final: 0.6184 (m-10) REVERT: C 528 LYS cc_start: 0.8938 (mmmm) cc_final: 0.8654 (mmmt) REVERT: C 558 LYS cc_start: 0.8587 (mptt) cc_final: 0.8085 (mppt) REVERT: C 562 PHE cc_start: 0.8193 (p90) cc_final: 0.7905 (p90) REVERT: C 574 ASP cc_start: 0.8001 (t70) cc_final: 0.7636 (t0) REVERT: C 602 THR cc_start: 0.8697 (m) cc_final: 0.8248 (p) REVERT: C 671 CYS cc_start: 0.6987 (m) cc_final: 0.6607 (m) REVERT: C 725 GLU cc_start: 0.8268 (tt0) cc_final: 0.7962 (tm-30) REVERT: C 726 ILE cc_start: 0.9317 (OUTLIER) cc_final: 0.8884 (mm) REVERT: C 739 THR cc_start: 0.8489 (m) cc_final: 0.8184 (t) REVERT: C 773 GLU cc_start: 0.8059 (tt0) cc_final: 0.7107 (tp30) REVERT: C 774 GLN cc_start: 0.8079 (mm-40) cc_final: 0.7554 (mp10) REVERT: C 776 LYS cc_start: 0.8761 (tmmt) cc_final: 0.8473 (ttmm) REVERT: C 777 ASN cc_start: 0.8402 (m-40) cc_final: 0.7541 (m110) REVERT: C 779 GLN cc_start: 0.8596 (tm-30) cc_final: 0.8390 (tm-30) REVERT: C 808 ASP cc_start: 0.8112 (t70) cc_final: 0.7845 (t0) REVERT: C 851 CYS cc_start: 0.8252 (t) cc_final: 0.7649 (t) REVERT: C 868 GLU cc_start: 0.8558 (mp0) cc_final: 0.8302 (mp0) REVERT: C 918 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8267 (mt-10) REVERT: C 933 LYS cc_start: 0.8678 (mtpp) cc_final: 0.8474 (mtmm) REVERT: C 949 GLN cc_start: 0.8774 (mm110) cc_final: 0.8404 (mm-40) REVERT: C 964 LYS cc_start: 0.8855 (tmtm) cc_final: 0.8456 (ttmm) REVERT: C 988 GLU cc_start: 0.8542 (tp30) cc_final: 0.7650 (tp30) REVERT: C 1002 GLN cc_start: 0.8354 (tp40) cc_final: 0.8050 (tp40) REVERT: C 1010 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.8132 (mp10) REVERT: C 1017 GLU cc_start: 0.8187 (tp30) cc_final: 0.7777 (tp30) REVERT: C 1027 THR cc_start: 0.8805 (m) cc_final: 0.8468 (t) REVERT: C 1050 MET cc_start: 0.8222 (mtm) cc_final: 0.7968 (mtm) REVERT: C 1072 GLU cc_start: 0.8537 (pm20) cc_final: 0.8242 (pm20) REVERT: C 1107 ARG cc_start: 0.7935 (mtt180) cc_final: 0.7460 (mtt180) REVERT: C 1111 GLU cc_start: 0.8674 (tt0) cc_final: 0.8453 (tt0) REVERT: D 208 MET cc_start: 0.0230 (tpp) cc_final: -0.0051 (tpp) outliers start: 139 outliers final: 114 residues processed: 627 average time/residue: 0.3909 time to fit residues: 379.2935 Evaluate side-chains 632 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 503 time to evaluate : 2.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 388 ASN 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 511 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 205 HIS Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 245 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 161 optimal weight: 5.9990 chunk 263 optimal weight: 0.0270 chunk 277 optimal weight: 0.9990 chunk 152 optimal weight: 0.4980 chunk 252 optimal weight: 0.0980 chunk 132 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 261 optimal weight: 0.8980 chunk 244 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 overall best weight: 0.5040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 205 HIS ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B 978 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1058 HIS C1101 HIS ** D 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 = 0.4040 r_free = 0.4040 target = 0.155872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.116361 restraints weight = 46183.122| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.88 r_work: 0.3329 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 26904 Z= 0.116 Angle : 0.635 15.881 36699 Z= 0.314 Chirality : 0.046 0.353 4216 Planarity : 0.004 0.049 4697 Dihedral : 6.476 59.579 4269 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 4.59 % Allowed : 20.90 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.11 (0.14), residues: 3276 helix: 1.24 (0.21), residues: 663 sheet: -1.45 (0.20), residues: 611 loop : -2.45 (0.13), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP A 64 HIS 0.016 0.001 HIS A 66 PHE 0.026 0.001 PHE C 392 TYR 0.025 0.001 TYR A 170 ARG 0.007 0.000 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00354 ( 28) link_NAG-ASN : angle 2.11678 ( 84) hydrogen bonds : bond 0.03176 ( 750) hydrogen bonds : angle 4.76517 ( 2004) SS BOND : bond 0.00240 ( 41) SS BOND : angle 1.46524 ( 82) covalent geometry : bond 0.00259 (26835) covalent geometry : angle 0.62419 (36533) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 511 time to evaluate : 2.672 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 109 THR cc_start: 0.8736 (p) cc_final: 0.8435 (t) REVERT: A 132 GLU cc_start: 0.6786 (pm20) cc_final: 0.6048 (pm20) REVERT: A 186 ASN cc_start: 0.7743 (p0) cc_final: 0.7423 (p0) REVERT: A 214 GLU cc_start: 0.7649 (pm20) cc_final: 0.7248 (pp20) REVERT: A 269 TYR cc_start: 0.8459 (m-80) cc_final: 0.7670 (m-80) REVERT: A 282 ASN cc_start: 0.8885 (OUTLIER) cc_final: 0.8470 (m-40) REVERT: A 297 SER cc_start: 0.8458 (m) cc_final: 0.8050 (p) REVERT: A 298 GLU cc_start: 0.8124 (tt0) cc_final: 0.7866 (tm-30) REVERT: A 356 LYS cc_start: 0.7647 (tmmm) cc_final: 0.7233 (tmmm) REVERT: A 386 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7388 (mtmm) REVERT: A 390 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7030 (tt) REVERT: A 392 PHE cc_start: 0.7593 (m-80) cc_final: 0.7201 (m-80) REVERT: A 542 ASN cc_start: 0.8670 (t0) cc_final: 0.8411 (t0) REVERT: A 569 ILE cc_start: 0.8565 (pt) cc_final: 0.8221 (mp) REVERT: A 580 GLN cc_start: 0.8245 (pt0) cc_final: 0.7828 (pt0) REVERT: A 602 THR cc_start: 0.8451 (OUTLIER) cc_final: 0.8245 (p) REVERT: A 664 ILE cc_start: 0.8982 (mt) cc_final: 0.8747 (mp) REVERT: A 675 GLN cc_start: 0.7465 (mm-40) cc_final: 0.7159 (mm-40) REVERT: A 708 SER cc_start: 0.8392 (t) cc_final: 0.8113 (m) REVERT: A 725 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7518 (tm-30) REVERT: A 773 GLU cc_start: 0.7737 (tm-30) cc_final: 0.7050 (tm-30) REVERT: A 780 GLU cc_start: 0.8032 (pt0) cc_final: 0.7663 (tm-30) REVERT: A 788 ILE cc_start: 0.8961 (mm) cc_final: 0.8747 (mm) REVERT: A 790 LYS cc_start: 0.8187 (mppt) cc_final: 0.7931 (mppt) REVERT: A 796 TYR cc_start: 0.8567 (t80) cc_final: 0.8339 (t80) REVERT: A 803 SER cc_start: 0.8550 (m) cc_final: 0.8336 (p) REVERT: A 851 CYS cc_start: 0.8703 (t) cc_final: 0.8067 (t) REVERT: A 855 PHE cc_start: 0.8213 (m-10) cc_final: 0.7996 (m-80) REVERT: A 868 GLU cc_start: 0.8283 (tp30) cc_final: 0.8038 (tm-30) REVERT: A 869 MET cc_start: 0.8531 (mtt) cc_final: 0.8309 (mtm) REVERT: A 933 LYS cc_start: 0.8321 (mtmt) cc_final: 0.8069 (mttp) REVERT: A 990 GLU cc_start: 0.8231 (tm-30) cc_final: 0.7856 (tm-30) REVERT: A 994 ASP cc_start: 0.7566 (t70) cc_final: 0.7257 (t70) REVERT: A 1017 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7775 (tp30) REVERT: A 1050 MET cc_start: 0.8086 (mtm) cc_final: 0.7872 (mtp) REVERT: A 1107 ARG cc_start: 0.7886 (mtt90) cc_final: 0.6043 (mtt90) REVERT: B 52 GLN cc_start: 0.8265 (tm-30) cc_final: 0.7920 (tm-30) REVERT: B 121 ASN cc_start: 0.7782 (p0) cc_final: 0.6979 (t0) REVERT: B 129 LYS cc_start: 0.8549 (ttmt) cc_final: 0.8092 (tmtt) REVERT: B 187 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8044 (mt) REVERT: B 298 GLU cc_start: 0.8033 (tt0) cc_final: 0.7812 (tt0) REVERT: B 307 THR cc_start: 0.8731 (m) cc_final: 0.8330 (p) REVERT: B 327 VAL cc_start: 0.8874 (t) cc_final: 0.8569 (m) REVERT: B 347 PHE cc_start: 0.3566 (OUTLIER) cc_final: 0.2899 (t80) REVERT: B 378 LYS cc_start: 0.8486 (mmtt) cc_final: 0.8015 (mmtt) REVERT: B 380 TYR cc_start: 0.7339 (m-80) cc_final: 0.6880 (m-80) REVERT: B 406 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7656 (mt-10) REVERT: B 551 VAL cc_start: 0.8932 (t) cc_final: 0.8696 (m) REVERT: B 558 LYS cc_start: 0.8810 (mmmt) cc_final: 0.8505 (mmmt) REVERT: B 580 GLN cc_start: 0.8602 (mm-40) cc_final: 0.8248 (mm-40) REVERT: B 586 ASP cc_start: 0.7759 (t0) cc_final: 0.7551 (t0) REVERT: B 707 TYR cc_start: 0.8495 (t80) cc_final: 0.8198 (t80) REVERT: B 725 GLU cc_start: 0.7999 (pt0) cc_final: 0.7662 (pt0) REVERT: B 764 LYS cc_start: 0.8679 (ttmm) cc_final: 0.8319 (ttpp) REVERT: B 773 GLU cc_start: 0.7604 (tm-30) cc_final: 0.6952 (tm-30) REVERT: B 776 LYS cc_start: 0.8916 (tptm) cc_final: 0.8696 (tptm) REVERT: B 796 TYR cc_start: 0.8681 (t80) cc_final: 0.8468 (t80) REVERT: B 816 SER cc_start: 0.8895 (m) cc_final: 0.8533 (p) REVERT: B 825 LYS cc_start: 0.8627 (mtmm) cc_final: 0.8419 (mtmm) REVERT: B 851 CYS cc_start: 0.8656 (t) cc_final: 0.8213 (t) REVERT: B 918 GLU cc_start: 0.7839 (mp0) cc_final: 0.7519 (mp0) REVERT: B 949 GLN cc_start: 0.8841 (mm-40) cc_final: 0.8485 (mm-40) REVERT: B 950 ASP cc_start: 0.7943 (t70) cc_final: 0.7591 (t70) REVERT: B 957 GLN cc_start: 0.8365 (pt0) cc_final: 0.8099 (pt0) REVERT: B 964 LYS cc_start: 0.8552 (mtmp) cc_final: 0.8268 (ttmm) REVERT: B 979 ASP cc_start: 0.8001 (m-30) cc_final: 0.7707 (m-30) REVERT: B 990 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7752 (tp30) REVERT: B 1010 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.7821 (mp10) REVERT: B 1017 GLU cc_start: 0.8326 (tm-30) cc_final: 0.7888 (tm-30) REVERT: B 1019 ARG cc_start: 0.7946 (ttp80) cc_final: 0.7278 (ttp80) REVERT: B 1031 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7681 (mt-10) REVERT: B 1041 ASP cc_start: 0.8455 (m-30) cc_final: 0.8016 (t0) REVERT: B 1118 ASP cc_start: 0.7783 (t70) cc_final: 0.7313 (t0) REVERT: C 40 ASP cc_start: 0.7916 (t0) cc_final: 0.7699 (t0) REVERT: C 41 LYS cc_start: 0.8472 (mtpt) cc_final: 0.8053 (ptpp) REVERT: C 177 MET cc_start: 0.6773 (tpp) cc_final: 0.5698 (tpp) REVERT: C 188 ARG cc_start: 0.8333 (ptp-170) cc_final: 0.7788 (ptp-170) REVERT: C 199 PHE cc_start: 0.8020 (t80) cc_final: 0.7704 (t80) REVERT: C 235 ILE cc_start: 0.8621 (mt) cc_final: 0.8386 (mm) REVERT: C 280 ASN cc_start: 0.8479 (t0) cc_final: 0.8206 (t0) REVERT: C 281 GLU cc_start: 0.7899 (pp20) cc_final: 0.7586 (pp20) REVERT: C 308 VAL cc_start: 0.8854 (OUTLIER) cc_final: 0.8574 (m) REVERT: C 335 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7330 (tt) REVERT: C 347 PHE cc_start: 0.8864 (t80) cc_final: 0.8037 (t80) REVERT: C 355 ARG cc_start: 0.8071 (ttm-80) cc_final: 0.7867 (tpt90) REVERT: C 378 LYS cc_start: 0.7553 (mmmm) cc_final: 0.7237 (mmmm) REVERT: C 386 LYS cc_start: 0.8074 (mttp) cc_final: 0.7506 (tttt) REVERT: C 462 LYS cc_start: 0.8050 (tptt) cc_final: 0.7653 (ttmm) REVERT: C 501 TYR cc_start: 0.6523 (OUTLIER) cc_final: 0.6186 (m-10) REVERT: C 528 LYS cc_start: 0.8887 (mmmm) cc_final: 0.8631 (mmmt) REVERT: C 558 LYS cc_start: 0.8417 (mptt) cc_final: 0.8012 (mppt) REVERT: C 574 ASP cc_start: 0.7836 (t70) cc_final: 0.7477 (t0) REVERT: C 592 PHE cc_start: 0.8116 (p90) cc_final: 0.7888 (p90) REVERT: C 602 THR cc_start: 0.8582 (m) cc_final: 0.8181 (p) REVERT: C 671 CYS cc_start: 0.6665 (m) cc_final: 0.6308 (m) REVERT: C 726 ILE cc_start: 0.9335 (OUTLIER) cc_final: 0.9008 (mm) REVERT: C 739 THR cc_start: 0.8390 (m) cc_final: 0.8093 (t) REVERT: C 773 GLU cc_start: 0.7805 (tt0) cc_final: 0.6850 (tp30) REVERT: C 774 GLN cc_start: 0.7930 (mm-40) cc_final: 0.7479 (mp10) REVERT: C 776 LYS cc_start: 0.8732 (tmmt) cc_final: 0.8489 (ttmm) REVERT: C 777 ASN cc_start: 0.8262 (m-40) cc_final: 0.7452 (m110) REVERT: C 808 ASP cc_start: 0.8126 (t70) cc_final: 0.7880 (t0) REVERT: C 851 CYS cc_start: 0.8274 (t) cc_final: 0.7681 (t) REVERT: C 904 TYR cc_start: 0.7934 (m-10) cc_final: 0.7587 (m-10) REVERT: C 918 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7882 (mt-10) REVERT: C 949 GLN cc_start: 0.8709 (mm110) cc_final: 0.8388 (mm-40) REVERT: C 964 LYS cc_start: 0.8772 (tmtm) cc_final: 0.8436 (ttmm) REVERT: C 1002 GLN cc_start: 0.8184 (tp40) cc_final: 0.7833 (tp40) REVERT: C 1010 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.7941 (mp10) REVERT: C 1017 GLU cc_start: 0.8246 (tp30) cc_final: 0.7788 (tp30) REVERT: C 1072 GLU cc_start: 0.8401 (pm20) cc_final: 0.8177 (pm20) REVERT: C 1139 ASP cc_start: 0.8098 (t0) cc_final: 0.7798 (t0) REVERT: D 208 MET cc_start: -0.0129 (tpp) cc_final: -0.0369 (tpp) outliers start: 131 outliers final: 98 residues processed: 608 average time/residue: 0.4065 time to fit residues: 383.8061 Evaluate side-chains 600 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 489 time to evaluate : 2.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 388 ASN 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 511 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 205 HIS Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 245 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 147 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 233 optimal weight: 7.9990 chunk 82 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 38 optimal weight: 20.0000 chunk 31 optimal weight: 0.0270 chunk 113 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 280 optimal weight: 2.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN B 955 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 563 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1058 HIS C1101 HIS ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.154868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.115405 restraints weight = 46249.203| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.88 r_work: 0.3326 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26904 Z= 0.132 Angle : 0.653 15.836 36699 Z= 0.324 Chirality : 0.046 0.330 4216 Planarity : 0.004 0.048 4697 Dihedral : 6.452 59.847 4268 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 4.34 % Allowed : 21.60 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.00 (0.14), residues: 3276 helix: 1.42 (0.21), residues: 652 sheet: -1.45 (0.20), residues: 616 loop : -2.37 (0.13), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 64 HIS 0.010 0.001 HIS A 205 PHE 0.028 0.001 PHE C 140 TYR 0.026 0.001 TYR A 170 ARG 0.010 0.000 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00355 ( 28) link_NAG-ASN : angle 2.08095 ( 84) hydrogen bonds : bond 0.03220 ( 750) hydrogen bonds : angle 4.77873 ( 2004) SS BOND : bond 0.00341 ( 41) SS BOND : angle 1.42305 ( 82) covalent geometry : bond 0.00296 (26835) covalent geometry : angle 0.64284 (36533) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 496 time to evaluate : 2.811 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 109 THR cc_start: 0.8742 (p) cc_final: 0.8431 (t) REVERT: A 132 GLU cc_start: 0.6835 (pm20) cc_final: 0.6005 (pm20) REVERT: A 164 ASN cc_start: 0.7955 (p0) cc_final: 0.7657 (p0) REVERT: A 186 ASN cc_start: 0.7741 (p0) cc_final: 0.7359 (p0) REVERT: A 269 TYR cc_start: 0.8466 (m-80) cc_final: 0.7713 (m-80) REVERT: A 282 ASN cc_start: 0.8914 (OUTLIER) cc_final: 0.8515 (m-40) REVERT: A 297 SER cc_start: 0.8454 (m) cc_final: 0.8099 (p) REVERT: A 356 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.7308 (tmmm) REVERT: A 386 LYS cc_start: 0.7699 (OUTLIER) cc_final: 0.7299 (mttm) REVERT: A 390 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7094 (tt) REVERT: A 392 PHE cc_start: 0.7664 (m-80) cc_final: 0.7253 (m-80) REVERT: A 542 ASN cc_start: 0.8709 (t0) cc_final: 0.8427 (t0) REVERT: A 569 ILE cc_start: 0.8578 (pt) cc_final: 0.8241 (mp) REVERT: A 580 GLN cc_start: 0.8236 (pt0) cc_final: 0.7840 (pt0) REVERT: A 591 SER cc_start: 0.9004 (t) cc_final: 0.8699 (p) REVERT: A 675 GLN cc_start: 0.7505 (mm-40) cc_final: 0.7173 (mm-40) REVERT: A 708 SER cc_start: 0.8391 (t) cc_final: 0.8091 (m) REVERT: A 725 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7511 (tm-30) REVERT: A 773 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7033 (tm-30) REVERT: A 780 GLU cc_start: 0.8114 (pt0) cc_final: 0.7656 (tm-30) REVERT: A 788 ILE cc_start: 0.8944 (mm) cc_final: 0.8731 (mm) REVERT: A 790 LYS cc_start: 0.8195 (mppt) cc_final: 0.7925 (mppt) REVERT: A 796 TYR cc_start: 0.8565 (t80) cc_final: 0.8343 (t80) REVERT: A 803 SER cc_start: 0.8561 (m) cc_final: 0.8348 (p) REVERT: A 851 CYS cc_start: 0.8714 (t) cc_final: 0.8099 (t) REVERT: A 868 GLU cc_start: 0.8359 (tp30) cc_final: 0.8092 (tm-30) REVERT: A 869 MET cc_start: 0.8574 (mtt) cc_final: 0.8343 (mtm) REVERT: A 933 LYS cc_start: 0.8290 (mtmt) cc_final: 0.8041 (mttp) REVERT: A 990 GLU cc_start: 0.8287 (tm-30) cc_final: 0.7981 (tm-30) REVERT: A 994 ASP cc_start: 0.7564 (t70) cc_final: 0.7249 (t70) REVERT: A 995 ARG cc_start: 0.8371 (ttp-170) cc_final: 0.8150 (ttp-110) REVERT: A 1017 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7810 (tp30) REVERT: A 1107 ARG cc_start: 0.7838 (mtt90) cc_final: 0.7567 (mtt90) REVERT: B 52 GLN cc_start: 0.8265 (tm-30) cc_final: 0.7920 (tm-30) REVERT: B 92 PHE cc_start: 0.8099 (t80) cc_final: 0.7722 (t80) REVERT: B 121 ASN cc_start: 0.7847 (p0) cc_final: 0.7401 (p0) REVERT: B 129 LYS cc_start: 0.8633 (ttmt) cc_final: 0.8227 (tmtt) REVERT: B 187 LEU cc_start: 0.8429 (tp) cc_final: 0.8017 (mt) REVERT: B 307 THR cc_start: 0.8757 (m) cc_final: 0.8317 (p) REVERT: B 327 VAL cc_start: 0.8858 (t) cc_final: 0.8545 (m) REVERT: B 347 PHE cc_start: 0.3584 (OUTLIER) cc_final: 0.2908 (t80) REVERT: B 378 LYS cc_start: 0.8497 (mmtt) cc_final: 0.7992 (mmtt) REVERT: B 380 TYR cc_start: 0.7507 (m-80) cc_final: 0.7044 (m-80) REVERT: B 551 VAL cc_start: 0.8925 (t) cc_final: 0.8680 (m) REVERT: B 558 LYS cc_start: 0.8869 (mmmt) cc_final: 0.8545 (mmmt) REVERT: B 580 GLN cc_start: 0.8624 (mm-40) cc_final: 0.8261 (mm-40) REVERT: B 586 ASP cc_start: 0.7708 (t0) cc_final: 0.7501 (t0) REVERT: B 707 TYR cc_start: 0.8500 (t80) cc_final: 0.8199 (t80) REVERT: B 725 GLU cc_start: 0.7999 (pt0) cc_final: 0.7666 (pt0) REVERT: B 764 LYS cc_start: 0.8768 (ttmm) cc_final: 0.8418 (ttpp) REVERT: B 773 GLU cc_start: 0.7613 (tm-30) cc_final: 0.6986 (tm-30) REVERT: B 776 LYS cc_start: 0.8933 (tptm) cc_final: 0.8719 (tptm) REVERT: B 825 LYS cc_start: 0.8645 (mtmm) cc_final: 0.8419 (mtmm) REVERT: B 851 CYS cc_start: 0.8653 (t) cc_final: 0.8216 (t) REVERT: B 904 TYR cc_start: 0.7772 (m-10) cc_final: 0.7143 (m-10) REVERT: B 918 GLU cc_start: 0.7858 (mp0) cc_final: 0.7551 (mp0) REVERT: B 949 GLN cc_start: 0.8860 (mm-40) cc_final: 0.8490 (mm-40) REVERT: B 950 ASP cc_start: 0.8025 (t70) cc_final: 0.7679 (t70) REVERT: B 964 LYS cc_start: 0.8595 (mtmp) cc_final: 0.8319 (ttmm) REVERT: B 979 ASP cc_start: 0.8009 (m-30) cc_final: 0.7731 (m-30) REVERT: B 990 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7802 (tp30) REVERT: B 1001 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.9039 (mt) REVERT: B 1010 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.7781 (mp10) REVERT: B 1017 GLU cc_start: 0.8340 (tm-30) cc_final: 0.7915 (tm-30) REVERT: B 1019 ARG cc_start: 0.7968 (ttp80) cc_final: 0.7311 (ttp80) REVERT: B 1031 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7765 (mt-10) REVERT: B 1041 ASP cc_start: 0.8468 (m-30) cc_final: 0.8011 (t0) REVERT: B 1118 ASP cc_start: 0.7843 (t70) cc_final: 0.7284 (t0) REVERT: B 1125 ASN cc_start: 0.8281 (t0) cc_final: 0.7989 (t0) REVERT: C 40 ASP cc_start: 0.7912 (t0) cc_final: 0.7699 (t0) REVERT: C 41 LYS cc_start: 0.8420 (mtpt) cc_final: 0.8041 (ptpp) REVERT: C 177 MET cc_start: 0.6883 (tpp) cc_final: 0.5775 (tpp) REVERT: C 188 ARG cc_start: 0.8366 (ptp-170) cc_final: 0.7795 (ptp-170) REVERT: C 199 PHE cc_start: 0.7948 (t80) cc_final: 0.7635 (t80) REVERT: C 235 ILE cc_start: 0.8608 (mt) cc_final: 0.8386 (mm) REVERT: C 280 ASN cc_start: 0.8470 (t0) cc_final: 0.8193 (t0) REVERT: C 281 GLU cc_start: 0.7888 (pp20) cc_final: 0.7570 (pp20) REVERT: C 308 VAL cc_start: 0.8872 (OUTLIER) cc_final: 0.8599 (m) REVERT: C 335 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7315 (tt) REVERT: C 347 PHE cc_start: 0.8878 (t80) cc_final: 0.8039 (t80) REVERT: C 355 ARG cc_start: 0.8137 (ttm-80) cc_final: 0.7865 (tpt90) REVERT: C 378 LYS cc_start: 0.7621 (mmmm) cc_final: 0.7288 (mmmm) REVERT: C 386 LYS cc_start: 0.8104 (mttp) cc_final: 0.7511 (tttt) REVERT: C 408 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.7572 (pmm-80) REVERT: C 462 LYS cc_start: 0.8125 (tptt) cc_final: 0.7747 (ttmm) REVERT: C 501 TYR cc_start: 0.6409 (OUTLIER) cc_final: 0.6132 (m-10) REVERT: C 528 LYS cc_start: 0.9024 (mmmm) cc_final: 0.8736 (mmmt) REVERT: C 574 ASP cc_start: 0.7813 (t70) cc_final: 0.7436 (t0) REVERT: C 602 THR cc_start: 0.8526 (m) cc_final: 0.8120 (p) REVERT: C 671 CYS cc_start: 0.6698 (m) cc_final: 0.6355 (m) REVERT: C 739 THR cc_start: 0.8380 (m) cc_final: 0.8095 (t) REVERT: C 773 GLU cc_start: 0.7860 (tt0) cc_final: 0.6866 (tp30) REVERT: C 774 GLN cc_start: 0.7977 (mm-40) cc_final: 0.7464 (mp10) REVERT: C 776 LYS cc_start: 0.8776 (tmmt) cc_final: 0.8529 (ttmm) REVERT: C 777 ASN cc_start: 0.8277 (m-40) cc_final: 0.7482 (m110) REVERT: C 808 ASP cc_start: 0.8131 (t70) cc_final: 0.7896 (t0) REVERT: C 851 CYS cc_start: 0.8282 (t) cc_final: 0.7673 (t) REVERT: C 868 GLU cc_start: 0.8419 (mp0) cc_final: 0.8196 (mp0) REVERT: C 918 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7935 (mt-10) REVERT: C 949 GLN cc_start: 0.8738 (mm110) cc_final: 0.8398 (mm-40) REVERT: C 964 LYS cc_start: 0.8841 (tmtm) cc_final: 0.8492 (ttmm) REVERT: C 1002 GLN cc_start: 0.8214 (tp40) cc_final: 0.7811 (tp40) REVERT: C 1010 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.7966 (mp10) REVERT: C 1017 GLU cc_start: 0.8269 (tp30) cc_final: 0.7806 (tp30) REVERT: C 1072 GLU cc_start: 0.8385 (pm20) cc_final: 0.8165 (pm20) REVERT: C 1107 ARG cc_start: 0.7791 (mtt180) cc_final: 0.7526 (mtt180) REVERT: C 1118 ASP cc_start: 0.7982 (t70) cc_final: 0.7685 (t0) REVERT: C 1139 ASP cc_start: 0.8136 (t0) cc_final: 0.7813 (t0) REVERT: D 208 MET cc_start: 0.0096 (tpp) cc_final: -0.0112 (tpp) outliers start: 124 outliers final: 100 residues processed: 588 average time/residue: 0.4057 time to fit residues: 368.7025 Evaluate side-chains 607 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 494 time to evaluate : 2.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 347 PHE 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 511 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 245 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 205 optimal weight: 3.9990 chunk 36 optimal weight: 0.0050 chunk 84 optimal weight: 0.9990 chunk 156 optimal weight: 4.9990 chunk 142 optimal weight: 0.0040 chunk 57 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 318 optimal weight: 10.0000 chunk 189 optimal weight: 0.0040 chunk 229 optimal weight: 3.9990 overall best weight: 0.6022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN B 762 GLN B 954 HIS B 955 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1058 HIS C1101 HIS D 40 GLN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.157062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.117561 restraints weight = 46198.802| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.95 r_work: 0.3317 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.4551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26904 Z= 0.128 Angle : 0.664 15.571 36699 Z= 0.330 Chirality : 0.047 0.387 4216 Planarity : 0.004 0.049 4697 Dihedral : 6.428 59.990 4268 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 4.31 % Allowed : 21.91 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.15), residues: 3276 helix: 1.52 (0.21), residues: 652 sheet: -1.49 (0.20), residues: 630 loop : -2.30 (0.13), residues: 1994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP A 64 HIS 0.008 0.001 HIS A 205 PHE 0.028 0.001 PHE C 140 TYR 0.026 0.001 TYR A 170 ARG 0.008 0.000 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00355 ( 28) link_NAG-ASN : angle 2.04666 ( 84) hydrogen bonds : bond 0.03158 ( 750) hydrogen bonds : angle 4.75511 ( 2004) SS BOND : bond 0.00333 ( 41) SS BOND : angle 1.45548 ( 82) covalent geometry : bond 0.00289 (26835) covalent geometry : angle 0.65432 (36533) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 501 time to evaluate : 2.613 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: A 109 THR cc_start: 0.8765 (p) cc_final: 0.8449 (t) REVERT: A 132 GLU cc_start: 0.6683 (pm20) cc_final: 0.5990 (pm20) REVERT: A 239 GLN cc_start: 0.7953 (tp-100) cc_final: 0.7709 (tm-30) REVERT: A 269 TYR cc_start: 0.8513 (m-80) cc_final: 0.7723 (m-80) REVERT: A 282 ASN cc_start: 0.8881 (OUTLIER) cc_final: 0.8466 (m-40) REVERT: A 297 SER cc_start: 0.8394 (m) cc_final: 0.7960 (p) REVERT: A 356 LYS cc_start: 0.7721 (OUTLIER) cc_final: 0.7373 (tmmm) REVERT: A 386 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.7314 (mttm) REVERT: A 390 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7084 (tt) REVERT: A 392 PHE cc_start: 0.7747 (m-80) cc_final: 0.7328 (m-80) REVERT: A 542 ASN cc_start: 0.8721 (t0) cc_final: 0.8428 (t0) REVERT: A 569 ILE cc_start: 0.8556 (pt) cc_final: 0.8212 (mp) REVERT: A 580 GLN cc_start: 0.8254 (pt0) cc_final: 0.7837 (pt0) REVERT: A 591 SER cc_start: 0.9020 (t) cc_final: 0.8691 (p) REVERT: A 708 SER cc_start: 0.8419 (t) cc_final: 0.8106 (m) REVERT: A 725 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7475 (tm-30) REVERT: A 773 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7024 (tm-30) REVERT: A 780 GLU cc_start: 0.8033 (pt0) cc_final: 0.7609 (tm-30) REVERT: A 788 ILE cc_start: 0.8946 (mm) cc_final: 0.8723 (mm) REVERT: A 790 LYS cc_start: 0.8211 (mppt) cc_final: 0.7915 (mppt) REVERT: A 796 TYR cc_start: 0.8578 (t80) cc_final: 0.8345 (t80) REVERT: A 803 SER cc_start: 0.8552 (m) cc_final: 0.8309 (p) REVERT: A 851 CYS cc_start: 0.8606 (t) cc_final: 0.8061 (t) REVERT: A 855 PHE cc_start: 0.8356 (m-80) cc_final: 0.8007 (m-80) REVERT: A 868 GLU cc_start: 0.8220 (tp30) cc_final: 0.7960 (tm-30) REVERT: A 869 MET cc_start: 0.8650 (mtt) cc_final: 0.8391 (mtm) REVERT: A 933 LYS cc_start: 0.8240 (mtmt) cc_final: 0.7954 (mttp) REVERT: A 990 GLU cc_start: 0.8341 (tm-30) cc_final: 0.8013 (tm-30) REVERT: A 994 ASP cc_start: 0.7628 (t70) cc_final: 0.7310 (t70) REVERT: A 1017 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7725 (tp30) REVERT: A 1107 ARG cc_start: 0.7989 (mtt90) cc_final: 0.7698 (mtt90) REVERT: B 52 GLN cc_start: 0.8268 (tm-30) cc_final: 0.7894 (tm-30) REVERT: B 65 PHE cc_start: 0.8245 (m-10) cc_final: 0.7399 (m-10) REVERT: B 95 ILE cc_start: 0.8692 (mt) cc_final: 0.8461 (mm) REVERT: B 121 ASN cc_start: 0.7815 (p0) cc_final: 0.7375 (p0) REVERT: B 208 ILE cc_start: 0.7896 (OUTLIER) cc_final: 0.7635 (mm) REVERT: B 274 THR cc_start: 0.8602 (OUTLIER) cc_final: 0.8069 (p) REVERT: B 275 PHE cc_start: 0.8615 (m-80) cc_final: 0.8301 (m-80) REVERT: B 298 GLU cc_start: 0.8168 (tt0) cc_final: 0.7560 (mt-10) REVERT: B 327 VAL cc_start: 0.8723 (t) cc_final: 0.8374 (m) REVERT: B 347 PHE cc_start: 0.4037 (OUTLIER) cc_final: 0.3290 (t80) REVERT: B 378 LYS cc_start: 0.8361 (mmtt) cc_final: 0.7910 (mmtt) REVERT: B 380 TYR cc_start: 0.7633 (m-80) cc_final: 0.7021 (m-80) REVERT: B 542 ASN cc_start: 0.8395 (t0) cc_final: 0.8130 (t0) REVERT: B 558 LYS cc_start: 0.8792 (mmmt) cc_final: 0.8473 (mmmt) REVERT: B 580 GLN cc_start: 0.8707 (mm-40) cc_final: 0.8289 (mm-40) REVERT: B 586 ASP cc_start: 0.7689 (t0) cc_final: 0.7467 (t0) REVERT: B 707 TYR cc_start: 0.8583 (t80) cc_final: 0.8286 (t80) REVERT: B 764 LYS cc_start: 0.8702 (ttmm) cc_final: 0.8347 (ttpp) REVERT: B 773 GLU cc_start: 0.7680 (tm-30) cc_final: 0.7036 (tm-30) REVERT: B 776 LYS cc_start: 0.8920 (tptm) cc_final: 0.8692 (tptm) REVERT: B 825 LYS cc_start: 0.8664 (mtmm) cc_final: 0.8441 (mtmm) REVERT: B 851 CYS cc_start: 0.8667 (t) cc_final: 0.8258 (t) REVERT: B 918 GLU cc_start: 0.7868 (mp0) cc_final: 0.7540 (mp0) REVERT: B 949 GLN cc_start: 0.8843 (mm-40) cc_final: 0.8532 (mm-40) REVERT: B 950 ASP cc_start: 0.8001 (t70) cc_final: 0.7635 (t70) REVERT: B 964 LYS cc_start: 0.8576 (mtmp) cc_final: 0.8371 (ttmm) REVERT: B 979 ASP cc_start: 0.8034 (m-30) cc_final: 0.7727 (m-30) REVERT: B 990 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7811 (tp30) REVERT: B 1010 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.7918 (mp10) REVERT: B 1017 GLU cc_start: 0.8297 (tm-30) cc_final: 0.7861 (tm-30) REVERT: B 1019 ARG cc_start: 0.7981 (ttp80) cc_final: 0.7336 (ttp80) REVERT: B 1031 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7755 (mt-10) REVERT: B 1041 ASP cc_start: 0.8393 (m-30) cc_final: 0.7995 (t0) REVERT: B 1118 ASP cc_start: 0.7845 (t70) cc_final: 0.7296 (t0) REVERT: C 40 ASP cc_start: 0.7867 (t0) cc_final: 0.7643 (t0) REVERT: C 41 LYS cc_start: 0.8418 (mtpt) cc_final: 0.8070 (ptpp) REVERT: C 177 MET cc_start: 0.6802 (tpp) cc_final: 0.5636 (tpp) REVERT: C 188 ARG cc_start: 0.8328 (ptp-170) cc_final: 0.7713 (ptp-170) REVERT: C 199 PHE cc_start: 0.8087 (t80) cc_final: 0.7723 (t80) REVERT: C 235 ILE cc_start: 0.8612 (mt) cc_final: 0.8341 (mm) REVERT: C 237 ARG cc_start: 0.8153 (mtm180) cc_final: 0.7801 (mtm180) REVERT: C 280 ASN cc_start: 0.8508 (t0) cc_final: 0.8179 (t0) REVERT: C 281 GLU cc_start: 0.7928 (pp20) cc_final: 0.7589 (pp20) REVERT: C 308 VAL cc_start: 0.8858 (OUTLIER) cc_final: 0.8573 (m) REVERT: C 335 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.7272 (tt) REVERT: C 347 PHE cc_start: 0.8803 (t80) cc_final: 0.7858 (t80) REVERT: C 355 ARG cc_start: 0.8213 (ttm-80) cc_final: 0.7989 (tpt90) REVERT: C 378 LYS cc_start: 0.7683 (mmmm) cc_final: 0.7294 (mmmm) REVERT: C 386 LYS cc_start: 0.8196 (mttp) cc_final: 0.7549 (tttt) REVERT: C 388 ASN cc_start: 0.8054 (p0) cc_final: 0.7845 (p0) REVERT: C 408 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.7483 (pmm-80) REVERT: C 462 LYS cc_start: 0.7966 (tptt) cc_final: 0.7630 (ttmm) REVERT: C 501 TYR cc_start: 0.6640 (OUTLIER) cc_final: 0.6232 (m-10) REVERT: C 528 LYS cc_start: 0.9023 (mmmm) cc_final: 0.8693 (mmmt) REVERT: C 574 ASP cc_start: 0.7797 (t70) cc_final: 0.7449 (t0) REVERT: C 602 THR cc_start: 0.8592 (m) cc_final: 0.8171 (p) REVERT: C 671 CYS cc_start: 0.6774 (m) cc_final: 0.6409 (m) REVERT: C 739 THR cc_start: 0.8323 (m) cc_final: 0.8034 (t) REVERT: C 751 ASN cc_start: 0.8511 (OUTLIER) cc_final: 0.8309 (t0) REVERT: C 773 GLU cc_start: 0.7866 (tt0) cc_final: 0.6835 (tp30) REVERT: C 774 GLN cc_start: 0.7934 (mm-40) cc_final: 0.7452 (mp10) REVERT: C 776 LYS cc_start: 0.8744 (tmmt) cc_final: 0.8479 (ttmm) REVERT: C 777 ASN cc_start: 0.8237 (m-40) cc_final: 0.7413 (m110) REVERT: C 808 ASP cc_start: 0.8111 (t70) cc_final: 0.7878 (t0) REVERT: C 851 CYS cc_start: 0.8270 (t) cc_final: 0.7703 (t) REVERT: C 868 GLU cc_start: 0.8413 (mp0) cc_final: 0.8158 (mp0) REVERT: C 918 GLU cc_start: 0.8294 (mt-10) cc_final: 0.8069 (mt-10) REVERT: C 949 GLN cc_start: 0.8750 (mm110) cc_final: 0.8396 (mm-40) REVERT: C 964 LYS cc_start: 0.8829 (tmtm) cc_final: 0.8472 (ttmm) REVERT: C 1002 GLN cc_start: 0.8325 (tp40) cc_final: 0.7888 (tp40) REVERT: C 1010 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.7976 (mp10) REVERT: C 1017 GLU cc_start: 0.8286 (tp30) cc_final: 0.7825 (tp30) REVERT: C 1019 ARG cc_start: 0.7897 (ttp80) cc_final: 0.7366 (ttp80) REVERT: C 1072 GLU cc_start: 0.8466 (pm20) cc_final: 0.8203 (pm20) REVERT: C 1118 ASP cc_start: 0.7998 (t70) cc_final: 0.7699 (t0) outliers start: 123 outliers final: 101 residues processed: 590 average time/residue: 0.4104 time to fit residues: 371.9190 Evaluate side-chains 604 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 488 time to evaluate : 3.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 347 PHE 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 511 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 226 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 294 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 chunk 191 optimal weight: 0.9980 chunk 137 optimal weight: 0.2980 chunk 156 optimal weight: 4.9990 chunk 177 optimal weight: 2.9990 chunk 144 optimal weight: 50.0000 chunk 95 optimal weight: 2.9990 chunk 212 optimal weight: 6.9990 chunk 171 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 205 HIS ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 955 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1058 HIS C1101 HIS D 40 GLN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.154877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.115426 restraints weight = 46025.459| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.90 r_work: 0.3284 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.4686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 26904 Z= 0.204 Angle : 0.700 16.617 36699 Z= 0.349 Chirality : 0.047 0.349 4216 Planarity : 0.004 0.048 4697 Dihedral : 6.574 59.684 4268 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.40 % Favored : 90.60 % Rotamer: Outliers : 4.27 % Allowed : 22.09 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.14), residues: 3276 helix: 1.41 (0.21), residues: 654 sheet: -1.54 (0.20), residues: 622 loop : -2.29 (0.13), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 64 HIS 0.009 0.001 HIS B1064 PHE 0.028 0.002 PHE C 140 TYR 0.029 0.001 TYR A 170 ARG 0.008 0.001 ARG A1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00364 ( 28) link_NAG-ASN : angle 2.15621 ( 84) hydrogen bonds : bond 0.03559 ( 750) hydrogen bonds : angle 4.84661 ( 2004) SS BOND : bond 0.00354 ( 41) SS BOND : angle 1.69026 ( 82) covalent geometry : bond 0.00450 (26835) covalent geometry : angle 0.68892 (36533) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16585.18 seconds wall clock time: 289 minutes 32.99 seconds (17372.99 seconds total)