Starting phenix.real_space_refine on Sun Jul 5 07:17:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7woq_32655/07_2026/7woq_32655.cif Found real_map, /net/cci-nas-00/data/ceres_data/7woq_32655/07_2026/7woq_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 { model { file = "/net/cci-nas-00/data/ceres_data/7woq_32655/07_2026/7woq_32655.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7woq_32655/07_2026/7woq_32655.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7woq_32655/07_2026/7woq_32655.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7woq_32655/07_2026/7woq_32655.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7woq_32655/07_2026/7woq_32655.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7woq_32655/07_2026/7woq_32655.cif" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.026 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'ARG:plan': 2, 'GLU:plan': 6, 'GLN:plan1': 1, '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: {'ARG:plan': 2, 'GLU:plan': 6, 'GLN:plan1': 1, '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: {'ARG:plan': 2, 'GLU:plan': 6, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "D" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1754 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 225} Chain breaks: 1 Chain: "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 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 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 chiralities: 9 Time building chain proxies: 4.80, per 1000 atoms: 0.18 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: 1.71 Conformation dependent library (CDL) restraints added in 1.0 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: 0.63 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: 4.53 Time building geometry restraints manager: 2.42 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: 15017 17.27 - 34.54: 611 34.54 - 51.82: 102 51.82 - 69.09: 21 69.09 - 86.36: 2 Dihedral angle restraints: 15753 sinusoidal: 6076 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 15750 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 1309)) selection = (chain 'B' and resid 26 through 1309) selection = (chain 'C' and (resid 26 through 243 or resid 262 through 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: 2.000 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: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 20.490 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.040 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 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 : 9.315 86.360 9410 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.001 0.000 ARG A1014 TYR 0.011 0.001 TYR C1067 PHE 0.010 0.001 PHE C 375 TRP 0.004 0.001 TRP D 162 HIS 0.002 0.000 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.20 (26835) covalent geometry : angle 0.56280 / 0.32 (36533) SS BOND : bond 0.00151 / 0.08 ( 41) SS BOND : angle 0.59250 / 0.43 ( 82) hydrogen bonds : bond 0.16242 / 10.11 ( 750) hydrogen bonds : angle 6.68850 / 4.55 ( 2004) link_NAG-ASN : bond 0.00537 / 0.30 ( 28) link_NAG-ASN : angle 2.14630 / 1.39 ( 84) *********************** 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 : 0.611 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: 0.7317 (p0) REVERT: A 43 PHE cc_start: 0.8230 (t80) cc_final: 0.8003 (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: 0.6673 (p0) REVERT: A 208 ILE cc_start: 0.8579 (pp) cc_final: 0.8378 (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: 0.8272 (mmmm) REVERT: A 563 GLN cc_start: 0.6738 (mt0) cc_final: 0.6379 (mt0) REVERT: A 574 ASP cc_start: 0.6988 (t70) cc_final: 0.6611 (t0) REVERT: A 581 THR cc_start: 0.8154 (t) cc_final: 0.7951 (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: 0.6751 (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: 0.7935 (p) REVERT: A 819 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7389 (mt-10) REVERT: A 820 ASP cc_start: 0.7516 (m-30) cc_final: 0.7258 (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: 0.7241 (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: 0.7032 (p0) REVERT: A 1017 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7573 (tm-30) REVERT: A 1048 HIS cc_start: 0.8225 (t70) cc_final: 0.7884 (t-170) REVERT: A 1050 MET cc_start: 0.7243 (mtm) cc_final: 0.6900 (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: 0.7937 (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: 0.7597 (mt) REVERT: B 204 LYS cc_start: 0.7540 (tptp) cc_final: 0.7179 (tptp) REVERT: B 280 ASN cc_start: 0.8334 (t0) cc_final: 0.8123 (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: 0.7924 (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: 0.6870 (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: 0.7948 (mm-40) REVERT: B 586 ASP cc_start: 0.7483 (t0) cc_final: 0.7267 (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: 0.7565 (p) REVERT: B 754 LEU cc_start: 0.8895 (mt) cc_final: 0.8670 (mm) REVERT: B 773 GLU cc_start: 0.6991 (tm-30) cc_final: 0.6437 (tm-30) REVERT: B 776 LYS cc_start: 0.8679 (ttpp) cc_final: 0.8219 (tptm) REVERT: B 780 GLU cc_start: 0.7006 (pt0) cc_final: 0.6740 (pt0) REVERT: B 795 LYS cc_start: 0.8590 (mttt) cc_final: 0.8388 (mttm) REVERT: B 821 LEU cc_start: 0.8647 (tp) cc_final: 0.8307 (tp) REVERT: B 851 CYS cc_start: 0.7665 (t) cc_final: 0.7358 (t) REVERT: B 856 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8668 (mmtm) REVERT: B 914 ASN cc_start: 0.7937 (p0) cc_final: 0.7265 (p0) REVERT: B 949 GLN cc_start: 0.8216 (mm110) cc_final: 0.7674 (mm-40) REVERT: B 953 ASN cc_start: 0.8268 (m-40) cc_final: 0.7774 (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: 0.7835 (mtmm) REVERT: B 979 ASP cc_start: 0.7866 (m-30) cc_final: 0.7426 (m-30) REVERT: B 991 VAL cc_start: 0.8878 (t) cc_final: 0.8099 (p) REVERT: B 1097 SER cc_start: 0.9232 (t) cc_final: 0.9019 (p) REVERT: B 1123 SER cc_start: 0.7890 (t) cc_final: 0.7574 (p) REVERT: C 54 LEU cc_start: 0.8543 (mt) cc_final: 0.8044 (mt) REVERT: C 91 TYR cc_start: 0.7331 (t80) cc_final: 0.6330 (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: 0.7872 (p) REVERT: C 133 PHE cc_start: 0.7496 (p90) cc_final: 0.7156 (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: 0.7852 (mm) REVERT: C 237 ARG cc_start: 0.7581 (mtm180) cc_final: 0.7290 (ptt180) REVERT: C 265 TYR cc_start: 0.7049 (p90) cc_final: 0.6827 (p90) REVERT: C 355 ARG cc_start: 0.8292 (ttt90) cc_final: 0.7843 (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: 0.7509 (tp) REVERT: C 560 LEU cc_start: 0.8183 (mt) cc_final: 0.7508 (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: 0.6090 (mp10) REVERT: C 574 ASP cc_start: 0.6799 (t70) cc_final: 0.6221 (t0) REVERT: C 615 VAL cc_start: 0.8413 (t) cc_final: 0.8181 (m) REVERT: C 663 ASP cc_start: 0.7719 (t70) cc_final: 0.7459 (t0) REVERT: C 693 ILE cc_start: 0.8725 (pt) cc_final: 0.8497 (pt) REVERT: C 732 THR cc_start: 0.8945 (OUTLIER) cc_final: 0.8528 (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: 0.6776 (tt0) REVERT: C 776 LYS cc_start: 0.8440 (tmmt) cc_final: 0.8134 (ttmm) REVERT: C 777 ASN cc_start: 0.7871 (m-40) cc_final: 0.7573 (m110) REVERT: C 797 PHE cc_start: 0.8037 (m-10) cc_final: 0.7827 (m-80) REVERT: C 803 SER cc_start: 0.8725 (m) cc_final: 0.8391 (p) REVERT: C 821 LEU cc_start: 0.8418 (tp) cc_final: 0.7946 (tt) REVERT: C 949 GLN cc_start: 0.7888 (mm110) cc_final: 0.7437 (mm-40) REVERT: C 953 ASN cc_start: 0.7906 (m-40) cc_final: 0.7592 (m110) REVERT: C 964 LYS cc_start: 0.8404 (tmtm) cc_final: 0.8122 (ttmm) REVERT: C 965 GLN cc_start: 0.7809 (mt0) cc_final: 0.7585 (tt0) REVERT: C 970 PHE cc_start: 0.8406 (m-10) cc_final: 0.8179 (m-10) REVERT: C 976 VAL cc_start: 0.8791 (t) cc_final: 0.8463 (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: 0.7167 (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: 59 residues processed: 855 average time/residue: 0.1672 time to fit residues: 220.4512 Evaluate side-chains 619 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 553 time to evaluate : 0.802 ------------------------------------------------------------------------------- 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 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 197 optimal weight: 1.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN A 173 GLN A 181 GLN A 186 ASN A 245 HIS ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN A1010 GLN A1048 HIS ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN B 164 ASN B 205 HIS B 218 GLN B 354 ASN B 370 ASN B 409 GLN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 580 GLN B 751 ASN B 784 GLN B 853 GLN B 872 GLN B 895 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 360 ASN C 394 ASN C 409 GLN C 414 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN C 564 GLN C 690 GLN C 784 GLN C 853 GLN C 901 GLN ** 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 33 ASN D 39 GLN D 40 GLN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 GLN D 165 GLN D 202 ASN Total number of N/Q/H flips: 61 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.197067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.166423 restraints weight = 56580.803| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.74 r_work: 0.3445 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 26904 Z= 0.231 Angle : 0.675 9.378 36699 Z= 0.338 Chirality : 0.048 0.320 4216 Planarity : 0.005 0.049 4697 Dihedral : 6.431 59.734 3720 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 5.29 % Allowed : 14.98 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.23 (0.13), residues: 3276 helix: 0.17 (0.21), residues: 658 sheet: -2.09 (0.20), residues: 592 loop : -3.16 (0.12), residues: 2026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C1019 TYR 0.024 0.002 TYR C1067 PHE 0.028 0.002 PHE C 375 TRP 0.032 0.002 TRP A 104 HIS 0.007 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.23 (26835) covalent geometry : angle 0.65641 / 0.33 (36533) SS BOND : bond 0.00515 / 0.37 ( 41) SS BOND : angle 2.14716 / 1.52 ( 82) hydrogen bonds : bond 0.04058 / 2.67 ( 750) hydrogen bonds : angle 5.03847 / 3.50 ( 2004) link_NAG-ASN : bond 0.00827 / 0.62 ( 28) link_NAG-ASN : angle 2.62685 / 1.74 ( 84) *********************** 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 721 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 570 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 PHE cc_start: 0.8674 (t80) cc_final: 0.8389 (t80) REVERT: A 46 SER cc_start: 0.9220 (m) cc_final: 0.9006 (p) REVERT: A 64 TRP cc_start: 0.8036 (t60) cc_final: 0.7785 (t-100) REVERT: A 66 HIS cc_start: 0.8134 (OUTLIER) cc_final: 0.7918 (m90) REVERT: A 97 LYS cc_start: 0.8283 (tppt) cc_final: 0.7981 (tppt) REVERT: A 104 TRP cc_start: 0.8575 (m-90) cc_final: 0.8146 (m-90) REVERT: A 109 THR cc_start: 0.8643 (p) cc_final: 0.8358 (t) REVERT: A 121 ASN cc_start: 0.7512 (m-40) cc_final: 0.7270 (p0) REVERT: A 132 GLU cc_start: 0.6766 (pm20) cc_final: 0.5570 (pm20) REVERT: A 198 TYR cc_start: 0.7903 (m-10) cc_final: 0.7556 (m-10) REVERT: A 208 ILE cc_start: 0.8651 (pp) cc_final: 0.8448 (pt) REVERT: A 224 GLU cc_start: 0.8115 (mp0) cc_final: 0.7603 (mp0) REVERT: A 269 TYR cc_start: 0.8533 (m-80) cc_final: 0.8082 (m-80) REVERT: A 275 PHE cc_start: 0.8574 (m-80) cc_final: 0.8318 (m-10) REVERT: A 297 SER cc_start: 0.8639 (m) cc_final: 0.8157 (p) REVERT: A 298 GLU cc_start: 0.8309 (tt0) cc_final: 0.7777 (tp30) REVERT: A 306 PHE cc_start: 0.8796 (m-10) cc_final: 0.8531 (m-80) REVERT: A 307 THR cc_start: 0.8735 (m) cc_final: 0.8326 (p) REVERT: A 574 ASP cc_start: 0.7979 (t70) cc_final: 0.7545 (t0) REVERT: A 602 THR cc_start: 0.8709 (OUTLIER) cc_final: 0.8455 (p) REVERT: A 615 VAL cc_start: 0.8381 (t) cc_final: 0.8110 (t) REVERT: A 663 ASP cc_start: 0.7984 (t70) cc_final: 0.7485 (t0) REVERT: A 664 ILE cc_start: 0.8889 (mt) cc_final: 0.8444 (mm) REVERT: A 675 GLN cc_start: 0.7642 (mm-40) cc_final: 0.7212 (mm-40) REVERT: A 708 SER cc_start: 0.8831 (t) cc_final: 0.8448 (m) REVERT: A 773 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7341 (tm-30) REVERT: A 780 GLU cc_start: 0.8183 (pt0) cc_final: 0.7646 (tm-30) REVERT: A 790 LYS cc_start: 0.8194 (mppt) cc_final: 0.7854 (mppt) REVERT: A 803 SER cc_start: 0.8560 (m) cc_final: 0.8295 (p) REVERT: A 820 ASP cc_start: 0.8190 (m-30) cc_final: 0.7970 (m-30) REVERT: A 851 CYS cc_start: 0.8592 (t) cc_final: 0.8288 (t) REVERT: A 855 PHE cc_start: 0.8284 (m-80) cc_final: 0.7805 (m-80) REVERT: A 868 GLU cc_start: 0.8348 (tp30) cc_final: 0.7931 (tm-30) REVERT: A 933 LYS cc_start: 0.8592 (mtmt) cc_final: 0.8302 (mttp) REVERT: A 960 ASN cc_start: 0.8423 (t0) cc_final: 0.8222 (t0) REVERT: A 994 ASP cc_start: 0.7691 (t70) cc_final: 0.7409 (t70) REVERT: A 995 ARG cc_start: 0.8459 (mtm-85) cc_final: 0.8222 (ttp-110) REVERT: A 996 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8378 (tp) REVERT: A 1001 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8801 (tp) REVERT: A 1002 GLN cc_start: 0.8203 (tp40) cc_final: 0.7990 (tp40) REVERT: A 1010 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.8234 (mp10) REVERT: A 1017 GLU cc_start: 0.8354 (tm-30) cc_final: 0.7820 (tp30) REVERT: A 1028 LYS cc_start: 0.8301 (mttm) cc_final: 0.8050 (ttmm) REVERT: A 1050 MET cc_start: 0.8207 (mtm) cc_final: 0.7848 (mtp) REVERT: A 1072 GLU cc_start: 0.8729 (pm20) cc_final: 0.8235 (pm20) REVERT: A 1107 ARG cc_start: 0.8068 (mtt90) cc_final: 0.7846 (mtt90) REVERT: A 1139 ASP cc_start: 0.7877 (p0) cc_final: 0.7656 (p0) REVERT: B 92 PHE cc_start: 0.8034 (t80) cc_final: 0.7739 (t80) REVERT: B 95 ILE cc_start: 0.8731 (mt) cc_final: 0.8141 (tt) REVERT: B 121 ASN cc_start: 0.7365 (p0) cc_final: 0.7009 (p0) REVERT: B 187 LEU cc_start: 0.8033 (tp) cc_final: 0.7804 (mp) REVERT: B 190 PHE cc_start: 0.8525 (m-10) cc_final: 0.8251 (m-10) REVERT: B 199 PHE cc_start: 0.8782 (t80) cc_final: 0.8369 (t80) REVERT: B 204 LYS cc_start: 0.8434 (tptp) cc_final: 0.8132 (tptp) REVERT: B 224 GLU cc_start: 0.7986 (pm20) cc_final: 0.7382 (mt-10) REVERT: B 229 LEU cc_start: 0.8311 (pp) cc_final: 0.8104 (pp) REVERT: B 271 GLN cc_start: 0.8240 (mt0) cc_final: 0.7959 (mt0) REVERT: B 281 GLU cc_start: 0.7763 (pp20) cc_final: 0.7558 (pp20) REVERT: B 297 SER cc_start: 0.8541 (m) cc_final: 0.8327 (p) REVERT: B 307 THR cc_start: 0.8930 (m) cc_final: 0.8559 (p) REVERT: B 361 CYS cc_start: 0.7287 (OUTLIER) cc_final: 0.6930 (t) REVERT: B 406 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7633 (mt-10) REVERT: B 542 ASN cc_start: 0.8398 (t0) cc_final: 0.7785 (t0) REVERT: B 558 LYS cc_start: 0.8919 (mmmt) cc_final: 0.8496 (mmmt) REVERT: B 580 GLN cc_start: 0.8687 (mm-40) cc_final: 0.8284 (mm-40) REVERT: B 586 ASP cc_start: 0.7954 (t0) cc_final: 0.7607 (t0) REVERT: B 589 PRO cc_start: 0.8718 (Cg_exo) cc_final: 0.8109 (Cg_endo) REVERT: B 719 THR cc_start: 0.8354 (t) cc_final: 0.8154 (p) REVERT: B 764 LYS cc_start: 0.8789 (ttmm) cc_final: 0.8533 (ttmm) REVERT: B 773 GLU cc_start: 0.7752 (tm-30) cc_final: 0.7105 (tm-30) REVERT: B 776 LYS cc_start: 0.9063 (ttpp) cc_final: 0.8595 (tptm) REVERT: B 795 LYS cc_start: 0.8916 (mttt) cc_final: 0.8701 (mttm) REVERT: B 796 TYR cc_start: 0.8999 (t80) cc_final: 0.8673 (t80) REVERT: B 850 ILE cc_start: 0.9064 (mm) cc_final: 0.8741 (tp) REVERT: B 851 CYS cc_start: 0.8481 (t) cc_final: 0.7701 (p) REVERT: B 904 TYR cc_start: 0.8344 (m-10) cc_final: 0.7273 (m-10) REVERT: B 914 ASN cc_start: 0.8195 (p0) cc_final: 0.7994 (p0) REVERT: B 949 GLN cc_start: 0.8636 (mm110) cc_final: 0.8341 (mm-40) REVERT: B 955 ASN cc_start: 0.8389 (m110) cc_final: 0.8069 (m110) REVERT: B 960 ASN cc_start: 0.8560 (m-40) cc_final: 0.8168 (t0) REVERT: B 964 LYS cc_start: 0.8587 (mtmp) cc_final: 0.8245 (ttmm) REVERT: B 979 ASP cc_start: 0.8192 (m-30) cc_final: 0.7677 (m-30) REVERT: B 1010 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8061 (mp10) REVERT: B 1050 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7833 (mtp) REVERT: B 1118 ASP cc_start: 0.7969 (t70) cc_final: 0.7463 (t0) REVERT: C 40 ASP cc_start: 0.8047 (t70) cc_final: 0.7745 (t70) REVERT: C 81 ASN cc_start: 0.7703 (p0) cc_final: 0.7492 (t0) REVERT: C 119 ILE cc_start: 0.8068 (OUTLIER) cc_final: 0.7784 (mm) REVERT: C 120 VAL cc_start: 0.8557 (m) cc_final: 0.8238 (p) REVERT: C 133 PHE cc_start: 0.7805 (p90) cc_final: 0.7404 (p90) REVERT: C 135 PHE cc_start: 0.7246 (p90) cc_final: 0.6875 (p90) REVERT: C 235 ILE cc_start: 0.8513 (mt) cc_final: 0.8102 (mm) REVERT: C 237 ARG cc_start: 0.8343 (mtm180) cc_final: 0.7788 (mtm180) REVERT: C 265 TYR cc_start: 0.7864 (p90) cc_final: 0.7657 (p90) REVERT: C 269 TYR cc_start: 0.8544 (m-80) cc_final: 0.8162 (m-80) REVERT: C 280 ASN cc_start: 0.8409 (t0) cc_final: 0.7986 (t0) REVERT: C 281 GLU cc_start: 0.7713 (pp20) cc_final: 0.7298 (pp20) REVERT: C 329 PHE cc_start: 0.8541 (OUTLIER) cc_final: 0.8165 (m-80) REVERT: C 378 LYS cc_start: 0.7799 (mmmm) cc_final: 0.7493 (mmmm) REVERT: C 386 LYS cc_start: 0.8183 (mttp) cc_final: 0.7680 (tttt) REVERT: C 388 ASN cc_start: 0.8115 (p0) cc_final: 0.7914 (p0) REVERT: C 392 PHE cc_start: 0.6763 (m-80) cc_final: 0.6374 (m-80) REVERT: C 462 LYS cc_start: 0.8061 (tptt) cc_final: 0.7636 (ttmm) REVERT: C 537 LYS cc_start: 0.8872 (tttp) cc_final: 0.8594 (mtpp) REVERT: C 546 LEU cc_start: 0.7929 (tm) cc_final: 0.7720 (tp) REVERT: C 562 PHE cc_start: 0.7970 (p90) cc_final: 0.7611 (p90) REVERT: C 564 GLN cc_start: 0.7069 (mp10) cc_final: 0.6653 (mp10) REVERT: C 574 ASP cc_start: 0.8056 (t70) cc_final: 0.7758 (t0) REVERT: C 615 VAL cc_start: 0.8404 (t) cc_final: 0.7801 (m) REVERT: C 693 ILE cc_start: 0.8871 (pt) cc_final: 0.8600 (pt) REVERT: C 725 GLU cc_start: 0.8304 (tt0) cc_final: 0.8016 (tm-30) REVERT: C 737 ASP cc_start: 0.8163 (t0) cc_final: 0.7933 (t0) REVERT: C 773 GLU cc_start: 0.8214 (tt0) cc_final: 0.7434 (tp30) REVERT: C 776 LYS cc_start: 0.8693 (tmmt) cc_final: 0.8407 (ttmm) REVERT: C 777 ASN cc_start: 0.8430 (m-40) cc_final: 0.7689 (m110) REVERT: C 779 GLN cc_start: 0.8458 (tm-30) cc_final: 0.8171 (tm-30) REVERT: C 792 PRO cc_start: 0.8323 (Cg_exo) cc_final: 0.8095 (Cg_endo) REVERT: C 803 SER cc_start: 0.9078 (m) cc_final: 0.8792 (p) REVERT: C 808 ASP cc_start: 0.8260 (t70) cc_final: 0.7737 (p0) REVERT: C 851 CYS cc_start: 0.8260 (t) cc_final: 0.7661 (t) REVERT: C 900 MET cc_start: 0.8535 (mtp) cc_final: 0.8245 (mtp) REVERT: C 964 LYS cc_start: 0.8795 (tmtm) cc_final: 0.8452 (ttmm) REVERT: C 990 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8069 (tm-30) REVERT: C 1002 GLN cc_start: 0.8217 (tp40) cc_final: 0.7671 (tp-100) REVERT: C 1010 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.8180 (mp10) REVERT: C 1038 LYS cc_start: 0.8895 (mtpt) cc_final: 0.8508 (mtmm) REVERT: C 1072 GLU cc_start: 0.8610 (pm20) cc_final: 0.8283 (pm20) REVERT: C 1107 ARG cc_start: 0.7925 (mtt180) cc_final: 0.7516 (mtt180) REVERT: C 1118 ASP cc_start: 0.8232 (t70) cc_final: 0.7839 (t0) REVERT: C 1138 TYR cc_start: 0.7976 (t80) cc_final: 0.7584 (t80) outliers start: 151 outliers final: 85 residues processed: 695 average time/residue: 0.1652 time to fit residues: 179.3631 Evaluate side-chains 613 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 517 time to evaluate : 0.752 ------------------------------------------------------------------------------- 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 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU 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 531 THR 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 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 996 LEU 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 1104 VAL 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 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 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 907 ASN Chi-restraints excluded: chain B residue 935 GLN 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 1050 MET 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 303 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 329 PHE 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 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 732 THR Chi-restraints excluded: chain C residue 980 ILE 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 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 5 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 251 optimal weight: 0.0370 chunk 188 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 286 optimal weight: 0.7980 chunk 247 optimal weight: 7.9990 chunk 220 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.3462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 205 HIS A 239 GLN A 321 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 949 GLN A1005 GLN A1011 GLN A1083 HIS A1125 ASN B 30 ASN B 542 ASN B 762 GLN B 913 GLN B 954 HIS B 957 GLN B 978 ASN ** 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 205 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 563 GLN C 955 ASN ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS ** 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** D 207 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.195887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.167018 restraints weight = 56582.968| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.32 r_work: 0.3417 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 26904 Z= 0.200 Angle : 0.657 13.621 36699 Z= 0.328 Chirality : 0.047 0.341 4216 Planarity : 0.005 0.049 4697 Dihedral : 6.349 59.147 3690 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 5.46 % Allowed : 16.73 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.83 (0.14), residues: 3276 helix: 0.57 (0.21), residues: 657 sheet: -1.81 (0.20), residues: 625 loop : -2.94 (0.12), residues: 1994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 328 TYR 0.022 0.001 TYR C1067 PHE 0.032 0.002 PHE B 759 TRP 0.016 0.001 TRP A 104 HIS 0.007 0.001 HIS A 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.20 (26835) covalent geometry : angle 0.63926 / 0.32 (36533) SS BOND : bond 0.00297 / 0.20 ( 41) SS BOND : angle 2.22828 / 1.62 ( 82) hydrogen bonds : bond 0.03833 / 2.54 ( 750) hydrogen bonds : angle 4.96560 / 3.46 ( 2004) link_NAG-ASN : bond 0.00485 / 0.34 ( 28) link_NAG-ASN : angle 2.43795 / 1.59 ( 84) *********************** 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 702 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 546 time to evaluate : 0.644 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 46 SER cc_start: 0.9203 (m) cc_final: 0.8968 (p) REVERT: A 64 TRP cc_start: 0.8106 (t60) cc_final: 0.7785 (t-100) REVERT: A 66 HIS cc_start: 0.8175 (OUTLIER) cc_final: 0.7623 (m90) REVERT: A 97 LYS cc_start: 0.8596 (tppt) cc_final: 0.8318 (tppt) REVERT: A 102 ARG cc_start: 0.8720 (ptp-170) cc_final: 0.8519 (ptp-170) REVERT: A 109 THR cc_start: 0.8644 (p) cc_final: 0.8373 (t) REVERT: A 129 LYS cc_start: 0.7421 (ttpt) cc_final: 0.7201 (tmtt) REVERT: A 132 GLU cc_start: 0.6709 (pm20) cc_final: 0.5900 (pm20) REVERT: A 164 ASN cc_start: 0.7590 (p0) cc_final: 0.6938 (p0) REVERT: A 186 ASN cc_start: 0.7757 (p0) cc_final: 0.7447 (p0) REVERT: A 198 TYR cc_start: 0.8129 (m-10) cc_final: 0.7778 (m-80) REVERT: A 224 GLU cc_start: 0.8201 (mp0) cc_final: 0.7866 (mp0) REVERT: A 269 TYR cc_start: 0.8594 (m-80) cc_final: 0.7749 (m-80) REVERT: A 297 SER cc_start: 0.8652 (m) cc_final: 0.8206 (p) REVERT: A 298 GLU cc_start: 0.8280 (tt0) cc_final: 0.7825 (tp30) REVERT: A 307 THR cc_start: 0.8700 (m) cc_final: 0.8432 (p) REVERT: A 324 GLU cc_start: 0.7459 (mp0) cc_final: 0.7030 (pm20) REVERT: A 356 LYS cc_start: 0.7438 (OUTLIER) cc_final: 0.7027 (tmmm) REVERT: A 542 ASN cc_start: 0.8617 (t0) cc_final: 0.8407 (t0) REVERT: A 580 GLN cc_start: 0.8064 (pt0) cc_final: 0.7711 (pt0) REVERT: A 602 THR cc_start: 0.8665 (OUTLIER) cc_final: 0.8450 (p) REVERT: A 663 ASP cc_start: 0.7954 (t70) cc_final: 0.7555 (t0) REVERT: A 664 ILE cc_start: 0.8866 (mt) cc_final: 0.8437 (mm) REVERT: A 675 GLN cc_start: 0.7652 (mm-40) cc_final: 0.7184 (mm-40) REVERT: A 707 TYR cc_start: 0.8414 (t80) cc_final: 0.8195 (t80) REVERT: A 708 SER cc_start: 0.8758 (t) cc_final: 0.8400 (m) REVERT: A 725 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7492 (tm-30) REVERT: A 731 MET cc_start: 0.8739 (ttt) cc_final: 0.8528 (ttm) REVERT: A 773 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7202 (tm-30) REVERT: A 780 GLU cc_start: 0.8132 (pt0) cc_final: 0.7599 (tm-30) REVERT: A 803 SER cc_start: 0.8584 (m) cc_final: 0.8326 (p) REVERT: A 851 CYS cc_start: 0.8521 (t) cc_final: 0.8184 (t) REVERT: A 855 PHE cc_start: 0.8383 (m-80) cc_final: 0.8024 (m-80) REVERT: A 868 GLU cc_start: 0.8249 (tp30) cc_final: 0.7875 (tm-30) REVERT: A 869 MET cc_start: 0.8732 (mtt) cc_final: 0.8422 (mtm) REVERT: A 933 LYS cc_start: 0.8589 (mtmt) cc_final: 0.8289 (mttp) REVERT: A 994 ASP cc_start: 0.7745 (t70) cc_final: 0.7450 (t70) REVERT: A 995 ARG cc_start: 0.8477 (mtm-85) cc_final: 0.8267 (ttp-110) REVERT: A 996 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8444 (tp) REVERT: A 1002 GLN cc_start: 0.8179 (tp40) cc_final: 0.7972 (tp40) REVERT: A 1006 THR cc_start: 0.8907 (p) cc_final: 0.8693 (t) REVERT: A 1017 GLU cc_start: 0.8387 (tm-30) cc_final: 0.7862 (tp30) REVERT: A 1050 MET cc_start: 0.8089 (mtm) cc_final: 0.7878 (mtp) REVERT: A 1072 GLU cc_start: 0.8684 (pm20) cc_final: 0.8205 (pm20) REVERT: A 1107 ARG cc_start: 0.8013 (mtt90) cc_final: 0.7714 (mtt90) REVERT: B 52 GLN cc_start: 0.8231 (tm-30) cc_final: 0.7929 (tm-30) REVERT: B 95 ILE cc_start: 0.8775 (mt) cc_final: 0.8282 (tt) REVERT: B 121 ASN cc_start: 0.7666 (p0) cc_final: 0.7263 (p0) REVERT: B 187 LEU cc_start: 0.8043 (tp) cc_final: 0.7725 (mt) REVERT: B 190 PHE cc_start: 0.8574 (m-10) cc_final: 0.8363 (m-10) REVERT: B 224 GLU cc_start: 0.7976 (pm20) cc_final: 0.7536 (pt0) REVERT: B 271 GLN cc_start: 0.8293 (mt0) cc_final: 0.8011 (mt0) REVERT: B 281 GLU cc_start: 0.7839 (pp20) cc_final: 0.7629 (pp20) REVERT: B 297 SER cc_start: 0.8589 (m) cc_final: 0.8368 (p) REVERT: B 307 THR cc_start: 0.8896 (m) cc_final: 0.8510 (p) REVERT: B 347 PHE cc_start: 0.4426 (OUTLIER) cc_final: 0.3601 (t80) REVERT: B 406 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7828 (mt-10) REVERT: B 542 ASN cc_start: 0.8364 (t160) cc_final: 0.8084 (t0) REVERT: B 558 LYS cc_start: 0.8914 (mmmt) cc_final: 0.8502 (mmmt) REVERT: B 580 GLN cc_start: 0.8783 (mm-40) cc_final: 0.8349 (mm-40) REVERT: B 586 ASP cc_start: 0.7958 (t0) cc_final: 0.7717 (t0) REVERT: B 589 PRO cc_start: 0.8994 (Cg_exo) cc_final: 0.8655 (Cg_endo) REVERT: B 674 TYR cc_start: 0.8474 (t80) cc_final: 0.8194 (t80) REVERT: B 725 GLU cc_start: 0.8095 (pt0) cc_final: 0.7718 (pt0) REVERT: B 764 LYS cc_start: 0.8747 (ttmm) cc_final: 0.8499 (ttpp) REVERT: B 773 GLU cc_start: 0.7686 (tm-30) cc_final: 0.6937 (tm-30) REVERT: B 776 LYS cc_start: 0.8959 (ttpp) cc_final: 0.8640 (tptm) REVERT: B 795 LYS cc_start: 0.8956 (mttt) cc_final: 0.8708 (mttm) REVERT: B 796 TYR cc_start: 0.9020 (t80) cc_final: 0.8700 (t80) REVERT: B 816 SER cc_start: 0.8921 (m) cc_final: 0.8543 (p) REVERT: B 850 ILE cc_start: 0.9048 (mm) cc_final: 0.8738 (tp) REVERT: B 851 CYS cc_start: 0.8554 (t) cc_final: 0.7699 (p) REVERT: B 904 TYR cc_start: 0.8270 (m-10) cc_final: 0.8002 (m-10) REVERT: B 921 LYS cc_start: 0.8333 (mmmm) cc_final: 0.8125 (mtpp) REVERT: B 949 GLN cc_start: 0.8677 (mm110) cc_final: 0.8440 (mm-40) REVERT: B 950 ASP cc_start: 0.7967 (t70) cc_final: 0.7598 (t70) REVERT: B 955 ASN cc_start: 0.8394 (m110) cc_final: 0.8069 (m110) REVERT: B 957 GLN cc_start: 0.8441 (pt0) cc_final: 0.8219 (pt0) REVERT: B 960 ASN cc_start: 0.8606 (m-40) cc_final: 0.8149 (t0) REVERT: B 964 LYS cc_start: 0.8595 (mtmp) cc_final: 0.8332 (ttmm) REVERT: B 979 ASP cc_start: 0.8182 (m-30) cc_final: 0.7843 (m-30) REVERT: B 1010 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.8025 (mp10) REVERT: B 1041 ASP cc_start: 0.8615 (m-30) cc_final: 0.8142 (t0) REVERT: B 1073 LYS cc_start: 0.8525 (ttpp) cc_final: 0.8321 (ttmm) REVERT: B 1118 ASP cc_start: 0.7989 (t70) cc_final: 0.7645 (t0) REVERT: C 40 ASP cc_start: 0.8014 (OUTLIER) cc_final: 0.7799 (t70) REVERT: C 120 VAL cc_start: 0.8424 (m) cc_final: 0.8144 (p) REVERT: C 135 PHE cc_start: 0.7519 (p90) cc_final: 0.7141 (p90) REVERT: C 188 ARG cc_start: 0.8121 (ptp-170) cc_final: 0.7701 (ptp-170) REVERT: C 235 ILE cc_start: 0.8601 (mt) cc_final: 0.8323 (mm) REVERT: C 237 ARG cc_start: 0.8358 (mtm180) cc_final: 0.7779 (mtm180) REVERT: C 242 LEU cc_start: 0.6886 (OUTLIER) cc_final: 0.6605 (pp) REVERT: C 269 TYR cc_start: 0.8540 (m-80) cc_final: 0.8115 (m-10) REVERT: C 280 ASN cc_start: 0.8428 (t0) cc_final: 0.8016 (t0) REVERT: C 281 GLU cc_start: 0.7752 (pp20) cc_final: 0.7380 (pp20) REVERT: C 355 ARG cc_start: 0.8512 (ttm-80) cc_final: 0.7884 (tpt90) REVERT: C 378 LYS cc_start: 0.7796 (mmmm) cc_final: 0.7429 (mmmm) REVERT: C 386 LYS cc_start: 0.8190 (mttp) cc_final: 0.7688 (tttt) REVERT: C 392 PHE cc_start: 0.6969 (m-80) cc_final: 0.6616 (m-80) REVERT: C 462 LYS cc_start: 0.7832 (tptt) cc_final: 0.7443 (ttmm) REVERT: C 528 LYS cc_start: 0.8762 (mmmm) cc_final: 0.8423 (mmmt) REVERT: C 537 LYS cc_start: 0.8863 (tttp) cc_final: 0.8360 (mtpp) REVERT: C 551 VAL cc_start: 0.8707 (OUTLIER) cc_final: 0.8486 (p) REVERT: C 562 PHE cc_start: 0.8031 (p90) cc_final: 0.7667 (p90) REVERT: C 563 GLN cc_start: 0.7172 (pt0) cc_final: 0.6935 (pt0) REVERT: C 569 ILE cc_start: 0.7903 (mm) cc_final: 0.7576 (mm) REVERT: C 574 ASP cc_start: 0.8057 (t70) cc_final: 0.7708 (t0) REVERT: C 602 THR cc_start: 0.8727 (m) cc_final: 0.8282 (p) REVERT: C 615 VAL cc_start: 0.8409 (t) cc_final: 0.8042 (m) REVERT: C 671 CYS cc_start: 0.6847 (m) cc_final: 0.6430 (m) REVERT: C 693 ILE cc_start: 0.8866 (pt) cc_final: 0.8661 (pt) REVERT: C 725 GLU cc_start: 0.8271 (tt0) cc_final: 0.7965 (tm-30) REVERT: C 773 GLU cc_start: 0.8108 (tt0) cc_final: 0.7354 (tp30) REVERT: C 776 LYS cc_start: 0.8576 (tmmt) cc_final: 0.8296 (ttmm) REVERT: C 777 ASN cc_start: 0.8334 (m-40) cc_final: 0.7557 (m110) REVERT: C 779 GLN cc_start: 0.8535 (tm-30) cc_final: 0.8152 (tm-30) REVERT: C 792 PRO cc_start: 0.8422 (Cg_exo) cc_final: 0.8215 (Cg_endo) REVERT: C 808 ASP cc_start: 0.8197 (t70) cc_final: 0.7611 (p0) REVERT: C 821 LEU cc_start: 0.8535 (tp) cc_final: 0.8275 (tt) REVERT: C 851 CYS cc_start: 0.8262 (t) cc_final: 0.7688 (t) REVERT: C 964 LYS cc_start: 0.8796 (tmtm) cc_final: 0.8393 (ttmm) REVERT: C 965 GLN cc_start: 0.8659 (tt0) cc_final: 0.8417 (tt0) REVERT: C 1002 GLN cc_start: 0.8321 (tp40) cc_final: 0.7959 (tp40) REVERT: C 1010 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8192 (mp10) REVERT: C 1072 GLU cc_start: 0.8584 (pm20) cc_final: 0.8267 (pm20) REVERT: C 1107 ARG cc_start: 0.7925 (mtt180) cc_final: 0.7570 (mpt-90) REVERT: C 1118 ASP cc_start: 0.8242 (t70) cc_final: 0.7839 (t0) REVERT: C 1138 TYR cc_start: 0.7946 (t80) cc_final: 0.7579 (t80) outliers start: 156 outliers final: 101 residues processed: 660 average time/residue: 0.1594 time to fit residues: 164.4003 Evaluate side-chains 618 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 507 time to evaluate : 0.815 ------------------------------------------------------------------------------- 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 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 531 THR 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 658 ASN Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 720 ILE 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 996 LEU 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 1114 ILE Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1141 LEU 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 177 MET 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 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 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 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 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 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 790 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1017 GLU 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 254 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 290 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 chunk 211 optimal weight: 0.0980 chunk 94 optimal weight: 0.6980 chunk 185 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 246 optimal weight: 0.0470 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN A 122 ASN ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 HIS ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN B 954 HIS ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN ** 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 955 ASN ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.196936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.168720 restraints weight = 56161.415| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.37 r_work: 0.3366 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 26904 Z= 0.134 Angle : 0.623 11.235 36699 Z= 0.309 Chirality : 0.046 0.316 4216 Planarity : 0.004 0.050 4697 Dihedral : 6.288 58.730 3683 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 4.87 % Allowed : 18.34 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.14), residues: 3276 helix: 0.86 (0.21), residues: 651 sheet: -1.73 (0.20), residues: 620 loop : -2.76 (0.12), residues: 2005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 328 TYR 0.020 0.001 TYR C 707 PHE 0.029 0.001 PHE B 199 TRP 0.015 0.001 TRP A 104 HIS 0.012 0.001 HIS A 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (26835) covalent geometry : angle 0.60587 / 0.30 (36533) SS BOND : bond 0.00292 / 0.22 ( 41) SS BOND : angle 2.15187 / 1.52 ( 82) hydrogen bonds : bond 0.03398 / 2.26 ( 750) hydrogen bonds : angle 4.82940 / 3.37 ( 2004) link_NAG-ASN : bond 0.00414 / 0.31 ( 28) link_NAG-ASN : angle 2.26584 / 1.49 ( 84) *********************** 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 674 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 535 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.9162 (m) cc_final: 0.8936 (p) REVERT: A 66 HIS cc_start: 0.8180 (OUTLIER) cc_final: 0.7653 (m90) REVERT: A 97 LYS cc_start: 0.8558 (tppt) cc_final: 0.8251 (tppt) REVERT: A 102 ARG cc_start: 0.8797 (ptp-170) cc_final: 0.8543 (ptp-170) REVERT: A 109 THR cc_start: 0.8648 (p) cc_final: 0.8380 (t) REVERT: A 132 GLU cc_start: 0.6662 (pm20) cc_final: 0.6111 (pm20) REVERT: A 164 ASN cc_start: 0.7700 (p0) cc_final: 0.7326 (p0) REVERT: A 186 ASN cc_start: 0.7821 (p0) cc_final: 0.7457 (p0) REVERT: A 224 GLU cc_start: 0.8168 (mp0) cc_final: 0.7874 (mp0) REVERT: A 239 GLN cc_start: 0.8104 (tp40) cc_final: 0.7779 (tp40) REVERT: A 269 TYR cc_start: 0.8631 (m-80) cc_final: 0.7667 (m-80) REVERT: A 297 SER cc_start: 0.8571 (m) cc_final: 0.8132 (p) REVERT: A 298 GLU cc_start: 0.8312 (tt0) cc_final: 0.7875 (tp30) REVERT: A 307 THR cc_start: 0.8755 (m) cc_final: 0.8510 (p) REVERT: A 390 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.6920 (tt) REVERT: A 519 HIS cc_start: 0.3926 (OUTLIER) cc_final: 0.3633 (p90) REVERT: A 537 LYS cc_start: 0.8770 (ttmt) cc_final: 0.8439 (ttmm) REVERT: A 542 ASN cc_start: 0.8676 (t0) cc_final: 0.8429 (t0) REVERT: A 580 GLN cc_start: 0.8053 (pt0) cc_final: 0.7695 (pt0) REVERT: A 602 THR cc_start: 0.8639 (m) cc_final: 0.8413 (p) REVERT: A 663 ASP cc_start: 0.7848 (t70) cc_final: 0.7489 (t0) REVERT: A 664 ILE cc_start: 0.8887 (mt) cc_final: 0.8435 (mm) REVERT: A 675 GLN cc_start: 0.7626 (mm-40) cc_final: 0.7127 (mm-40) REVERT: A 703 ASN cc_start: 0.8272 (t0) cc_final: 0.7998 (t0) REVERT: A 708 SER cc_start: 0.8788 (t) cc_final: 0.8470 (m) REVERT: A 725 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7431 (tm-30) REVERT: A 773 GLU cc_start: 0.7919 (tm-30) cc_final: 0.7177 (tm-30) REVERT: A 780 GLU cc_start: 0.8241 (pt0) cc_final: 0.7722 (tm-30) REVERT: A 787 GLN cc_start: 0.8824 (mp10) cc_final: 0.8507 (mp10) REVERT: A 803 SER cc_start: 0.8544 (m) cc_final: 0.8278 (p) REVERT: A 851 CYS cc_start: 0.8505 (t) cc_final: 0.8227 (t) REVERT: A 868 GLU cc_start: 0.8277 (tp30) cc_final: 0.7961 (tm-30) REVERT: A 869 MET cc_start: 0.8713 (mtt) cc_final: 0.8429 (mtm) REVERT: A 933 LYS cc_start: 0.8419 (mtmt) cc_final: 0.8124 (mttp) REVERT: A 994 ASP cc_start: 0.7657 (t70) cc_final: 0.7354 (t70) REVERT: A 1002 GLN cc_start: 0.8231 (tp40) cc_final: 0.7956 (tp40) REVERT: A 1017 GLU cc_start: 0.8385 (tm-30) cc_final: 0.7845 (tp30) REVERT: A 1050 MET cc_start: 0.8089 (mtm) cc_final: 0.7847 (mtp) REVERT: A 1072 GLU cc_start: 0.8702 (pm20) cc_final: 0.8495 (pm20) REVERT: A 1107 ARG cc_start: 0.7999 (mtt90) cc_final: 0.7796 (mtt90) REVERT: B 52 GLN cc_start: 0.8185 (tm-30) cc_final: 0.7834 (tm-30) REVERT: B 95 ILE cc_start: 0.8775 (mt) cc_final: 0.8094 (tt) REVERT: B 121 ASN cc_start: 0.7891 (p0) cc_final: 0.7398 (p0) REVERT: B 129 LYS cc_start: 0.8605 (ttmt) cc_final: 0.7918 (tmtt) REVERT: B 187 LEU cc_start: 0.8168 (tp) cc_final: 0.7863 (mt) REVERT: B 190 PHE cc_start: 0.8634 (m-10) cc_final: 0.8403 (m-10) REVERT: B 199 PHE cc_start: 0.8902 (t80) cc_final: 0.8512 (t80) REVERT: B 239 GLN cc_start: 0.7992 (tp40) cc_final: 0.7785 (tm-30) REVERT: B 271 GLN cc_start: 0.8316 (mt0) cc_final: 0.8084 (mt0) REVERT: B 297 SER cc_start: 0.8559 (m) cc_final: 0.8304 (p) REVERT: B 307 THR cc_start: 0.8897 (m) cc_final: 0.8488 (p) REVERT: B 347 PHE cc_start: 0.4303 (OUTLIER) cc_final: 0.3463 (t80) REVERT: B 406 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7832 (mt-10) REVERT: B 542 ASN cc_start: 0.8369 (t0) cc_final: 0.8089 (t0) REVERT: B 558 LYS cc_start: 0.8910 (mmmt) cc_final: 0.8419 (mmmt) REVERT: B 580 GLN cc_start: 0.8714 (mm-40) cc_final: 0.8283 (mm-40) REVERT: B 586 ASP cc_start: 0.7914 (t0) cc_final: 0.7652 (t0) REVERT: B 674 TYR cc_start: 0.8423 (t80) cc_final: 0.8140 (t80) REVERT: B 707 TYR cc_start: 0.8542 (t80) cc_final: 0.8216 (t80) REVERT: B 725 GLU cc_start: 0.8084 (pt0) cc_final: 0.7731 (pt0) REVERT: B 764 LYS cc_start: 0.8734 (ttmm) cc_final: 0.8447 (ttpp) REVERT: B 773 GLU cc_start: 0.7723 (tm-30) cc_final: 0.6958 (tm-30) REVERT: B 776 LYS cc_start: 0.8937 (ttpp) cc_final: 0.8679 (tptm) REVERT: B 795 LYS cc_start: 0.8978 (mttt) cc_final: 0.8760 (mttm) REVERT: B 796 TYR cc_start: 0.9044 (t80) cc_final: 0.8796 (t80) REVERT: B 816 SER cc_start: 0.8909 (m) cc_final: 0.8466 (p) REVERT: B 820 ASP cc_start: 0.8022 (m-30) cc_final: 0.7768 (t0) REVERT: B 851 CYS cc_start: 0.8540 (t) cc_final: 0.7645 (p) REVERT: B 904 TYR cc_start: 0.8159 (m-10) cc_final: 0.7050 (m-10) REVERT: B 918 GLU cc_start: 0.7909 (mp0) cc_final: 0.7703 (mp0) REVERT: B 949 GLN cc_start: 0.8698 (mm110) cc_final: 0.8412 (mm-40) REVERT: B 950 ASP cc_start: 0.8064 (t70) cc_final: 0.7706 (t70) REVERT: B 955 ASN cc_start: 0.8394 (m110) cc_final: 0.8106 (m-40) REVERT: B 957 GLN cc_start: 0.8499 (pt0) cc_final: 0.8272 (pt0) REVERT: B 979 ASP cc_start: 0.8216 (m-30) cc_final: 0.7858 (m-30) REVERT: B 1010 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.8433 (mm-40) REVERT: B 1031 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7941 (mt-10) REVERT: B 1041 ASP cc_start: 0.8626 (m-30) cc_final: 0.8125 (t0) REVERT: B 1073 LYS cc_start: 0.8532 (ttpp) cc_final: 0.8267 (ttmm) REVERT: B 1118 ASP cc_start: 0.8011 (t70) cc_final: 0.7475 (t0) REVERT: C 120 VAL cc_start: 0.8389 (m) cc_final: 0.8039 (p) REVERT: C 235 ILE cc_start: 0.8497 (mt) cc_final: 0.8236 (mm) REVERT: C 237 ARG cc_start: 0.8437 (mtm180) cc_final: 0.7867 (mtm180) REVERT: C 269 TYR cc_start: 0.8555 (m-80) cc_final: 0.8156 (m-80) REVERT: C 280 ASN cc_start: 0.8468 (t0) cc_final: 0.8113 (t0) REVERT: C 281 GLU cc_start: 0.7859 (pp20) cc_final: 0.7422 (pp20) REVERT: C 355 ARG cc_start: 0.8444 (ttm-80) cc_final: 0.7977 (tpt90) REVERT: C 357 ARG cc_start: 0.7829 (ttp-110) cc_final: 0.6658 (mtp85) REVERT: C 378 LYS cc_start: 0.7777 (mmmm) cc_final: 0.7427 (mmmm) REVERT: C 386 LYS cc_start: 0.8245 (mttp) cc_final: 0.7603 (tttt) REVERT: C 392 PHE cc_start: 0.6866 (m-80) cc_final: 0.6445 (m-80) REVERT: C 462 LYS cc_start: 0.7822 (tptt) cc_final: 0.7418 (ttmm) REVERT: C 528 LYS cc_start: 0.8691 (mmmm) cc_final: 0.8361 (mmmt) REVERT: C 537 LYS cc_start: 0.8774 (tttp) cc_final: 0.8361 (mtpp) REVERT: C 551 VAL cc_start: 0.8675 (OUTLIER) cc_final: 0.8384 (p) REVERT: C 562 PHE cc_start: 0.8031 (p90) cc_final: 0.7790 (p90) REVERT: C 569 ILE cc_start: 0.7844 (mm) cc_final: 0.7494 (mm) REVERT: C 574 ASP cc_start: 0.8011 (t70) cc_final: 0.7631 (t0) REVERT: C 602 THR cc_start: 0.8715 (m) cc_final: 0.8208 (p) REVERT: C 619 GLU cc_start: 0.7408 (mp0) cc_final: 0.7138 (pm20) REVERT: C 671 CYS cc_start: 0.6931 (m) cc_final: 0.6549 (m) REVERT: C 725 GLU cc_start: 0.8249 (tt0) cc_final: 0.7975 (tm-30) REVERT: C 726 ILE cc_start: 0.9349 (OUTLIER) cc_final: 0.8973 (mm) REVERT: C 773 GLU cc_start: 0.8129 (tt0) cc_final: 0.7099 (tp30) REVERT: C 776 LYS cc_start: 0.8722 (tmmt) cc_final: 0.8464 (ttmm) REVERT: C 777 ASN cc_start: 0.8445 (m-40) cc_final: 0.7455 (m110) REVERT: C 779 GLN cc_start: 0.8539 (tm-30) cc_final: 0.8145 (tm-30) REVERT: C 792 PRO cc_start: 0.8399 (Cg_exo) cc_final: 0.8185 (Cg_endo) REVERT: C 808 ASP cc_start: 0.8217 (t70) cc_final: 0.7498 (p0) REVERT: C 821 LEU cc_start: 0.8456 (tp) cc_final: 0.8113 (tt) REVERT: C 851 CYS cc_start: 0.8298 (t) cc_final: 0.7695 (t) REVERT: C 933 LYS cc_start: 0.8579 (mtpp) cc_final: 0.8344 (mtmm) REVERT: C 953 ASN cc_start: 0.8501 (m-40) cc_final: 0.8287 (m-40) REVERT: C 964 LYS cc_start: 0.8765 (tmtm) cc_final: 0.8345 (ttmm) REVERT: C 1002 GLN cc_start: 0.8321 (tp40) cc_final: 0.7945 (tp40) REVERT: C 1010 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.8191 (mp10) REVERT: C 1027 THR cc_start: 0.8713 (m) cc_final: 0.8375 (t) REVERT: C 1072 GLU cc_start: 0.8604 (pm20) cc_final: 0.8265 (pm20) REVERT: C 1107 ARG cc_start: 0.7918 (mtt180) cc_final: 0.7507 (mtt180) REVERT: C 1118 ASP cc_start: 0.8287 (t70) cc_final: 0.7873 (t0) REVERT: C 1138 TYR cc_start: 0.7947 (t80) cc_final: 0.7586 (t80) REVERT: C 1139 ASP cc_start: 0.8071 (t70) cc_final: 0.7854 (t0) REVERT: C 1144 GLU cc_start: 0.8105 (pp20) cc_final: 0.7812 (pp20) outliers start: 139 outliers final: 89 residues processed: 643 average time/residue: 0.1598 time to fit residues: 160.4229 Evaluate side-chains 610 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 513 time to evaluate : 0.915 ------------------------------------------------------------------------------- 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 131 CYS 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 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 519 HIS 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 747 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 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 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 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 763 LEU 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 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 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 221 SER 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 697 MET Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 955 ASN Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1017 GLU 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 Chi-restraints excluded: chain D residue 245 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 176 optimal weight: 0.7980 chunk 253 optimal weight: 2.9990 chunk 258 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 248 optimal weight: 8.9990 chunk 278 optimal weight: 4.9990 chunk 193 optimal weight: 3.9990 chunk 180 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 178 optimal weight: 0.8980 chunk 177 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN A 394 ASN A 544 ASN A1083 HIS B 30 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN B 949 GLN B 954 HIS ** 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 450 ASN C 563 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1064 HIS ** D 81 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 = 0.4029 r_free = 0.4029 target = 0.155984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.115986 restraints weight = 46366.236| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 3.03 r_work: 0.3259 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 26904 Z= 0.197 Angle : 0.649 11.006 36699 Z= 0.325 Chirality : 0.047 0.329 4216 Planarity : 0.004 0.049 4697 Dihedral : 6.339 59.471 3680 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 5.11 % Allowed : 19.18 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.46 (0.14), residues: 3276 helix: 0.84 (0.21), residues: 654 sheet: -1.60 (0.20), residues: 604 loop : -2.66 (0.12), residues: 2018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 328 TYR 0.021 0.001 TYR C1067 PHE 0.024 0.002 PHE A 168 TRP 0.032 0.001 TRP A 64 HIS 0.007 0.001 HIS C1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.20 (26835) covalent geometry : angle 0.63502 / 0.32 (36533) SS BOND : bond 0.00295 / 0.21 ( 41) SS BOND : angle 1.84344 / 1.27 ( 82) hydrogen bonds : bond 0.03765 / 2.50 ( 750) hydrogen bonds : angle 4.90133 / 3.42 ( 2004) link_NAG-ASN : bond 0.00390 / 0.29 ( 28) link_NAG-ASN : angle 2.29378 / 1.50 ( 84) *********************** 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 677 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 531 time to evaluate : 0.753 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 43 PHE cc_start: 0.8621 (t80) cc_final: 0.8420 (t80) REVERT: A 46 SER cc_start: 0.9219 (m) cc_final: 0.8989 (p) REVERT: A 66 HIS cc_start: 0.8180 (OUTLIER) cc_final: 0.7643 (m90) REVERT: A 97 LYS cc_start: 0.8646 (tppt) cc_final: 0.8266 (tppt) REVERT: A 109 THR cc_start: 0.8700 (p) cc_final: 0.8417 (t) REVERT: A 132 GLU cc_start: 0.6693 (pm20) cc_final: 0.6065 (pm20) REVERT: A 164 ASN cc_start: 0.7764 (p0) cc_final: 0.7375 (p0) REVERT: A 186 ASN cc_start: 0.7793 (p0) cc_final: 0.7341 (p0) REVERT: A 224 GLU cc_start: 0.8194 (mp0) cc_final: 0.7877 (mp0) REVERT: A 239 GLN cc_start: 0.8029 (tp40) cc_final: 0.7689 (tp40) REVERT: A 269 TYR cc_start: 0.8636 (m-80) cc_final: 0.7678 (m-80) REVERT: A 282 ASN cc_start: 0.8913 (OUTLIER) cc_final: 0.8331 (m-40) REVERT: A 297 SER cc_start: 0.8595 (m) cc_final: 0.8229 (p) REVERT: A 298 GLU cc_start: 0.8193 (tt0) cc_final: 0.7935 (tp30) REVERT: A 307 THR cc_start: 0.8714 (m) cc_final: 0.8412 (p) REVERT: A 356 LYS cc_start: 0.7598 (OUTLIER) cc_final: 0.7126 (tmmm) REVERT: A 390 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.7046 (tt) REVERT: A 537 LYS cc_start: 0.8893 (ttmt) cc_final: 0.8523 (ttmm) REVERT: A 542 ASN cc_start: 0.8692 (t0) cc_final: 0.8383 (t0) REVERT: A 544 ASN cc_start: 0.8553 (m-40) cc_final: 0.8242 (t0) REVERT: A 569 ILE cc_start: 0.8613 (pt) cc_final: 0.8306 (mp) REVERT: A 580 GLN cc_start: 0.8171 (pt0) cc_final: 0.7755 (pt0) REVERT: A 708 SER cc_start: 0.8552 (t) cc_final: 0.8235 (m) REVERT: A 725 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7408 (tm-30) REVERT: A 726 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8552 (mm) REVERT: A 739 THR cc_start: 0.8484 (m) cc_final: 0.8239 (m) REVERT: A 773 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7137 (tm-30) REVERT: A 780 GLU cc_start: 0.8161 (pt0) cc_final: 0.7719 (tm-30) REVERT: A 788 ILE cc_start: 0.8936 (mm) cc_final: 0.8678 (mm) REVERT: A 790 LYS cc_start: 0.8221 (mppt) cc_final: 0.7821 (mppt) REVERT: A 803 SER cc_start: 0.8726 (m) cc_final: 0.8451 (p) REVERT: A 851 CYS cc_start: 0.8643 (t) cc_final: 0.8257 (t) REVERT: A 868 GLU cc_start: 0.8377 (tp30) cc_final: 0.8107 (tm-30) REVERT: A 869 MET cc_start: 0.8680 (mtt) cc_final: 0.8400 (mtm) REVERT: A 933 LYS cc_start: 0.8513 (mtmt) cc_final: 0.8217 (mttp) REVERT: A 984 LEU cc_start: 0.9041 (mt) cc_final: 0.8839 (mt) REVERT: A 994 ASP cc_start: 0.7703 (t70) cc_final: 0.7438 (t70) REVERT: A 1017 GLU cc_start: 0.8312 (tm-30) cc_final: 0.7820 (tp30) REVERT: A 1050 MET cc_start: 0.8119 (mtm) cc_final: 0.7895 (mtp) REVERT: A 1107 ARG cc_start: 0.7840 (mtt90) cc_final: 0.7605 (mtt90) REVERT: B 52 GLN cc_start: 0.8277 (tm-30) cc_final: 0.7933 (tm-30) REVERT: B 95 ILE cc_start: 0.8782 (mt) cc_final: 0.8233 (tt) REVERT: B 121 ASN cc_start: 0.7924 (p0) cc_final: 0.7436 (p0) REVERT: B 129 LYS cc_start: 0.8657 (ttmt) cc_final: 0.8122 (tmtt) REVERT: B 187 LEU cc_start: 0.8287 (tp) cc_final: 0.7927 (mt) REVERT: B 297 SER cc_start: 0.8588 (m) cc_final: 0.8308 (p) REVERT: B 299 THR cc_start: 0.8821 (m) cc_final: 0.8538 (p) REVERT: B 307 THR cc_start: 0.8866 (m) cc_final: 0.8464 (p) REVERT: B 347 PHE cc_start: 0.3639 (OUTLIER) cc_final: 0.2989 (t80) REVERT: B 406 GLU cc_start: 0.8457 (mt-10) cc_final: 0.7987 (mt-10) REVERT: B 534 VAL cc_start: 0.8701 (t) cc_final: 0.8478 (m) REVERT: B 558 LYS cc_start: 0.8891 (mmmt) cc_final: 0.8404 (mmmt) REVERT: B 580 GLN cc_start: 0.8737 (mm-40) cc_final: 0.8318 (mm-40) REVERT: B 674 TYR cc_start: 0.8486 (t80) cc_final: 0.8201 (t80) REVERT: B 725 GLU cc_start: 0.8059 (pt0) cc_final: 0.7728 (pt0) REVERT: B 764 LYS cc_start: 0.8770 (ttmm) cc_final: 0.8447 (ttpp) REVERT: B 773 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7043 (tm-30) REVERT: B 796 TYR cc_start: 0.8999 (t80) cc_final: 0.8694 (t80) REVERT: B 816 SER cc_start: 0.8913 (m) cc_final: 0.8500 (p) REVERT: B 820 ASP cc_start: 0.8053 (m-30) cc_final: 0.7833 (t0) REVERT: B 851 CYS cc_start: 0.8580 (t) cc_final: 0.8159 (t) REVERT: B 904 TYR cc_start: 0.8162 (m-10) cc_final: 0.7026 (m-10) REVERT: B 949 GLN cc_start: 0.8748 (mm-40) cc_final: 0.8396 (mm-40) REVERT: B 950 ASP cc_start: 0.8102 (t70) cc_final: 0.7747 (t70) REVERT: B 955 ASN cc_start: 0.8327 (m110) cc_final: 0.8110 (m-40) REVERT: B 957 GLN cc_start: 0.8445 (pt0) cc_final: 0.8242 (pt0) REVERT: B 979 ASP cc_start: 0.8117 (m-30) cc_final: 0.7757 (m-30) REVERT: B 990 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7850 (tp30) REVERT: B 1010 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.7908 (mp10) REVERT: B 1017 GLU cc_start: 0.8350 (tm-30) cc_final: 0.7857 (tm-30) REVERT: B 1031 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7939 (mt-10) REVERT: B 1041 ASP cc_start: 0.8539 (m-30) cc_final: 0.8062 (t0) REVERT: B 1073 LYS cc_start: 0.8503 (ttpp) cc_final: 0.8266 (ttmm) REVERT: B 1118 ASP cc_start: 0.8048 (t70) cc_final: 0.7566 (t0) REVERT: C 81 ASN cc_start: 0.7109 (t0) cc_final: 0.6003 (t0) REVERT: C 120 VAL cc_start: 0.8448 (m) cc_final: 0.8125 (p) REVERT: C 135 PHE cc_start: 0.6281 (p90) cc_final: 0.5990 (p90) REVERT: C 199 PHE cc_start: 0.8042 (t80) cc_final: 0.7623 (t80) REVERT: C 235 ILE cc_start: 0.8650 (mt) cc_final: 0.8193 (mm) REVERT: C 237 ARG cc_start: 0.8416 (mtm180) cc_final: 0.7829 (mtm180) REVERT: C 239 GLN cc_start: 0.6767 (tp40) cc_final: 0.5980 (tp40) REVERT: C 280 ASN cc_start: 0.8466 (t0) cc_final: 0.8173 (t0) REVERT: C 281 GLU cc_start: 0.7908 (pp20) cc_final: 0.7570 (pp20) REVERT: C 319 ARG cc_start: 0.8440 (ttm-80) cc_final: 0.8208 (ttm-80) REVERT: C 355 ARG cc_start: 0.8326 (ttm-80) cc_final: 0.7774 (tpt90) REVERT: C 378 LYS cc_start: 0.7802 (mmmm) cc_final: 0.7424 (mmmm) REVERT: C 386 LYS cc_start: 0.8177 (mttp) cc_final: 0.7559 (ttmt) REVERT: C 392 PHE cc_start: 0.7115 (m-80) cc_final: 0.6680 (m-80) REVERT: C 462 LYS cc_start: 0.8158 (tptt) cc_final: 0.7714 (ttmm) REVERT: C 501 TYR cc_start: 0.6291 (OUTLIER) cc_final: 0.5985 (m-10) REVERT: C 511 VAL cc_start: 0.7832 (t) cc_final: 0.7621 (p) REVERT: C 528 LYS cc_start: 0.8892 (mmmm) cc_final: 0.8609 (mmmt) REVERT: C 551 VAL cc_start: 0.8760 (OUTLIER) cc_final: 0.8483 (p) REVERT: C 592 PHE cc_start: 0.8519 (p90) cc_final: 0.8291 (p90) REVERT: C 602 THR cc_start: 0.8707 (m) cc_final: 0.8301 (p) REVERT: C 615 VAL cc_start: 0.8740 (t) cc_final: 0.8498 (m) REVERT: C 671 CYS cc_start: 0.6791 (m) cc_final: 0.6422 (m) REVERT: C 725 GLU cc_start: 0.8258 (tt0) cc_final: 0.8035 (tm-30) REVERT: C 726 ILE cc_start: 0.9353 (OUTLIER) cc_final: 0.8954 (mm) REVERT: C 773 GLU cc_start: 0.8083 (tt0) cc_final: 0.7345 (tp30) REVERT: C 776 LYS cc_start: 0.8737 (tmmt) cc_final: 0.8483 (ttmm) REVERT: C 777 ASN cc_start: 0.8464 (m-40) cc_final: 0.7784 (m110) REVERT: C 779 GLN cc_start: 0.8596 (tm-30) cc_final: 0.8366 (tm-30) REVERT: C 808 ASP cc_start: 0.8181 (t70) cc_final: 0.7913 (t0) REVERT: C 851 CYS cc_start: 0.8251 (t) cc_final: 0.7649 (t) REVERT: C 868 GLU cc_start: 0.8341 (mp0) cc_final: 0.8063 (mp0) REVERT: C 933 LYS cc_start: 0.8627 (mtpp) cc_final: 0.8400 (mtmm) REVERT: C 964 LYS cc_start: 0.8809 (tmtm) cc_final: 0.8400 (ttmm) REVERT: C 991 VAL cc_start: 0.9007 (OUTLIER) cc_final: 0.8765 (p) REVERT: C 1002 GLN cc_start: 0.8325 (tp40) cc_final: 0.7917 (tp40) REVERT: C 1010 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.8184 (mp10) REVERT: C 1027 THR cc_start: 0.8845 (m) cc_final: 0.8498 (t) REVERT: C 1072 GLU cc_start: 0.8479 (pm20) cc_final: 0.8174 (pm20) REVERT: C 1107 ARG cc_start: 0.7908 (mtt180) cc_final: 0.7565 (mtt180) REVERT: C 1118 ASP cc_start: 0.8201 (t70) cc_final: 0.7782 (t0) REVERT: C 1138 TYR cc_start: 0.7904 (t80) cc_final: 0.7627 (t80) REVERT: C 1144 GLU cc_start: 0.8072 (pp20) cc_final: 0.7757 (pp20) outliers start: 146 outliers final: 105 residues processed: 641 average time/residue: 0.1610 time to fit residues: 161.0650 Evaluate side-chains 627 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 509 time to evaluate : 0.838 ------------------------------------------------------------------------------- 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 68 ILE Chi-restraints excluded: chain A residue 108 THR 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 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 549 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 764 LYS 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 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 1141 LEU 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 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 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 731 MET Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 976 VAL 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 1129 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 30 ASN 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 203 SER Chi-restraints excluded: chain C residue 221 SER 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 501 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 697 MET Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 751 ASN 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 957 GLN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1017 GLU 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 313 optimal weight: 0.8980 chunk 244 optimal weight: 9.9990 chunk 284 optimal weight: 0.2980 chunk 35 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 127 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 437 ASN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 ASN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN B 762 GLN B 913 GLN B 954 HIS ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 563 GLN C 955 ASN ** D 81 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 = 0.4049 r_free = 0.4049 target = 0.158805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.118804 restraints weight = 46773.915| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 3.12 r_work: 0.3248 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 26904 Z= 0.144 Angle : 0.626 10.416 36699 Z= 0.312 Chirality : 0.046 0.321 4216 Planarity : 0.004 0.069 4697 Dihedral : 6.228 59.577 3679 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 5.08 % Allowed : 19.67 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.14), residues: 3276 helix: 0.98 (0.21), residues: 656 sheet: -1.57 (0.20), residues: 594 loop : -2.57 (0.13), residues: 2026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 328 TYR 0.021 0.001 TYR B 707 PHE 0.028 0.001 PHE B 199 TRP 0.033 0.001 TRP A 64 HIS 0.008 0.001 HIS A1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (26835) covalent geometry : angle 0.61325 / 0.31 (36533) SS BOND : bond 0.00292 / 0.20 ( 41) SS BOND : angle 1.62643 / 1.11 ( 82) hydrogen bonds : bond 0.03432 / 2.29 ( 750) hydrogen bonds : angle 4.83665 / 3.37 ( 2004) link_NAG-ASN : bond 0.00374 / 0.27 ( 28) link_NAG-ASN : angle 2.19321 / 1.43 ( 84) *********************** 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 667 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 522 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ASN cc_start: 0.8874 (t0) cc_final: 0.8451 (p0) REVERT: A 43 PHE cc_start: 0.8567 (t80) cc_final: 0.8202 (t80) REVERT: A 46 SER cc_start: 0.9196 (m) cc_final: 0.8973 (p) REVERT: A 66 HIS cc_start: 0.8237 (OUTLIER) cc_final: 0.7786 (m90) REVERT: A 97 LYS cc_start: 0.8660 (tppt) cc_final: 0.8383 (tppt) REVERT: A 102 ARG cc_start: 0.8721 (ptp-170) cc_final: 0.8520 (ptp-170) REVERT: A 109 THR cc_start: 0.8603 (p) cc_final: 0.8322 (t) REVERT: A 186 ASN cc_start: 0.7751 (OUTLIER) cc_final: 0.7233 (p0) REVERT: A 224 GLU cc_start: 0.8267 (mp0) cc_final: 0.8043 (mp0) REVERT: A 239 GLN cc_start: 0.8094 (tp40) cc_final: 0.7741 (tp40) REVERT: A 269 TYR cc_start: 0.8674 (m-80) cc_final: 0.7703 (m-80) REVERT: A 282 ASN cc_start: 0.8857 (OUTLIER) cc_final: 0.8264 (m-40) REVERT: A 297 SER cc_start: 0.8591 (m) cc_final: 0.8153 (p) REVERT: A 298 GLU cc_start: 0.8190 (tt0) cc_final: 0.7901 (tp30) REVERT: A 307 THR cc_start: 0.8789 (m) cc_final: 0.8451 (t) REVERT: A 324 GLU cc_start: 0.7621 (pm20) cc_final: 0.7409 (pm20) REVERT: A 356 LYS cc_start: 0.7574 (OUTLIER) cc_final: 0.7111 (tmmm) REVERT: A 390 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.6847 (tt) REVERT: A 392 PHE cc_start: 0.7331 (m-80) cc_final: 0.7060 (m-80) REVERT: A 449 TYR cc_start: 0.6564 (OUTLIER) cc_final: 0.6356 (p90) REVERT: A 537 LYS cc_start: 0.8913 (ttmt) cc_final: 0.8408 (mtpp) REVERT: A 542 ASN cc_start: 0.8676 (t0) cc_final: 0.8394 (t0) REVERT: A 562 PHE cc_start: 0.8048 (p90) cc_final: 0.7733 (p90) REVERT: A 569 ILE cc_start: 0.8607 (pt) cc_final: 0.8314 (mp) REVERT: A 580 GLN cc_start: 0.8290 (pt0) cc_final: 0.7840 (pt0) REVERT: A 664 ILE cc_start: 0.8827 (mt) cc_final: 0.8553 (mp) REVERT: A 675 GLN cc_start: 0.7616 (mm-40) cc_final: 0.7163 (mm110) REVERT: A 708 SER cc_start: 0.8541 (t) cc_final: 0.8249 (m) REVERT: A 725 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7425 (tm-30) REVERT: A 726 ILE cc_start: 0.8766 (OUTLIER) cc_final: 0.8409 (mm) REVERT: A 739 THR cc_start: 0.8494 (m) cc_final: 0.8264 (m) REVERT: A 773 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7161 (tm-30) REVERT: A 775 ASP cc_start: 0.8366 (t0) cc_final: 0.8093 (m-30) REVERT: A 780 GLU cc_start: 0.8231 (pt0) cc_final: 0.7755 (tm-30) REVERT: A 787 GLN cc_start: 0.8851 (mp10) cc_final: 0.8558 (mp10) REVERT: A 788 ILE cc_start: 0.8930 (mm) cc_final: 0.8658 (mm) REVERT: A 790 LYS cc_start: 0.8253 (mppt) cc_final: 0.7950 (mppt) REVERT: A 803 SER cc_start: 0.8657 (m) cc_final: 0.8366 (p) REVERT: A 851 CYS cc_start: 0.8550 (t) cc_final: 0.8215 (t) REVERT: A 868 GLU cc_start: 0.8372 (tp30) cc_final: 0.8076 (tm-30) REVERT: A 869 MET cc_start: 0.8677 (mtt) cc_final: 0.8390 (mtm) REVERT: A 933 LYS cc_start: 0.8460 (mtmt) cc_final: 0.8168 (mttp) REVERT: A 984 LEU cc_start: 0.9016 (mt) cc_final: 0.8808 (mt) REVERT: A 990 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7874 (tm-30) REVERT: A 994 ASP cc_start: 0.7641 (t70) cc_final: 0.7358 (t70) REVERT: A 995 ARG cc_start: 0.8399 (ttp-110) cc_final: 0.8180 (ttp-110) REVERT: A 1017 GLU cc_start: 0.8331 (tm-30) cc_final: 0.7827 (tp30) REVERT: A 1050 MET cc_start: 0.8117 (mtm) cc_final: 0.7888 (mtp) REVERT: A 1107 ARG cc_start: 0.7962 (mtt90) cc_final: 0.7711 (mtt90) REVERT: B 52 GLN cc_start: 0.8270 (tm-30) cc_final: 0.7899 (tm-30) REVERT: B 95 ILE cc_start: 0.8676 (mt) cc_final: 0.8090 (tt) REVERT: B 104 TRP cc_start: 0.7757 (m-10) cc_final: 0.7214 (m-10) REVERT: B 121 ASN cc_start: 0.7974 (p0) cc_final: 0.7529 (p0) REVERT: B 129 LYS cc_start: 0.8555 (ttmt) cc_final: 0.7931 (tmtt) REVERT: B 169 GLU cc_start: 0.8254 (mp0) cc_final: 0.7971 (mp0) REVERT: B 190 PHE cc_start: 0.8536 (m-80) cc_final: 0.8125 (m-10) REVERT: B 201 ILE cc_start: 0.8851 (mt) cc_final: 0.8619 (mp) REVERT: B 208 ILE cc_start: 0.7940 (OUTLIER) cc_final: 0.7425 (pt) REVERT: B 297 SER cc_start: 0.8547 (m) cc_final: 0.8258 (p) REVERT: B 327 VAL cc_start: 0.8859 (t) cc_final: 0.8546 (m) REVERT: B 347 PHE cc_start: 0.3769 (OUTLIER) cc_final: 0.3088 (t80) REVERT: B 361 CYS cc_start: 0.7011 (OUTLIER) cc_final: 0.6732 (t) REVERT: B 406 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8041 (mt-10) REVERT: B 558 LYS cc_start: 0.8911 (mmmt) cc_final: 0.8393 (mmmt) REVERT: B 559 PHE cc_start: 0.8790 (m-10) cc_final: 0.8530 (m-10) REVERT: B 580 GLN cc_start: 0.8746 (mm-40) cc_final: 0.8310 (mm-40) REVERT: B 674 TYR cc_start: 0.8425 (t80) cc_final: 0.8139 (t80) REVERT: B 707 TYR cc_start: 0.8618 (t80) cc_final: 0.8310 (t80) REVERT: B 725 GLU cc_start: 0.8097 (pt0) cc_final: 0.7751 (pt0) REVERT: B 764 LYS cc_start: 0.8708 (ttmm) cc_final: 0.8384 (ttpp) REVERT: B 773 GLU cc_start: 0.7714 (tm-30) cc_final: 0.6963 (tm-30) REVERT: B 776 LYS cc_start: 0.8914 (tptm) cc_final: 0.8682 (tptm) REVERT: B 796 TYR cc_start: 0.9026 (t80) cc_final: 0.8715 (t80) REVERT: B 816 SER cc_start: 0.8862 (m) cc_final: 0.8405 (p) REVERT: B 820 ASP cc_start: 0.8034 (m-30) cc_final: 0.7770 (t0) REVERT: B 851 CYS cc_start: 0.8598 (t) cc_final: 0.8140 (t) REVERT: B 904 TYR cc_start: 0.8150 (m-10) cc_final: 0.6971 (m-10) REVERT: B 914 ASN cc_start: 0.8515 (p0) cc_final: 0.8246 (p0) REVERT: B 918 GLU cc_start: 0.7906 (mp0) cc_final: 0.7689 (mp0) REVERT: B 949 GLN cc_start: 0.8784 (mm-40) cc_final: 0.8397 (mm-40) REVERT: B 950 ASP cc_start: 0.8083 (t70) cc_final: 0.7747 (t70) REVERT: B 979 ASP cc_start: 0.8179 (m-30) cc_final: 0.7792 (m-30) REVERT: B 990 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7820 (tp30) REVERT: B 1010 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.7937 (mp10) REVERT: B 1017 GLU cc_start: 0.8425 (tm-30) cc_final: 0.7967 (tm-30) REVERT: B 1019 ARG cc_start: 0.7991 (ttp80) cc_final: 0.7791 (ttp80) REVERT: B 1031 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7896 (mt-10) REVERT: B 1041 ASP cc_start: 0.8512 (m-30) cc_final: 0.8070 (t0) REVERT: B 1073 LYS cc_start: 0.8529 (ttpp) cc_final: 0.8275 (ttmm) REVERT: B 1118 ASP cc_start: 0.8031 (t70) cc_final: 0.7544 (t0) REVERT: B 1125 ASN cc_start: 0.8354 (t0) cc_final: 0.7920 (t0) REVERT: C 81 ASN cc_start: 0.6930 (t0) cc_final: 0.5828 (t0) REVERT: C 86 PHE cc_start: 0.8258 (t80) cc_final: 0.7760 (t80) REVERT: C 120 VAL cc_start: 0.8396 (m) cc_final: 0.8072 (p) REVERT: C 133 PHE cc_start: 0.7292 (p90) cc_final: 0.6227 (p90) REVERT: C 135 PHE cc_start: 0.6994 (p90) cc_final: 0.6356 (p90) REVERT: C 188 ARG cc_start: 0.8390 (ptp-170) cc_final: 0.7905 (ptp-110) REVERT: C 199 PHE cc_start: 0.8117 (t80) cc_final: 0.7728 (t80) REVERT: C 235 ILE cc_start: 0.8547 (mt) cc_final: 0.8137 (mm) REVERT: C 237 ARG cc_start: 0.8428 (mtm180) cc_final: 0.7912 (mtm180) REVERT: C 239 GLN cc_start: 0.6848 (tp40) cc_final: 0.5974 (tp40) REVERT: C 269 TYR cc_start: 0.8570 (m-80) cc_final: 0.8258 (m-80) REVERT: C 280 ASN cc_start: 0.8460 (t0) cc_final: 0.8144 (t0) REVERT: C 281 GLU cc_start: 0.7922 (pp20) cc_final: 0.7577 (pp20) REVERT: C 328 ARG cc_start: 0.7322 (mtp85) cc_final: 0.6991 (mtp85) REVERT: C 335 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7380 (tt) REVERT: C 355 ARG cc_start: 0.8329 (ttm-80) cc_final: 0.7977 (tpt90) REVERT: C 357 ARG cc_start: 0.7882 (ttp-110) cc_final: 0.6813 (mtp85) REVERT: C 378 LYS cc_start: 0.7778 (mmmm) cc_final: 0.7379 (mmmm) REVERT: C 386 LYS cc_start: 0.8182 (mttp) cc_final: 0.7725 (mtpt) REVERT: C 462 LYS cc_start: 0.7804 (tptt) cc_final: 0.7433 (ttmm) REVERT: C 501 TYR cc_start: 0.6536 (OUTLIER) cc_final: 0.6143 (m-10) REVERT: C 511 VAL cc_start: 0.7602 (t) cc_final: 0.7383 (p) REVERT: C 528 LYS cc_start: 0.8861 (mmmm) cc_final: 0.8570 (mmmt) REVERT: C 574 ASP cc_start: 0.8003 (t70) cc_final: 0.7572 (t0) REVERT: C 602 THR cc_start: 0.8723 (m) cc_final: 0.8296 (p) REVERT: C 671 CYS cc_start: 0.6865 (m) cc_final: 0.6497 (m) REVERT: C 675 GLN cc_start: 0.7470 (tm-30) cc_final: 0.7024 (tm-30) REVERT: C 725 GLU cc_start: 0.8323 (tt0) cc_final: 0.7974 (tm-30) REVERT: C 726 ILE cc_start: 0.9327 (OUTLIER) cc_final: 0.8902 (mm) REVERT: C 773 GLU cc_start: 0.8095 (tt0) cc_final: 0.7092 (tp30) REVERT: C 774 GLN cc_start: 0.8035 (mm-40) cc_final: 0.7529 (mp10) REVERT: C 776 LYS cc_start: 0.8719 (tmmt) cc_final: 0.8422 (ttmm) REVERT: C 777 ASN cc_start: 0.8400 (m-40) cc_final: 0.7503 (m110) REVERT: C 779 GLN cc_start: 0.8573 (tm-30) cc_final: 0.8363 (tm-30) REVERT: C 808 ASP cc_start: 0.8143 (t70) cc_final: 0.7861 (t0) REVERT: C 851 CYS cc_start: 0.8228 (t) cc_final: 0.7632 (t) REVERT: C 868 GLU cc_start: 0.8432 (mp0) cc_final: 0.8123 (mp0) REVERT: C 918 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8254 (mt-10) REVERT: C 933 LYS cc_start: 0.8624 (mtpp) cc_final: 0.8402 (mtmm) REVERT: C 935 GLN cc_start: 0.8623 (mm-40) cc_final: 0.8138 (mm-40) REVERT: C 964 LYS cc_start: 0.8791 (tmtm) cc_final: 0.8376 (ttmm) REVERT: C 1002 GLN cc_start: 0.8420 (tp40) cc_final: 0.7900 (tp-100) REVERT: C 1010 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.8240 (mp10) REVERT: C 1072 GLU cc_start: 0.8516 (pm20) cc_final: 0.8183 (pm20) REVERT: C 1107 ARG cc_start: 0.7939 (mtt180) cc_final: 0.7460 (mtt180) REVERT: C 1118 ASP cc_start: 0.8218 (t70) cc_final: 0.7779 (t0) REVERT: C 1138 TYR cc_start: 0.7928 (t80) cc_final: 0.7592 (t80) REVERT: C 1144 GLU cc_start: 0.8095 (pp20) cc_final: 0.7771 (pp20) outliers start: 145 outliers final: 96 residues processed: 637 average time/residue: 0.1566 time to fit residues: 156.4633 Evaluate side-chains 617 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 505 time to evaluate : 0.891 ------------------------------------------------------------------------------- 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 68 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 186 ASN 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 449 TYR 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 549 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 726 ILE 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 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 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL 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 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 738 CYS Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 974 SER 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 1129 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 30 ASN 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 203 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 303 LEU 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 515 PHE Chi-restraints excluded: chain C residue 518 LEU 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 791 THR Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1017 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 148 optimal weight: 0.1980 chunk 195 optimal weight: 2.9990 chunk 302 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 318 optimal weight: 20.0000 chunk 146 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 110 optimal weight: 0.0670 chunk 109 optimal weight: 0.9990 chunk 214 optimal weight: 0.0470 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 544 ASN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN B 762 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN B 935 GLN B 954 HIS B 955 ASN B1011 GLN C 317 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.161025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.121277 restraints weight = 46911.865| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 3.14 r_work: 0.3272 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 26904 Z= 0.108 Angle : 0.606 11.522 36699 Z= 0.301 Chirality : 0.045 0.334 4216 Planarity : 0.004 0.050 4697 Dihedral : 6.020 58.853 3677 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 4.59 % Allowed : 20.13 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.14), residues: 3276 helix: 1.12 (0.21), residues: 663 sheet: -1.52 (0.20), residues: 600 loop : -2.50 (0.13), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 328 TYR 0.018 0.001 TYR B 707 PHE 0.029 0.001 PHE C 592 TRP 0.032 0.001 TRP A 64 HIS 0.008 0.001 HIS A1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (26835) covalent geometry : angle 0.59511 / 0.30 (36533) SS BOND : bond 0.00284 / 0.16 ( 41) SS BOND : angle 1.43879 / 1.01 ( 82) hydrogen bonds : bond 0.03129 / 2.10 ( 750) hydrogen bonds : angle 4.74567 / 3.31 ( 2004) link_NAG-ASN : bond 0.00396 / 0.29 ( 28) link_NAG-ASN : angle 2.07719 / 1.36 ( 84) *********************** 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 654 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 523 time to evaluate : 0.769 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 30 ASN cc_start: 0.8712 (t0) cc_final: 0.8397 (p0) REVERT: A 43 PHE cc_start: 0.8448 (t80) cc_final: 0.8124 (t80) REVERT: A 46 SER cc_start: 0.9149 (m) cc_final: 0.8931 (p) REVERT: A 97 LYS cc_start: 0.8561 (tppt) cc_final: 0.8311 (tppt) REVERT: A 102 ARG cc_start: 0.8720 (ptp-170) cc_final: 0.8502 (ptp-170) REVERT: A 109 THR cc_start: 0.8632 (p) cc_final: 0.8351 (t) REVERT: A 186 ASN cc_start: 0.7782 (OUTLIER) cc_final: 0.7254 (p0) REVERT: A 224 GLU cc_start: 0.8265 (mp0) cc_final: 0.8036 (mp0) REVERT: A 239 GLN cc_start: 0.8118 (tp40) cc_final: 0.7756 (tp40) REVERT: A 269 TYR cc_start: 0.8643 (m-80) cc_final: 0.7762 (m-80) REVERT: A 282 ASN cc_start: 0.8815 (OUTLIER) cc_final: 0.8294 (m-40) REVERT: A 297 SER cc_start: 0.8581 (m) cc_final: 0.8163 (p) REVERT: A 298 GLU cc_start: 0.8217 (tt0) cc_final: 0.7934 (tp30) REVERT: A 356 LYS cc_start: 0.7552 (tmmm) cc_final: 0.7133 (tmmm) REVERT: A 386 LYS cc_start: 0.7771 (OUTLIER) cc_final: 0.7327 (mttp) REVERT: A 390 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.6892 (tt) REVERT: A 392 PHE cc_start: 0.7432 (m-80) cc_final: 0.7110 (m-80) REVERT: A 449 TYR cc_start: 0.6516 (OUTLIER) cc_final: 0.6301 (p90) REVERT: A 537 LYS cc_start: 0.8858 (ttmt) cc_final: 0.8363 (mtpp) REVERT: A 542 ASN cc_start: 0.8669 (t0) cc_final: 0.8441 (t0) REVERT: A 569 ILE cc_start: 0.8566 (pt) cc_final: 0.8258 (mp) REVERT: A 580 GLN cc_start: 0.8230 (pt0) cc_final: 0.7784 (pt0) REVERT: A 675 GLN cc_start: 0.7548 (mm-40) cc_final: 0.7098 (mm110) REVERT: A 708 SER cc_start: 0.8479 (t) cc_final: 0.8200 (m) REVERT: A 725 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7382 (tm-30) REVERT: A 726 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8339 (mm) REVERT: A 739 THR cc_start: 0.8403 (m) cc_final: 0.8189 (m) REVERT: A 773 GLU cc_start: 0.7737 (tm-30) cc_final: 0.7064 (tm-30) REVERT: A 775 ASP cc_start: 0.8304 (t0) cc_final: 0.8048 (m-30) REVERT: A 780 GLU cc_start: 0.8204 (pt0) cc_final: 0.7735 (tm-30) REVERT: A 788 ILE cc_start: 0.8921 (mm) cc_final: 0.8673 (mm) REVERT: A 790 LYS cc_start: 0.8302 (mppt) cc_final: 0.7999 (mppt) REVERT: A 796 TYR cc_start: 0.8624 (t80) cc_final: 0.8337 (t80) REVERT: A 803 SER cc_start: 0.8543 (m) cc_final: 0.8289 (p) REVERT: A 851 CYS cc_start: 0.8573 (t) cc_final: 0.8075 (t) REVERT: A 855 PHE cc_start: 0.8296 (m-80) cc_final: 0.8079 (m-80) REVERT: A 868 GLU cc_start: 0.8336 (tp30) cc_final: 0.8056 (tm-30) REVERT: A 869 MET cc_start: 0.8681 (mtt) cc_final: 0.8421 (mtm) REVERT: A 933 LYS cc_start: 0.8360 (mtmt) cc_final: 0.8101 (mttp) REVERT: A 964 LYS cc_start: 0.8789 (ttpp) cc_final: 0.8579 (ttpp) REVERT: A 984 LEU cc_start: 0.8994 (mt) cc_final: 0.8783 (mt) REVERT: A 990 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7952 (tm-30) REVERT: A 994 ASP cc_start: 0.7548 (t70) cc_final: 0.7223 (t70) REVERT: A 1017 GLU cc_start: 0.8357 (tm-30) cc_final: 0.7892 (tp30) REVERT: A 1050 MET cc_start: 0.8068 (mtm) cc_final: 0.7823 (mtp) REVERT: A 1107 ARG cc_start: 0.7855 (mtt90) cc_final: 0.7588 (mtt90) REVERT: A 1139 ASP cc_start: 0.7861 (p0) cc_final: 0.7650 (p0) REVERT: B 52 GLN cc_start: 0.8265 (tm-30) cc_final: 0.7897 (tm-30) REVERT: B 95 ILE cc_start: 0.8593 (mt) cc_final: 0.7907 (tt) REVERT: B 104 TRP cc_start: 0.7623 (m-10) cc_final: 0.7019 (m-10) REVERT: B 121 ASN cc_start: 0.7946 (p0) cc_final: 0.7489 (p0) REVERT: B 187 LEU cc_start: 0.8270 (tp) cc_final: 0.7703 (mt) REVERT: B 190 PHE cc_start: 0.8416 (m-80) cc_final: 0.8041 (m-10) REVERT: B 201 ILE cc_start: 0.8880 (mt) cc_final: 0.8659 (mp) REVERT: B 293 LEU cc_start: 0.9128 (tp) cc_final: 0.8858 (tp) REVERT: B 297 SER cc_start: 0.8500 (m) cc_final: 0.8237 (p) REVERT: B 327 VAL cc_start: 0.8805 (t) cc_final: 0.8497 (m) REVERT: B 347 PHE cc_start: 0.3598 (OUTLIER) cc_final: 0.2922 (t80) REVERT: B 361 CYS cc_start: 0.7196 (OUTLIER) cc_final: 0.6952 (t) REVERT: B 406 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8029 (mt-10) REVERT: B 558 LYS cc_start: 0.8874 (mmmt) cc_final: 0.8327 (mmmt) REVERT: B 580 GLN cc_start: 0.8736 (mm-40) cc_final: 0.8320 (mm-40) REVERT: B 674 TYR cc_start: 0.8433 (t80) cc_final: 0.8152 (t80) REVERT: B 707 TYR cc_start: 0.8581 (t80) cc_final: 0.8284 (t80) REVERT: B 725 GLU cc_start: 0.8110 (pt0) cc_final: 0.7761 (pt0) REVERT: B 764 LYS cc_start: 0.8673 (ttmm) cc_final: 0.8350 (ttpp) REVERT: B 773 GLU cc_start: 0.7744 (tm-30) cc_final: 0.7017 (tm-30) REVERT: B 776 LYS cc_start: 0.8942 (tptm) cc_final: 0.8689 (tptm) REVERT: B 816 SER cc_start: 0.8853 (m) cc_final: 0.8200 (p) REVERT: B 820 ASP cc_start: 0.7971 (m-30) cc_final: 0.7647 (m-30) REVERT: B 851 CYS cc_start: 0.8589 (t) cc_final: 0.8122 (t) REVERT: B 914 ASN cc_start: 0.8474 (p0) cc_final: 0.8108 (p0) REVERT: B 918 GLU cc_start: 0.7964 (mp0) cc_final: 0.7655 (mp0) REVERT: B 949 GLN cc_start: 0.8764 (mm-40) cc_final: 0.8401 (mm-40) REVERT: B 950 ASP cc_start: 0.8044 (t70) cc_final: 0.7707 (t70) REVERT: B 979 ASP cc_start: 0.8118 (m-30) cc_final: 0.7754 (m-30) REVERT: B 990 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7862 (tp30) REVERT: B 1017 GLU cc_start: 0.8428 (tm-30) cc_final: 0.7984 (tm-30) REVERT: B 1019 ARG cc_start: 0.7941 (ttp80) cc_final: 0.7628 (ttp80) REVERT: B 1031 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7898 (mt-10) REVERT: B 1041 ASP cc_start: 0.8498 (m-30) cc_final: 0.8041 (t0) REVERT: B 1118 ASP cc_start: 0.7958 (t70) cc_final: 0.7464 (t0) REVERT: C 41 LYS cc_start: 0.8695 (mtpt) cc_final: 0.8253 (ptpt) REVERT: C 120 VAL cc_start: 0.8318 (m) cc_final: 0.8071 (p) REVERT: C 188 ARG cc_start: 0.8413 (ptp-170) cc_final: 0.7946 (ptp-170) REVERT: C 235 ILE cc_start: 0.8473 (mt) cc_final: 0.8166 (mm) REVERT: C 237 ARG cc_start: 0.8443 (mtm180) cc_final: 0.7938 (mtm180) REVERT: C 269 TYR cc_start: 0.8504 (m-80) cc_final: 0.8289 (m-80) REVERT: C 280 ASN cc_start: 0.8470 (t0) cc_final: 0.8217 (t0) REVERT: C 281 GLU cc_start: 0.7923 (pp20) cc_final: 0.7652 (pp20) REVERT: C 328 ARG cc_start: 0.7248 (mtp85) cc_final: 0.6964 (mtp85) REVERT: C 335 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.7211 (tt) REVERT: C 347 PHE cc_start: 0.8776 (t80) cc_final: 0.7821 (t80) REVERT: C 355 ARG cc_start: 0.8299 (ttm-80) cc_final: 0.8022 (tpt90) REVERT: C 378 LYS cc_start: 0.7728 (mmmm) cc_final: 0.7323 (mmmm) REVERT: C 386 LYS cc_start: 0.8023 (mttp) cc_final: 0.7551 (mtpt) REVERT: C 462 LYS cc_start: 0.7841 (tptt) cc_final: 0.7461 (ttmm) REVERT: C 501 TYR cc_start: 0.6434 (OUTLIER) cc_final: 0.6047 (m-10) REVERT: C 511 VAL cc_start: 0.7505 (t) cc_final: 0.7258 (p) REVERT: C 528 LYS cc_start: 0.8853 (mmmm) cc_final: 0.8512 (mmmt) REVERT: C 574 ASP cc_start: 0.7914 (t70) cc_final: 0.7545 (t0) REVERT: C 592 PHE cc_start: 0.8289 (p90) cc_final: 0.8024 (p90) REVERT: C 602 THR cc_start: 0.8657 (m) cc_final: 0.8193 (p) REVERT: C 658 ASN cc_start: 0.7597 (t0) cc_final: 0.7048 (t0) REVERT: C 671 CYS cc_start: 0.6852 (m) cc_final: 0.6473 (m) REVERT: C 675 GLN cc_start: 0.7503 (tm-30) cc_final: 0.7028 (tm-30) REVERT: C 725 GLU cc_start: 0.8328 (tt0) cc_final: 0.8018 (tm-30) REVERT: C 726 ILE cc_start: 0.9332 (OUTLIER) cc_final: 0.8968 (mm) REVERT: C 773 GLU cc_start: 0.7988 (tt0) cc_final: 0.6853 (tp30) REVERT: C 774 GLN cc_start: 0.7972 (mm-40) cc_final: 0.7442 (mp10) REVERT: C 776 LYS cc_start: 0.8734 (tmmt) cc_final: 0.8424 (ttmm) REVERT: C 777 ASN cc_start: 0.8308 (m-40) cc_final: 0.7407 (m110) REVERT: C 779 GLN cc_start: 0.8524 (tm-30) cc_final: 0.8318 (tm-30) REVERT: C 808 ASP cc_start: 0.8166 (t70) cc_final: 0.7893 (t0) REVERT: C 851 CYS cc_start: 0.8253 (t) cc_final: 0.7654 (t) REVERT: C 918 GLU cc_start: 0.8462 (mt-10) cc_final: 0.8193 (mt-10) REVERT: C 933 LYS cc_start: 0.8641 (mtpp) cc_final: 0.8430 (mtmm) REVERT: C 935 GLN cc_start: 0.8594 (mm-40) cc_final: 0.8102 (mm-40) REVERT: C 953 ASN cc_start: 0.8494 (m-40) cc_final: 0.8124 (m-40) REVERT: C 964 LYS cc_start: 0.8759 (tmtm) cc_final: 0.8342 (ttmm) REVERT: C 1002 GLN cc_start: 0.8351 (tp40) cc_final: 0.7861 (tp-100) REVERT: C 1010 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8124 (mp10) REVERT: C 1027 THR cc_start: 0.8756 (m) cc_final: 0.8290 (t) REVERT: C 1072 GLU cc_start: 0.8473 (pm20) cc_final: 0.8152 (pm20) REVERT: C 1118 ASP cc_start: 0.8223 (t70) cc_final: 0.7778 (t0) REVERT: C 1144 GLU cc_start: 0.8064 (pp20) cc_final: 0.7792 (pp20) outliers start: 131 outliers final: 91 residues processed: 625 average time/residue: 0.1601 time to fit residues: 156.9483 Evaluate side-chains 602 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 498 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS 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 186 ASN 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 421 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 511 VAL 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 726 ILE 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 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 66 HIS Chi-restraints excluded: chain B residue 90 VAL 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 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 730 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 762 GLN 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 1104 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 30 ASN 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 130 VAL Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 221 SER 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 375 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 515 PHE Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 534 VAL 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 775 ASP Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1017 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 58 optimal weight: 2.9990 chunk 230 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 144 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 262 optimal weight: 0.9990 chunk 311 optimal weight: 3.9990 chunk 286 optimal weight: 2.9990 chunk 256 optimal weight: 2.9990 chunk 98 optimal weight: 0.0030 chunk 19 optimal weight: 0.7980 overall best weight: 0.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1083 HIS ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN B 762 GLN B 954 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.161526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.119597 restraints weight = 45369.523| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 3.29 r_work: 0.3240 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.4257 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 : 0.637 15.419 36699 Z= 0.316 Chirality : 0.047 0.364 4216 Planarity : 0.004 0.048 4697 Dihedral : 6.098 59.856 3675 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.55 % Favored : 90.45 % Rotamer: Outliers : 4.48 % Allowed : 20.83 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.14), residues: 3276 helix: 1.17 (0.21), residues: 658 sheet: -1.46 (0.20), residues: 598 loop : -2.46 (0.13), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 328 TYR 0.018 0.001 TYR B 707 PHE 0.030 0.001 PHE B 168 TRP 0.037 0.001 TRP A 64 HIS 0.008 0.001 HIS A1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (26835) covalent geometry : angle 0.62490 / 0.31 (36533) SS BOND : bond 0.00303 / 0.21 ( 41) SS BOND : angle 1.72452 / 1.20 ( 82) hydrogen bonds : bond 0.03306 / 2.22 ( 750) hydrogen bonds : angle 4.76117 / 3.33 ( 2004) link_NAG-ASN : bond 0.00365 / 0.27 ( 28) link_NAG-ASN : angle 2.10614 / 1.38 ( 84) *********************** 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 635 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 507 time to evaluate : 0.758 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 30 ASN cc_start: 0.8755 (t0) cc_final: 0.8394 (p0) REVERT: A 43 PHE cc_start: 0.8476 (t80) cc_final: 0.8273 (t80) REVERT: A 46 SER cc_start: 0.9147 (m) cc_final: 0.8926 (p) REVERT: A 109 THR cc_start: 0.8668 (p) cc_final: 0.8384 (t) REVERT: A 186 ASN cc_start: 0.7816 (OUTLIER) cc_final: 0.7265 (p0) REVERT: A 224 GLU cc_start: 0.8214 (mp0) cc_final: 0.7981 (mp0) REVERT: A 239 GLN cc_start: 0.8110 (tp40) cc_final: 0.7706 (tp40) REVERT: A 269 TYR cc_start: 0.8677 (m-80) cc_final: 0.7769 (m-80) REVERT: A 282 ASN cc_start: 0.8833 (OUTLIER) cc_final: 0.8288 (m-40) REVERT: A 297 SER cc_start: 0.8579 (m) cc_final: 0.8174 (p) REVERT: A 298 GLU cc_start: 0.8171 (tt0) cc_final: 0.7854 (tp30) REVERT: A 356 LYS cc_start: 0.7681 (OUTLIER) cc_final: 0.7268 (tmmm) REVERT: A 386 LYS cc_start: 0.7756 (OUTLIER) cc_final: 0.7300 (mttm) REVERT: A 390 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.6990 (tt) REVERT: A 392 PHE cc_start: 0.7514 (m-80) cc_final: 0.7164 (m-80) REVERT: A 537 LYS cc_start: 0.8892 (ttmt) cc_final: 0.8414 (mtpp) REVERT: A 542 ASN cc_start: 0.8688 (t0) cc_final: 0.8444 (t0) REVERT: A 569 ILE cc_start: 0.8576 (pt) cc_final: 0.8274 (mp) REVERT: A 580 GLN cc_start: 0.8289 (pt0) cc_final: 0.7854 (pt0) REVERT: A 664 ILE cc_start: 0.8861 (mt) cc_final: 0.8587 (mm) REVERT: A 675 GLN cc_start: 0.7570 (mm-40) cc_final: 0.7126 (mm110) REVERT: A 708 SER cc_start: 0.8502 (t) cc_final: 0.8210 (m) REVERT: A 725 GLU cc_start: 0.7909 (tm-30) cc_final: 0.7368 (tm-30) REVERT: A 726 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8350 (mm) REVERT: A 731 MET cc_start: 0.8647 (ttt) cc_final: 0.8445 (ttm) REVERT: A 739 THR cc_start: 0.8434 (m) cc_final: 0.8215 (m) REVERT: A 773 GLU cc_start: 0.7749 (tm-30) cc_final: 0.7112 (tm-30) REVERT: A 775 ASP cc_start: 0.8318 (t0) cc_final: 0.8063 (m-30) REVERT: A 780 GLU cc_start: 0.8170 (pt0) cc_final: 0.7716 (tm-30) REVERT: A 788 ILE cc_start: 0.8914 (mm) cc_final: 0.8655 (mm) REVERT: A 790 LYS cc_start: 0.8324 (mppt) cc_final: 0.8014 (mppt) REVERT: A 796 TYR cc_start: 0.8647 (t80) cc_final: 0.8347 (t80) REVERT: A 803 SER cc_start: 0.8607 (m) cc_final: 0.8330 (p) REVERT: A 851 CYS cc_start: 0.8568 (t) cc_final: 0.8119 (t) REVERT: A 868 GLU cc_start: 0.8328 (tp30) cc_final: 0.8041 (tm-30) REVERT: A 869 MET cc_start: 0.8740 (mtt) cc_final: 0.8451 (mtm) REVERT: A 933 LYS cc_start: 0.8345 (mtmt) cc_final: 0.8052 (mttp) REVERT: A 964 LYS cc_start: 0.8791 (ttpp) cc_final: 0.8572 (ttpp) REVERT: A 994 ASP cc_start: 0.7640 (t70) cc_final: 0.7331 (t70) REVERT: A 1017 GLU cc_start: 0.8348 (tm-30) cc_final: 0.7755 (tp30) REVERT: A 1050 MET cc_start: 0.8114 (mtm) cc_final: 0.7893 (mtp) REVERT: A 1107 ARG cc_start: 0.7898 (mtt90) cc_final: 0.7606 (mtt90) REVERT: B 52 GLN cc_start: 0.8282 (tm-30) cc_final: 0.7899 (tm-30) REVERT: B 95 ILE cc_start: 0.8707 (mt) cc_final: 0.8139 (tt) REVERT: B 104 TRP cc_start: 0.7610 (m-10) cc_final: 0.7054 (m-10) REVERT: B 121 ASN cc_start: 0.7903 (p0) cc_final: 0.6922 (t0) REVERT: B 187 LEU cc_start: 0.8259 (tp) cc_final: 0.7738 (mt) REVERT: B 190 PHE cc_start: 0.8353 (m-80) cc_final: 0.8025 (m-10) REVERT: B 297 SER cc_start: 0.8550 (m) cc_final: 0.8299 (p) REVERT: B 327 VAL cc_start: 0.8839 (t) cc_final: 0.8535 (m) REVERT: B 347 PHE cc_start: 0.3806 (OUTLIER) cc_final: 0.3162 (t80) REVERT: B 406 GLU cc_start: 0.8423 (mt-10) cc_final: 0.7989 (mt-10) REVERT: B 551 VAL cc_start: 0.9006 (t) cc_final: 0.8713 (m) REVERT: B 558 LYS cc_start: 0.8939 (mmmt) cc_final: 0.8500 (mmmt) REVERT: B 580 GLN cc_start: 0.8746 (mm-40) cc_final: 0.8323 (mm-40) REVERT: B 674 TYR cc_start: 0.8496 (t80) cc_final: 0.8210 (t80) REVERT: B 707 TYR cc_start: 0.8637 (t80) cc_final: 0.8303 (t80) REVERT: B 725 GLU cc_start: 0.8063 (pt0) cc_final: 0.7705 (pt0) REVERT: B 773 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7064 (tm-30) REVERT: B 776 LYS cc_start: 0.8943 (tptm) cc_final: 0.8697 (tptm) REVERT: B 796 TYR cc_start: 0.8835 (t80) cc_final: 0.8559 (t80) REVERT: B 816 SER cc_start: 0.8865 (m) cc_final: 0.8463 (m) REVERT: B 820 ASP cc_start: 0.7952 (m-30) cc_final: 0.7654 (m-30) REVERT: B 851 CYS cc_start: 0.8601 (t) cc_final: 0.8133 (t) REVERT: B 904 TYR cc_start: 0.7992 (m-10) cc_final: 0.7098 (m-10) REVERT: B 914 ASN cc_start: 0.8499 (p0) cc_final: 0.8158 (p0) REVERT: B 918 GLU cc_start: 0.7949 (mp0) cc_final: 0.7633 (mp0) REVERT: B 949 GLN cc_start: 0.8798 (mm-40) cc_final: 0.8424 (mm-40) REVERT: B 950 ASP cc_start: 0.8096 (t70) cc_final: 0.7822 (m-30) REVERT: B 979 ASP cc_start: 0.8115 (m-30) cc_final: 0.7767 (m-30) REVERT: B 990 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7876 (tp30) REVERT: B 1010 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.7962 (mp10) REVERT: B 1017 GLU cc_start: 0.8421 (tm-30) cc_final: 0.7984 (tm-30) REVERT: B 1019 ARG cc_start: 0.7933 (ttp80) cc_final: 0.7608 (ttp80) REVERT: B 1031 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7901 (mt-10) REVERT: B 1041 ASP cc_start: 0.8539 (m-30) cc_final: 0.8036 (t0) REVERT: B 1118 ASP cc_start: 0.7977 (t70) cc_final: 0.7496 (t0) REVERT: B 1125 ASN cc_start: 0.8314 (t0) cc_final: 0.7984 (t0) REVERT: C 120 VAL cc_start: 0.8398 (m) cc_final: 0.8110 (p) REVERT: C 130 VAL cc_start: 0.8436 (OUTLIER) cc_final: 0.8108 (p) REVERT: C 188 ARG cc_start: 0.8378 (ptp-170) cc_final: 0.7900 (ptp-170) REVERT: C 199 PHE cc_start: 0.8028 (t80) cc_final: 0.7571 (t80) REVERT: C 235 ILE cc_start: 0.8559 (mt) cc_final: 0.8252 (mm) REVERT: C 237 ARG cc_start: 0.8415 (mtm180) cc_final: 0.7872 (mtm180) REVERT: C 269 TYR cc_start: 0.8517 (m-80) cc_final: 0.8219 (m-80) REVERT: C 280 ASN cc_start: 0.8508 (t0) cc_final: 0.8215 (t0) REVERT: C 281 GLU cc_start: 0.8011 (pp20) cc_final: 0.7670 (pp20) REVERT: C 328 ARG cc_start: 0.7250 (mtp85) cc_final: 0.6990 (mtp85) REVERT: C 335 LEU cc_start: 0.7519 (OUTLIER) cc_final: 0.7251 (tt) REVERT: C 347 PHE cc_start: 0.8842 (t80) cc_final: 0.7902 (t80) REVERT: C 378 LYS cc_start: 0.7703 (mmmm) cc_final: 0.7315 (mmmm) REVERT: C 386 LYS cc_start: 0.8114 (mttp) cc_final: 0.7441 (ttmt) REVERT: C 388 ASN cc_start: 0.8146 (p0) cc_final: 0.7941 (p0) REVERT: C 462 LYS cc_start: 0.8015 (tptt) cc_final: 0.7626 (ttmm) REVERT: C 501 TYR cc_start: 0.6394 (OUTLIER) cc_final: 0.6077 (m-10) REVERT: C 511 VAL cc_start: 0.7625 (t) cc_final: 0.7350 (p) REVERT: C 528 LYS cc_start: 0.8982 (mmmm) cc_final: 0.8581 (mmmt) REVERT: C 574 ASP cc_start: 0.7917 (t70) cc_final: 0.7517 (t0) REVERT: C 602 THR cc_start: 0.8668 (OUTLIER) cc_final: 0.8226 (p) REVERT: C 671 CYS cc_start: 0.6840 (m) cc_final: 0.6460 (m) REVERT: C 675 GLN cc_start: 0.7561 (tm-30) cc_final: 0.7039 (tm-30) REVERT: C 725 GLU cc_start: 0.8308 (tt0) cc_final: 0.7999 (tm-30) REVERT: C 726 ILE cc_start: 0.9339 (OUTLIER) cc_final: 0.8984 (mm) REVERT: C 732 THR cc_start: 0.8992 (OUTLIER) cc_final: 0.8784 (p) REVERT: C 773 GLU cc_start: 0.8027 (tt0) cc_final: 0.6954 (tp30) REVERT: C 774 GLN cc_start: 0.8117 (mm-40) cc_final: 0.7593 (mp10) REVERT: C 776 LYS cc_start: 0.8744 (tmmt) cc_final: 0.8454 (ttmm) REVERT: C 777 ASN cc_start: 0.8338 (m-40) cc_final: 0.7467 (m110) REVERT: C 808 ASP cc_start: 0.8135 (t70) cc_final: 0.7871 (t0) REVERT: C 851 CYS cc_start: 0.8206 (t) cc_final: 0.7623 (t) REVERT: C 918 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8173 (mt-10) REVERT: C 933 LYS cc_start: 0.8648 (mtpp) cc_final: 0.8439 (mtmm) REVERT: C 935 GLN cc_start: 0.8576 (mm-40) cc_final: 0.8058 (mm-40) REVERT: C 953 ASN cc_start: 0.8547 (m-40) cc_final: 0.8142 (m-40) REVERT: C 964 LYS cc_start: 0.8771 (tmtm) cc_final: 0.8347 (ttmm) REVERT: C 1002 GLN cc_start: 0.8377 (tp40) cc_final: 0.7850 (tp-100) REVERT: C 1010 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8151 (mp10) REVERT: C 1019 ARG cc_start: 0.7969 (ttp80) cc_final: 0.7567 (ttp80) REVERT: C 1072 GLU cc_start: 0.8461 (pm20) cc_final: 0.8146 (pm20) REVERT: C 1107 ARG cc_start: 0.7863 (mtt180) cc_final: 0.7385 (mtt-85) REVERT: C 1118 ASP cc_start: 0.8225 (t70) cc_final: 0.7785 (t0) REVERT: C 1144 GLU cc_start: 0.8013 (pp20) cc_final: 0.7785 (pp20) outliers start: 128 outliers final: 97 residues processed: 603 average time/residue: 0.1604 time to fit residues: 150.9773 Evaluate side-chains 610 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 497 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 186 ASN 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 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 726 ILE Chi-restraints excluded: chain A residue 752 LEU 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 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL 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 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 304 LYS 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 730 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 976 VAL 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 1104 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 30 ASN 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 130 VAL Chi-restraints excluded: chain C residue 221 SER 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 515 PHE Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 602 THR 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 751 ASN Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1017 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 253 optimal weight: 0.5980 chunk 159 optimal weight: 3.9990 chunk 232 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 211 optimal weight: 0.0370 chunk 122 optimal weight: 4.9990 chunk 274 optimal weight: 3.9990 chunk 282 optimal weight: 2.9990 chunk 161 optimal weight: 6.9990 chunk 236 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 overall best weight: 0.9262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 205 HIS A1083 HIS ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 954 HIS B 955 ASN B 978 ASN C 317 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 563 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.161179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.119382 restraints weight = 45442.444| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 3.28 r_work: 0.3234 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26904 Z= 0.154 Angle : 0.664 14.512 36699 Z= 0.330 Chirality : 0.047 0.375 4216 Planarity : 0.004 0.047 4697 Dihedral : 6.117 59.844 3675 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 4.34 % Allowed : 20.97 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.14), residues: 3276 helix: 1.20 (0.21), residues: 658 sheet: -1.51 (0.20), residues: 606 loop : -2.44 (0.13), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1019 TYR 0.018 0.001 TYR C1067 PHE 0.040 0.001 PHE A 168 TRP 0.043 0.001 TRP A 64 HIS 0.010 0.001 HIS C1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (26835) covalent geometry : angle 0.64950 / 0.33 (36533) SS BOND : bond 0.00402 / 0.32 ( 41) SS BOND : angle 2.18779 / 1.40 ( 82) hydrogen bonds : bond 0.03404 / 2.28 ( 750) hydrogen bonds : angle 4.80554 / 3.36 ( 2004) link_NAG-ASN : bond 0.00360 / 0.27 ( 28) link_NAG-ASN : angle 2.09754 / 1.37 ( 84) *********************** 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 626 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 502 time to evaluate : 0.905 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 30 ASN cc_start: 0.8734 (t0) cc_final: 0.8377 (p0) REVERT: A 43 PHE cc_start: 0.8482 (t80) cc_final: 0.8266 (t80) REVERT: A 46 SER cc_start: 0.9152 (m) cc_final: 0.8938 (p) REVERT: A 102 ARG cc_start: 0.8831 (ptp-170) cc_final: 0.8625 (ptp-170) REVERT: A 109 THR cc_start: 0.8664 (p) cc_final: 0.8372 (t) REVERT: A 186 ASN cc_start: 0.7835 (OUTLIER) cc_final: 0.7334 (p0) REVERT: A 224 GLU cc_start: 0.8191 (mp0) cc_final: 0.7916 (mp0) REVERT: A 239 GLN cc_start: 0.8094 (tp40) cc_final: 0.7696 (tp40) REVERT: A 269 TYR cc_start: 0.8691 (m-80) cc_final: 0.7807 (m-80) REVERT: A 282 ASN cc_start: 0.8842 (OUTLIER) cc_final: 0.8296 (m-40) REVERT: A 297 SER cc_start: 0.8597 (m) cc_final: 0.8195 (p) REVERT: A 298 GLU cc_start: 0.8168 (tt0) cc_final: 0.7924 (tp30) REVERT: A 356 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7313 (tmmm) REVERT: A 386 LYS cc_start: 0.7747 (OUTLIER) cc_final: 0.7285 (mttm) REVERT: A 390 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7052 (tt) REVERT: A 392 PHE cc_start: 0.7573 (m-80) cc_final: 0.7201 (m-80) REVERT: A 537 LYS cc_start: 0.8888 (ttmt) cc_final: 0.8411 (mtpp) REVERT: A 542 ASN cc_start: 0.8679 (t0) cc_final: 0.8397 (t0) REVERT: A 544 ASN cc_start: 0.8688 (m-40) cc_final: 0.8332 (t0) REVERT: A 562 PHE cc_start: 0.7966 (p90) cc_final: 0.7582 (p90) REVERT: A 569 ILE cc_start: 0.8587 (pt) cc_final: 0.8285 (mp) REVERT: A 580 GLN cc_start: 0.8310 (pt0) cc_final: 0.7878 (pt0) REVERT: A 664 ILE cc_start: 0.8888 (mt) cc_final: 0.8598 (mm) REVERT: A 702 GLU cc_start: 0.7984 (mp0) cc_final: 0.7740 (mp0) REVERT: A 708 SER cc_start: 0.8527 (t) cc_final: 0.8227 (m) REVERT: A 725 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7377 (tm-30) REVERT: A 726 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8340 (mm) REVERT: A 731 MET cc_start: 0.8660 (ttt) cc_final: 0.8456 (ttm) REVERT: A 739 THR cc_start: 0.8467 (m) cc_final: 0.8226 (m) REVERT: A 773 GLU cc_start: 0.7765 (tm-30) cc_final: 0.7128 (tm-30) REVERT: A 775 ASP cc_start: 0.8341 (t0) cc_final: 0.8080 (m-30) REVERT: A 780 GLU cc_start: 0.8171 (pt0) cc_final: 0.7711 (tm-30) REVERT: A 788 ILE cc_start: 0.8915 (mm) cc_final: 0.8646 (mm) REVERT: A 790 LYS cc_start: 0.8302 (mppt) cc_final: 0.7984 (mppt) REVERT: A 796 TYR cc_start: 0.8650 (t80) cc_final: 0.8354 (t80) REVERT: A 803 SER cc_start: 0.8676 (m) cc_final: 0.8380 (p) REVERT: A 851 CYS cc_start: 0.8491 (t) cc_final: 0.8078 (t) REVERT: A 859 THR cc_start: 0.8310 (OUTLIER) cc_final: 0.8017 (p) REVERT: A 868 GLU cc_start: 0.8349 (tp30) cc_final: 0.8056 (tm-30) REVERT: A 869 MET cc_start: 0.8759 (mtt) cc_final: 0.8465 (mtm) REVERT: A 933 LYS cc_start: 0.8327 (mtmt) cc_final: 0.8035 (mttp) REVERT: A 964 LYS cc_start: 0.8783 (ttpp) cc_final: 0.8558 (ttpp) REVERT: A 990 GLU cc_start: 0.8343 (tm-30) cc_final: 0.8002 (tm-30) REVERT: A 994 ASP cc_start: 0.7669 (t70) cc_final: 0.7382 (t70) REVERT: A 1017 GLU cc_start: 0.8360 (tm-30) cc_final: 0.7758 (tp30) REVERT: A 1107 ARG cc_start: 0.7888 (mtt90) cc_final: 0.7610 (mtt90) REVERT: B 52 GLN cc_start: 0.8294 (tm-30) cc_final: 0.7901 (tm-30) REVERT: B 95 ILE cc_start: 0.8672 (mt) cc_final: 0.8151 (tt) REVERT: B 104 TRP cc_start: 0.7614 (m-10) cc_final: 0.7028 (m-10) REVERT: B 121 ASN cc_start: 0.7907 (p0) cc_final: 0.7003 (t0) REVERT: B 187 LEU cc_start: 0.8229 (tp) cc_final: 0.7688 (mt) REVERT: B 190 PHE cc_start: 0.8292 (m-80) cc_final: 0.8005 (m-10) REVERT: B 297 SER cc_start: 0.8539 (m) cc_final: 0.8279 (p) REVERT: B 327 VAL cc_start: 0.8861 (t) cc_final: 0.8564 (m) REVERT: B 347 PHE cc_start: 0.3936 (OUTLIER) cc_final: 0.3288 (t80) REVERT: B 380 TYR cc_start: 0.7708 (m-80) cc_final: 0.7204 (m-80) REVERT: B 406 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8007 (mt-10) REVERT: B 551 VAL cc_start: 0.9015 (t) cc_final: 0.8745 (m) REVERT: B 558 LYS cc_start: 0.8919 (mmmt) cc_final: 0.8508 (mmmt) REVERT: B 580 GLN cc_start: 0.8768 (mm-40) cc_final: 0.8338 (mm-40) REVERT: B 674 TYR cc_start: 0.8495 (t80) cc_final: 0.8209 (t80) REVERT: B 707 TYR cc_start: 0.8664 (t80) cc_final: 0.8339 (t80) REVERT: B 725 GLU cc_start: 0.8031 (pt0) cc_final: 0.7661 (pt0) REVERT: B 773 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7082 (tm-30) REVERT: B 776 LYS cc_start: 0.8965 (tptm) cc_final: 0.8744 (tptm) REVERT: B 796 TYR cc_start: 0.8818 (t80) cc_final: 0.8550 (t80) REVERT: B 816 SER cc_start: 0.8908 (m) cc_final: 0.8296 (p) REVERT: B 820 ASP cc_start: 0.7900 (m-30) cc_final: 0.7578 (m-30) REVERT: B 851 CYS cc_start: 0.8579 (t) cc_final: 0.8108 (t) REVERT: B 914 ASN cc_start: 0.8526 (p0) cc_final: 0.8186 (p0) REVERT: B 918 GLU cc_start: 0.7958 (mp0) cc_final: 0.7613 (mp0) REVERT: B 949 GLN cc_start: 0.8790 (mm-40) cc_final: 0.8365 (mm-40) REVERT: B 950 ASP cc_start: 0.8091 (t70) cc_final: 0.7759 (t70) REVERT: B 979 ASP cc_start: 0.8104 (m-30) cc_final: 0.7752 (m-30) REVERT: B 990 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7882 (tp30) REVERT: B 1010 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.7954 (mp10) REVERT: B 1017 GLU cc_start: 0.8426 (tm-30) cc_final: 0.7982 (tm-30) REVERT: B 1019 ARG cc_start: 0.7939 (ttp80) cc_final: 0.7590 (ttp80) REVERT: B 1031 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7880 (mt-10) REVERT: B 1041 ASP cc_start: 0.8533 (m-30) cc_final: 0.8010 (t0) REVERT: B 1118 ASP cc_start: 0.7959 (t70) cc_final: 0.7466 (t0) REVERT: C 67 VAL cc_start: 0.8474 (p) cc_final: 0.8244 (m) REVERT: C 120 VAL cc_start: 0.8428 (m) cc_final: 0.8125 (p) REVERT: C 130 VAL cc_start: 0.8440 (OUTLIER) cc_final: 0.8101 (p) REVERT: C 188 ARG cc_start: 0.8349 (ptp-170) cc_final: 0.7878 (ptp-110) REVERT: C 199 PHE cc_start: 0.8058 (t80) cc_final: 0.7583 (t80) REVERT: C 235 ILE cc_start: 0.8595 (mt) cc_final: 0.8309 (mm) REVERT: C 237 ARG cc_start: 0.8415 (mtm180) cc_final: 0.7896 (mtm180) REVERT: C 269 TYR cc_start: 0.8520 (m-80) cc_final: 0.8181 (m-80) REVERT: C 280 ASN cc_start: 0.8458 (t0) cc_final: 0.8162 (t0) REVERT: C 281 GLU cc_start: 0.8015 (pp20) cc_final: 0.7723 (pp20) REVERT: C 328 ARG cc_start: 0.7313 (mtp85) cc_final: 0.6854 (mtp85) REVERT: C 335 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.7250 (tt) REVERT: C 347 PHE cc_start: 0.8825 (t80) cc_final: 0.7822 (t80) REVERT: C 357 ARG cc_start: 0.7749 (ttp-110) cc_final: 0.6948 (ttm110) REVERT: C 378 LYS cc_start: 0.7703 (mmmm) cc_final: 0.7324 (mmmm) REVERT: C 386 LYS cc_start: 0.8120 (mttp) cc_final: 0.7461 (ttmt) REVERT: C 408 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7543 (pmm-80) REVERT: C 462 LYS cc_start: 0.7962 (tptt) cc_final: 0.7597 (ttmm) REVERT: C 501 TYR cc_start: 0.6467 (OUTLIER) cc_final: 0.6111 (m-10) REVERT: C 511 VAL cc_start: 0.7644 (t) cc_final: 0.7394 (p) REVERT: C 528 LYS cc_start: 0.8973 (mmmm) cc_final: 0.8637 (mmmt) REVERT: C 533 LEU cc_start: 0.8118 (pt) cc_final: 0.7182 (pt) REVERT: C 574 ASP cc_start: 0.7914 (t70) cc_final: 0.7507 (t0) REVERT: C 602 THR cc_start: 0.8673 (OUTLIER) cc_final: 0.8240 (p) REVERT: C 671 CYS cc_start: 0.6863 (m) cc_final: 0.6500 (m) REVERT: C 675 GLN cc_start: 0.7576 (tm-30) cc_final: 0.7039 (tm-30) REVERT: C 725 GLU cc_start: 0.8327 (tt0) cc_final: 0.8017 (tm-30) REVERT: C 726 ILE cc_start: 0.9324 (OUTLIER) cc_final: 0.8909 (mm) REVERT: C 773 GLU cc_start: 0.8059 (tt0) cc_final: 0.7003 (tp30) REVERT: C 774 GLN cc_start: 0.8132 (mm-40) cc_final: 0.7617 (mp10) REVERT: C 776 LYS cc_start: 0.8737 (tmmt) cc_final: 0.8465 (ttmm) REVERT: C 777 ASN cc_start: 0.8349 (m-40) cc_final: 0.7476 (m110) REVERT: C 808 ASP cc_start: 0.8139 (t70) cc_final: 0.7875 (t0) REVERT: C 851 CYS cc_start: 0.8187 (t) cc_final: 0.7600 (t) REVERT: C 918 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8216 (mt-10) REVERT: C 933 LYS cc_start: 0.8665 (mtpp) cc_final: 0.8455 (mtmm) REVERT: C 935 GLN cc_start: 0.8547 (mm-40) cc_final: 0.8008 (mm-40) REVERT: C 953 ASN cc_start: 0.8544 (m-40) cc_final: 0.8134 (m-40) REVERT: C 964 LYS cc_start: 0.8783 (tmtm) cc_final: 0.8360 (ttmm) REVERT: C 1002 GLN cc_start: 0.8384 (tp40) cc_final: 0.7811 (tp-100) REVERT: C 1010 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8158 (mp10) REVERT: C 1019 ARG cc_start: 0.7946 (ttp80) cc_final: 0.7537 (ttp80) REVERT: C 1027 THR cc_start: 0.8722 (m) cc_final: 0.8338 (t) REVERT: C 1072 GLU cc_start: 0.8464 (pm20) cc_final: 0.8147 (pm20) REVERT: C 1118 ASP cc_start: 0.8243 (t70) cc_final: 0.7824 (t0) outliers start: 124 outliers final: 102 residues processed: 592 average time/residue: 0.1732 time to fit residues: 160.8837 Evaluate side-chains 614 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 495 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 186 ASN 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 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 726 ILE Chi-restraints excluded: chain A residue 752 LEU 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 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL 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 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 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 730 SER Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 976 VAL 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 1104 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 30 ASN 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 130 VAL Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 221 SER 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 390 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 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 515 PHE Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 602 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 756 TYR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1017 GLU 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 247 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 42 optimal weight: 30.0000 chunk 69 optimal weight: 0.8980 chunk 285 optimal weight: 0.8980 chunk 243 optimal weight: 9.9990 chunk 150 optimal weight: 0.6980 chunk 265 optimal weight: 3.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 205 HIS A1083 HIS ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 954 HIS B 955 ASN B 978 ASN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C1101 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.155264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.115634 restraints weight = 46170.315| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.91 r_work: 0.3287 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.4508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 26904 Z= 0.192 Angle : 0.689 13.122 36699 Z= 0.344 Chirality : 0.048 0.416 4216 Planarity : 0.004 0.047 4697 Dihedral : 6.199 59.425 3675 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Rotamer: Outliers : 4.45 % Allowed : 21.07 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.14), residues: 3276 helix: 1.15 (0.21), residues: 657 sheet: -1.46 (0.20), residues: 600 loop : -2.41 (0.13), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 188 TYR 0.020 0.001 TYR C1067 PHE 0.034 0.002 PHE B 199 TRP 0.046 0.002 TRP A 64 HIS 0.009 0.001 HIS A1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.19 (26835) covalent geometry : angle 0.67457 / 0.34 (36533) SS BOND : bond 0.00349 / 0.25 ( 41) SS BOND : angle 2.23507 / 1.44 ( 82) hydrogen bonds : bond 0.03594 / 2.41 ( 750) hydrogen bonds : angle 4.87326 / 3.41 ( 2004) link_NAG-ASN : bond 0.00366 / 0.27 ( 28) link_NAG-ASN : angle 2.14315 / 1.40 ( 84) ********************** 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 633 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 506 time to evaluate : 0.812 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 30 ASN cc_start: 0.8664 (t0) cc_final: 0.8344 (p0) REVERT: A 43 PHE cc_start: 0.8449 (t80) cc_final: 0.8220 (t80) REVERT: A 109 THR cc_start: 0.8745 (p) cc_final: 0.8435 (t) REVERT: A 186 ASN cc_start: 0.7925 (p0) cc_final: 0.7380 (p0) REVERT: A 224 GLU cc_start: 0.8130 (mp0) cc_final: 0.7870 (mp0) REVERT: A 239 GLN cc_start: 0.8013 (tp40) cc_final: 0.7611 (tp40) REVERT: A 269 TYR cc_start: 0.8648 (m-80) cc_final: 0.7774 (m-80) REVERT: A 282 ASN cc_start: 0.8888 (OUTLIER) cc_final: 0.8312 (m-40) REVERT: A 297 SER cc_start: 0.8539 (m) cc_final: 0.8157 (p) REVERT: A 298 GLU cc_start: 0.8134 (tt0) cc_final: 0.7888 (tp30) REVERT: A 356 LYS cc_start: 0.7827 (OUTLIER) cc_final: 0.7363 (tmmm) REVERT: A 386 LYS cc_start: 0.7714 (OUTLIER) cc_final: 0.7326 (mttm) REVERT: A 390 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7119 (tt) REVERT: A 392 PHE cc_start: 0.7719 (m-80) cc_final: 0.7303 (m-80) REVERT: A 537 LYS cc_start: 0.8866 (ttmt) cc_final: 0.8384 (mtpp) REVERT: A 542 ASN cc_start: 0.8697 (t0) cc_final: 0.8412 (t0) REVERT: A 544 ASN cc_start: 0.8615 (m-40) cc_final: 0.8278 (t0) REVERT: A 562 PHE cc_start: 0.7932 (p90) cc_final: 0.7703 (p90) REVERT: A 569 ILE cc_start: 0.8564 (pt) cc_final: 0.8270 (mp) REVERT: A 580 GLN cc_start: 0.8247 (pt0) cc_final: 0.7890 (pt0) REVERT: A 664 ILE cc_start: 0.8888 (mt) cc_final: 0.8673 (mm) REVERT: A 702 GLU cc_start: 0.7877 (mp0) cc_final: 0.7664 (mp0) REVERT: A 708 SER cc_start: 0.8465 (t) cc_final: 0.8152 (m) REVERT: A 725 GLU cc_start: 0.7830 (tm-30) cc_final: 0.7347 (tm-30) REVERT: A 726 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8403 (mm) REVERT: A 739 THR cc_start: 0.8465 (m) cc_final: 0.8225 (m) REVERT: A 740 MET cc_start: 0.8307 (ttp) cc_final: 0.8089 (ttp) REVERT: A 773 GLU cc_start: 0.7736 (tm-30) cc_final: 0.7149 (tm-30) REVERT: A 780 GLU cc_start: 0.8072 (pt0) cc_final: 0.7715 (tm-30) REVERT: A 788 ILE cc_start: 0.8935 (mm) cc_final: 0.8687 (mm) REVERT: A 790 LYS cc_start: 0.8237 (mppt) cc_final: 0.7947 (mppt) REVERT: A 803 SER cc_start: 0.8741 (m) cc_final: 0.8452 (p) REVERT: A 851 CYS cc_start: 0.8658 (t) cc_final: 0.8295 (t) REVERT: A 859 THR cc_start: 0.8388 (OUTLIER) cc_final: 0.8091 (p) REVERT: A 868 GLU cc_start: 0.8297 (tp30) cc_final: 0.8034 (tm-30) REVERT: A 869 MET cc_start: 0.8719 (mtt) cc_final: 0.8426 (mtm) REVERT: A 933 LYS cc_start: 0.8406 (mtmt) cc_final: 0.8107 (mttp) REVERT: A 964 LYS cc_start: 0.8730 (ttpp) cc_final: 0.8484 (ttpp) REVERT: A 990 GLU cc_start: 0.8350 (tm-30) cc_final: 0.7980 (tm-30) REVERT: A 994 ASP cc_start: 0.7694 (t70) cc_final: 0.7411 (t70) REVERT: A 1017 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7770 (tp30) REVERT: A 1107 ARG cc_start: 0.7805 (mtt90) cc_final: 0.7520 (mtt90) REVERT: B 52 GLN cc_start: 0.8363 (tm-30) cc_final: 0.7980 (tm-30) REVERT: B 95 ILE cc_start: 0.8686 (mt) cc_final: 0.8163 (tt) REVERT: B 104 TRP cc_start: 0.7743 (m-10) cc_final: 0.7210 (m-10) REVERT: B 121 ASN cc_start: 0.7791 (p0) cc_final: 0.6982 (t0) REVERT: B 187 LEU cc_start: 0.8254 (tp) cc_final: 0.7760 (mt) REVERT: B 190 PHE cc_start: 0.8263 (m-80) cc_final: 0.8012 (m-10) REVERT: B 224 GLU cc_start: 0.7981 (pm20) cc_final: 0.7551 (mp0) REVERT: B 297 SER cc_start: 0.8482 (m) cc_final: 0.8245 (p) REVERT: B 327 VAL cc_start: 0.8886 (t) cc_final: 0.8592 (m) REVERT: B 347 PHE cc_start: 0.4157 (OUTLIER) cc_final: 0.3433 (t80) REVERT: B 380 TYR cc_start: 0.7559 (m-80) cc_final: 0.6981 (m-80) REVERT: B 406 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8064 (mt-10) REVERT: B 551 VAL cc_start: 0.9048 (t) cc_final: 0.8788 (m) REVERT: B 558 LYS cc_start: 0.8791 (mmmt) cc_final: 0.8433 (mmmt) REVERT: B 580 GLN cc_start: 0.8737 (mm-40) cc_final: 0.8323 (mm-40) REVERT: B 674 TYR cc_start: 0.8530 (t80) cc_final: 0.8242 (t80) REVERT: B 725 GLU cc_start: 0.7987 (pt0) cc_final: 0.7651 (pt0) REVERT: B 773 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7095 (tm-30) REVERT: B 776 LYS cc_start: 0.8924 (tptm) cc_final: 0.8663 (tptm) REVERT: B 796 TYR cc_start: 0.8773 (t80) cc_final: 0.8539 (t80) REVERT: B 816 SER cc_start: 0.8981 (m) cc_final: 0.8585 (p) REVERT: B 851 CYS cc_start: 0.8649 (t) cc_final: 0.8234 (t) REVERT: B 914 ASN cc_start: 0.8532 (p0) cc_final: 0.8243 (p0) REVERT: B 918 GLU cc_start: 0.7792 (mp0) cc_final: 0.7489 (mp0) REVERT: B 949 GLN cc_start: 0.8851 (mm-40) cc_final: 0.8486 (mm-40) REVERT: B 979 ASP cc_start: 0.8060 (m-30) cc_final: 0.7731 (m-30) REVERT: B 990 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7865 (tp30) REVERT: B 1010 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.7880 (mp10) REVERT: B 1017 GLU cc_start: 0.8278 (tm-30) cc_final: 0.7830 (tm-30) REVERT: B 1019 ARG cc_start: 0.7901 (ttp80) cc_final: 0.7562 (ttp80) REVERT: B 1031 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7880 (mt-10) REVERT: B 1041 ASP cc_start: 0.8407 (m-30) cc_final: 0.7972 (t0) REVERT: B 1118 ASP cc_start: 0.7912 (t70) cc_final: 0.7431 (t0) REVERT: C 120 VAL cc_start: 0.8501 (m) cc_final: 0.8209 (p) REVERT: C 188 ARG cc_start: 0.8308 (ptp-170) cc_final: 0.7829 (ptp-110) REVERT: C 199 PHE cc_start: 0.8147 (t80) cc_final: 0.7725 (t80) REVERT: C 235 ILE cc_start: 0.8677 (mt) cc_final: 0.8415 (mm) REVERT: C 237 ARG cc_start: 0.8264 (mtm180) cc_final: 0.7767 (mtm180) REVERT: C 269 TYR cc_start: 0.8503 (m-80) cc_final: 0.8163 (m-80) REVERT: C 280 ASN cc_start: 0.8465 (t0) cc_final: 0.8177 (t0) REVERT: C 281 GLU cc_start: 0.8011 (pp20) cc_final: 0.7755 (pp20) REVERT: C 308 VAL cc_start: 0.8874 (OUTLIER) cc_final: 0.8574 (m) REVERT: C 335 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.7207 (tt) REVERT: C 347 PHE cc_start: 0.8835 (t80) cc_final: 0.7894 (t80) REVERT: C 357 ARG cc_start: 0.7869 (ttp-110) cc_final: 0.7129 (ttm110) REVERT: C 378 LYS cc_start: 0.7710 (mmmm) cc_final: 0.7318 (mmmm) REVERT: C 386 LYS cc_start: 0.8123 (mttp) cc_final: 0.7524 (ttmt) REVERT: C 408 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7547 (pmm-80) REVERT: C 462 LYS cc_start: 0.8004 (tptt) cc_final: 0.7640 (ttmm) REVERT: C 501 TYR cc_start: 0.6672 (OUTLIER) cc_final: 0.6211 (m-10) REVERT: C 511 VAL cc_start: 0.7745 (t) cc_final: 0.7492 (p) REVERT: C 528 LYS cc_start: 0.8950 (mmmm) cc_final: 0.8685 (mmmt) REVERT: C 574 ASP cc_start: 0.7903 (t70) cc_final: 0.7510 (t0) REVERT: C 602 THR cc_start: 0.8659 (OUTLIER) cc_final: 0.8253 (p) REVERT: C 671 CYS cc_start: 0.6735 (m) cc_final: 0.6387 (m) REVERT: C 675 GLN cc_start: 0.7425 (tm-30) cc_final: 0.6971 (tm-30) REVERT: C 726 ILE cc_start: 0.9337 (OUTLIER) cc_final: 0.8985 (mm) REVERT: C 739 THR cc_start: 0.8556 (m) cc_final: 0.8153 (t) REVERT: C 773 GLU cc_start: 0.7953 (tt0) cc_final: 0.7157 (tp30) REVERT: C 774 GLN cc_start: 0.8051 (mm-40) cc_final: 0.7617 (mp10) REVERT: C 776 LYS cc_start: 0.8739 (tmmt) cc_final: 0.8493 (ttmm) REVERT: C 777 ASN cc_start: 0.8323 (m-40) cc_final: 0.7495 (m110) REVERT: C 808 ASP cc_start: 0.8161 (t70) cc_final: 0.7927 (t0) REVERT: C 851 CYS cc_start: 0.8237 (t) cc_final: 0.7707 (t) REVERT: C 933 LYS cc_start: 0.8676 (mtpp) cc_final: 0.8473 (mtmm) REVERT: C 935 GLN cc_start: 0.8462 (mm-40) cc_final: 0.8047 (mm-40) REVERT: C 964 LYS cc_start: 0.8804 (tmtm) cc_final: 0.8416 (ttmm) REVERT: C 1002 GLN cc_start: 0.8318 (tp40) cc_final: 0.7801 (tp-100) REVERT: C 1010 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.8051 (mp10) REVERT: C 1072 GLU cc_start: 0.8410 (pm20) cc_final: 0.8138 (pm20) REVERT: C 1107 ARG cc_start: 0.7835 (mtt180) cc_final: 0.7633 (mtt90) REVERT: C 1118 ASP cc_start: 0.8164 (t70) cc_final: 0.7750 (t0) REVERT: C 1144 GLU cc_start: 0.8063 (pp20) cc_final: 0.7795 (pp20) outliers start: 127 outliers final: 102 residues processed: 594 average time/residue: 0.1611 time to fit residues: 149.9605 Evaluate side-chains 612 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 494 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 227 VAL 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 556 ASN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 752 LEU 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 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL 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 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 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 730 SER Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 976 VAL 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 1104 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 30 ASN 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 130 VAL Chi-restraints excluded: chain C residue 203 SER 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 392 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 515 PHE Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 602 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 756 TYR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1017 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 90 optimal weight: 4.9990 chunk 152 optimal weight: 0.3980 chunk 310 optimal weight: 9.9990 chunk 135 optimal weight: 7.9990 chunk 81 optimal weight: 0.9980 chunk 174 optimal weight: 0.7980 chunk 111 optimal weight: 0.8980 chunk 171 optimal weight: 0.9980 chunk 283 optimal weight: 0.9980 chunk 242 optimal weight: 5.9990 chunk 147 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 205 HIS A1083 HIS ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 913 GLN B 954 HIS B 955 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 ASN C 955 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.156159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.116660 restraints weight = 46251.566| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.92 r_work: 0.3300 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.4567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 26904 Z= 0.147 Angle : 0.675 13.161 36699 Z= 0.337 Chirality : 0.047 0.345 4216 Planarity : 0.004 0.047 4697 Dihedral : 6.173 59.879 3675 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 4.38 % Allowed : 21.04 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.14), residues: 3276 helix: 1.22 (0.21), residues: 661 sheet: -1.58 (0.20), residues: 624 loop : -2.38 (0.13), residues: 1991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 328 TYR 0.021 0.001 TYR B 707 PHE 0.042 0.001 PHE C 133 TRP 0.048 0.002 TRP A 64 HIS 0.014 0.001 HIS A 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (26835) covalent geometry : angle 0.66207 / 0.33 (36533) SS BOND : bond 0.00306 / 0.22 ( 41) SS BOND : angle 2.10038 / 1.34 ( 82) hydrogen bonds : bond 0.03428 / 2.32 ( 750) hydrogen bonds : angle 4.85506 / 3.39 ( 2004) link_NAG-ASN : bond 0.00352 / 0.26 ( 28) link_NAG-ASN : angle 2.09006 / 1.37 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6859.53 seconds wall clock time: 118 minutes 15.02 seconds (7095.02 seconds total)