Starting phenix.real_space_refine on Fri Mar 6 09:04:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wor_32656/03_2026/7wor_32656.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wor_32656/03_2026/7wor_32656.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wor_32656/03_2026/7wor_32656.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wor_32656/03_2026/7wor_32656.map" model { file = "/net/cci-nas-00/data/ceres_data/7wor_32656/03_2026/7wor_32656.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wor_32656/03_2026/7wor_32656.cif" } resolution = 3.7 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= 0.001 sd= 0.023 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 134 5.16 5 C 18904 2.51 5 N 4911 2.21 5 O 5721 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29670 Number of models: 1 Model: "" Number of chains: 9 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: 8043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8043 Classifications: {'peptide': 1033} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 58, 'TRANS': 974} Chain breaks: 7 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 6, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "C" Number of atoms: 7989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 7989 Classifications: {'peptide': 1026} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 56, 'TRANS': 969} Chain breaks: 7 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 6, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "D" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1754 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 225} Chain breaks: 1 Chain: "E" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1765 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "F" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1754 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 225} Chain breaks: 1 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 5.80, per 1000 atoms: 0.20 Number of scatterers: 29670 At special positions: 0 Unit cell: (146.832, 161.728, 203.224, 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 134 16.00 O 5721 8.00 N 4911 7.00 C 18904 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 90 " distance=2.03 Simple disulfide: pdb=" SG CYS D 148 " - pdb=" SG CYS D 221 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS E 146 " - pdb=" SG CYS E 220 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 90 " distance=2.03 Simple disulfide: pdb=" SG CYS F 148 " - pdb=" SG CYS F 221 " distance=2.03 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 616 " " NAG A1303 " - " ASN A 709 " " NAG A1304 " - " ASN A 717 " " NAG A1305 " - " ASN A 801 " " NAG A1306 " - " ASN A1098 " " NAG A1307 " - " ASN A1134 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B 717 " " NAG B1306 " - " ASN B 801 " " NAG B1307 " - " ASN B1098 " " NAG B1308 " - " ASN B1134 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 709 " " NAG C1305 " - " ASN C 717 " " NAG C1306 " - " ASN C 801 " " NAG C1307 " - " ASN C1098 " " NAG C1308 " - " ASN C1134 " Time building additional restraints: 2.31 Conformation dependent library (CDL) restraints added in 1.3 seconds 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7038 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 57 sheets defined 18.3% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 367 through 371 removed outlier: 4.054A pdb=" N ASN A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 444 through 448 removed outlier: 3.815A pdb=" N GLY A 447 " --> pdb=" O LYS A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 757 removed outlier: 3.545A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 783 removed outlier: 3.814A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 848 through 855 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.084A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 removed outlier: 3.544A pdb=" N GLY A 908 " --> pdb=" O TYR A 904 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY A 910 " --> pdb=" O PHE A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 929 Processing helix chain 'A' and resid 930 through 941 removed outlier: 3.537A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.604A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 983 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.093A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 3.984A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 336 through 341 removed outlier: 4.102A pdb=" N ASP B 339 " --> pdb=" O CYS B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 370 Processing helix chain 'B' and resid 383 through 388 removed outlier: 3.701A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 756 removed outlier: 3.563A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 781 removed outlier: 3.564A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 848 through 855 Processing helix chain 'B' and resid 866 through 883 Processing helix chain 'B' and resid 897 through 907 removed outlier: 3.659A pdb=" N ASN B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 939 removed outlier: 4.337A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER B 939 " --> pdb=" O GLN B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.540A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 983 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.548A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1143 through 1147 removed outlier: 3.862A pdb=" N ASP B1146 " --> pdb=" O PRO B1143 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER B1147 " --> pdb=" O GLU B1144 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1143 through 1147' Processing helix chain 'C' and resid 294 through 302 Processing helix chain 'C' and resid 336 through 341 removed outlier: 4.122A pdb=" N ASP C 339 " --> pdb=" O CYS C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 370 Processing helix chain 'C' and resid 383 through 388 removed outlier: 3.941A pdb=" N ASN C 388 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.590A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 747 through 755 removed outlier: 3.872A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 780 removed outlier: 3.657A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 823 Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.631A pdb=" N ALA C 903 " --> pdb=" O PRO C 899 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG C 905 " --> pdb=" O GLN C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 938 Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.072A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN C 965 " --> pdb=" O THR C 961 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 980 removed outlier: 3.605A pdb=" N ASP C 979 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE C 980 " --> pdb=" O LEU C 977 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 976 through 980' Processing helix chain 'C' and resid 985 through 993 removed outlier: 4.427A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 1033 removed outlier: 3.670A pdb=" N GLY C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.902A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 84 Processing helix chain 'E' and resid 152 through 156 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 29 removed outlier: 3.670A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.676A pdb=" N ARG B 567 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.359A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.707A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU A 117 " --> pdb=" O PHE A 106 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 90 through 93 removed outlier: 3.557A pdb=" N VAL A 191 " --> pdb=" O TYR A 202 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER A 203 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU A 224 " --> pdb=" O SER A 203 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 316 removed outlier: 5.492A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 376 through 377 removed outlier: 3.955A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N TRP A 436 " --> pdb=" O ARG A 509 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG A 509 " --> pdb=" O TRP A 436 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB1, first strand: chain 'A' and resid 538 through 543 Processing sheet with id=AB2, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.783A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.525A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB5, first strand: chain 'A' and resid 712 through 722 removed outlier: 6.762A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 725 through 728 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 1120 through 1121 Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.633A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.902A 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 224 through 229 removed outlier: 3.702A pdb=" N LEU B 226 " --> pdb=" O ILE B 201 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ILE B 201 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ASP B 228 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N PHE B 199 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR B 91 " --> pdb=" O GLY B 268 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 120 through 122 Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.686A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 325 through 326 removed outlier: 3.522A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 356 through 358 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.736A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 712 through 718 removed outlier: 7.066A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 721 through 728 removed outlier: 7.113A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 734 through 735 Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.808A pdb=" N LYS C 278 " --> pdb=" O ASP C 287 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AD8, first strand: chain 'C' and resid 93 through 96 removed outlier: 3.935A pdb=" N SER C 94 " --> pdb=" O ARG C 188 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU C 96 " --> pdb=" O ASN C 186 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN C 186 " --> pdb=" O GLU C 96 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 192 through 194 removed outlier: 7.495A pdb=" N ILE C 201 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU C 224 " --> pdb=" O SER C 203 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.999A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 325 through 326 removed outlier: 3.524A pdb=" N ASN C 542 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 356 through 358 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 660 removed outlier: 5.716A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 712 through 713 Processing sheet with id=AE6, first strand: chain 'C' and resid 717 through 718 Processing sheet with id=AE7, first strand: chain 'C' and resid 721 through 728 removed outlier: 3.782A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 734 through 735 Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 3.812A pdb=" N SER C1123 " --> pdb=" O ALA C1087 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF2, first strand: chain 'D' and resid 47 through 50 removed outlier: 6.126A pdb=" N LEU D 48 " --> pdb=" O GLN D 39 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLN D 39 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE D 50 " --> pdb=" O TRP D 37 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 68 through 69 Processing sheet with id=AF4, first strand: chain 'D' and resid 172 through 177 removed outlier: 6.088A pdb=" N TRP D 173 " --> pdb=" O ARG D 164 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ARG D 164 " --> pdb=" O TRP D 173 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE D 177 " --> pdb=" O MET D 160 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N MET D 160 " --> pdb=" O ILE D 177 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 21 through 23 Processing sheet with id=AF6, first strand: chain 'E' and resid 46 through 49 removed outlier: 5.006A pdb=" N LEU E 47 " --> pdb=" O GLN E 38 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N GLN E 38 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN E 97 " --> pdb=" O ASP E 93 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 46 through 49 removed outlier: 5.006A pdb=" N LEU E 47 " --> pdb=" O GLN E 38 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N GLN E 38 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR E 87 " --> pdb=" O THR E 104 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 130 through 131 removed outlier: 3.557A pdb=" N SER E 131 " --> pdb=" O SER E 145 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 182 through 184 removed outlier: 6.648A pdb=" N TRP E 160 " --> pdb=" O VAL E 172 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N VAL E 174 " --> pdb=" O MET E 158 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N MET E 158 " --> pdb=" O VAL E 174 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 47 through 50 removed outlier: 6.138A pdb=" N LEU F 48 " --> pdb=" O GLN F 39 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLN F 39 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE F 50 " --> pdb=" O TRP F 37 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 64 through 69 removed outlier: 5.373A pdb=" N SER F 65 " --> pdb=" O THR F 76 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER F 67 " --> pdb=" O SER F 74 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 172 through 176 removed outlier: 6.082A pdb=" N TRP F 173 " --> pdb=" O ARG F 164 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ARG F 164 " --> pdb=" O TRP F 173 " (cutoff:3.500A) 808 hydrogen bonds defined for protein. 2136 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.54 Time building geometry restraints manager: 3.12 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: 7896 1.33 - 1.45: 5888 1.45 - 1.57: 16409 1.57 - 1.69: 0 1.69 - 1.82: 172 Bond restraints: 30365 Sorted by residual: bond pdb=" CA ASN B1134 " pdb=" C ASN B1134 " ideal model delta sigma weight residual 1.523 1.438 0.085 1.23e-02 6.61e+03 4.74e+01 bond pdb=" CA ASN C1134 " pdb=" C ASN C1134 " ideal model delta sigma weight residual 1.523 1.459 0.065 1.19e-02 7.06e+03 2.95e+01 bond pdb=" CA TYR B 707 " pdb=" C TYR B 707 " ideal model delta sigma weight residual 1.525 1.465 0.060 1.28e-02 6.10e+03 2.17e+01 bond pdb=" CA ASN B 801 " pdb=" C ASN B 801 " ideal model delta sigma weight residual 1.522 1.475 0.047 1.08e-02 8.57e+03 1.87e+01 bond pdb=" CA ASN C 280 " pdb=" C ASN C 280 " ideal model delta sigma weight residual 1.523 1.468 0.055 1.34e-02 5.57e+03 1.67e+01 ... (remaining 30360 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 40772 2.07 - 4.14: 500 4.14 - 6.22: 51 6.22 - 8.29: 5 8.29 - 10.36: 1 Bond angle restraints: 41329 Sorted by residual: angle pdb=" N ASN A 616 " pdb=" CA ASN A 616 " pdb=" C ASN A 616 " ideal model delta sigma weight residual 112.93 107.19 5.74 1.12e+00 7.97e-01 2.63e+01 angle pdb=" N GLU A 281 " pdb=" CA GLU A 281 " pdb=" C GLU A 281 " ideal model delta sigma weight residual 111.71 106.00 5.71 1.15e+00 7.56e-01 2.47e+01 angle pdb=" N ASN B1134 " pdb=" CA ASN B1134 " pdb=" C ASN B1134 " ideal model delta sigma weight residual 109.24 101.31 7.93 1.63e+00 3.76e-01 2.37e+01 angle pdb=" N ALA C 27 " pdb=" CA ALA C 27 " pdb=" C ALA C 27 " ideal model delta sigma weight residual 110.80 100.44 10.36 2.13e+00 2.20e-01 2.37e+01 angle pdb=" N ILE B 418 " pdb=" CA ILE B 418 " pdb=" C ILE B 418 " ideal model delta sigma weight residual 113.53 108.78 4.75 9.80e-01 1.04e+00 2.35e+01 ... (remaining 41324 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.86: 17451 16.86 - 33.72: 712 33.72 - 50.58: 124 50.58 - 67.45: 35 67.45 - 84.31: 4 Dihedral angle restraints: 18326 sinusoidal: 7335 harmonic: 10991 Sorted by residual: dihedral pdb=" CA ALA C 27 " pdb=" C ALA C 27 " pdb=" N TYR C 28 " pdb=" CA TYR C 28 " ideal model delta harmonic sigma weight residual 180.00 152.02 27.98 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA TYR C 28 " pdb=" C TYR C 28 " pdb=" N THR C 29 " pdb=" CA THR C 29 " ideal model delta harmonic sigma weight residual 180.00 154.37 25.63 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA CYS B 336 " pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " ideal model delta sinusoidal sigma weight residual 79.00 20.41 58.59 1 2.00e+01 2.50e-03 1.15e+01 ... (remaining 18323 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.294: 4707 0.294 - 0.588: 2 0.588 - 0.881: 1 0.881 - 1.175: 0 1.175 - 1.469: 1 Chirality restraints: 4711 Sorted by residual: chirality pdb=" C1 NAG B1308 " pdb=" ND2 ASN B1134 " pdb=" C2 NAG B1308 " pdb=" O5 NAG B1308 " both_signs ideal model delta sigma weight residual False -2.40 -0.93 -1.47 2.00e-01 2.50e+01 5.39e+01 chirality pdb=" C1 NAG B1304 " pdb=" ND2 ASN B 709 " pdb=" C2 NAG B1304 " pdb=" O5 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.63 -0.77 2.00e-01 2.50e+01 1.50e+01 chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.43e+00 ... (remaining 4708 not shown) Planarity restraints: 5356 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1304 " 0.357 2.00e-02 2.50e+03 3.07e-01 1.18e+03 pdb=" C7 NAG C1304 " -0.086 2.00e-02 2.50e+03 pdb=" C8 NAG C1304 " 0.131 2.00e-02 2.50e+03 pdb=" N2 NAG C1304 " -0.545 2.00e-02 2.50e+03 pdb=" O7 NAG C1304 " 0.143 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1307 " 0.350 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C7 NAG C1307 " -0.082 2.00e-02 2.50e+03 pdb=" C8 NAG C1307 " 0.088 2.00e-02 2.50e+03 pdb=" N2 NAG C1307 " -0.536 2.00e-02 2.50e+03 pdb=" O7 NAG C1307 " 0.180 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1308 " -0.350 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C7 NAG C1308 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG C1308 " -0.089 2.00e-02 2.50e+03 pdb=" N2 NAG C1308 " 0.536 2.00e-02 2.50e+03 pdb=" O7 NAG C1308 " -0.178 2.00e-02 2.50e+03 ... (remaining 5353 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 3132 2.75 - 3.29: 29561 3.29 - 3.83: 48424 3.83 - 4.36: 55090 4.36 - 4.90: 95448 Nonbonded interactions: 231655 Sorted by model distance: nonbonded pdb=" OE1 GLN B 52 " pdb=" OG1 THR B 274 " model vdw 2.216 3.040 nonbonded pdb=" OG SER F 91 " pdb=" OE1 GLN F 227 " model vdw 2.219 3.040 nonbonded pdb=" OG1 THR C 719 " pdb=" O VAL C1068 " model vdw 2.236 3.040 nonbonded pdb=" OG SER D 91 " pdb=" OE1 GLN D 227 " model vdw 2.239 3.040 nonbonded pdb=" OG1 THR B 719 " pdb=" O VAL B1068 " model vdw 2.240 3.040 ... (remaining 231650 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 1307)) selection = (chain 'B' and (resid 26 through 243 or resid 262 through 1307)) selection = (chain 'C' and resid 26 through 1307) } ncs_group { reference = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 25.990 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 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 0.085 30432 Z= 0.199 Angle : 0.540 10.359 41486 Z= 0.294 Chirality : 0.049 1.469 4711 Planarity : 0.014 0.307 5333 Dihedral : 9.284 84.306 11156 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.68 % Favored : 92.22 % Rotamer: Outliers : 5.34 % Allowed : 8.31 % Favored : 86.35 % 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: -4.04 (0.11), residues: 3739 helix: -0.58 (0.19), residues: 658 sheet: -2.46 (0.18), residues: 630 loop : -3.61 (0.10), residues: 2451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 466 TYR 0.011 0.001 TYR A1067 PHE 0.011 0.001 PHE A 375 TRP 0.006 0.001 TRP E 98 HIS 0.001 0.000 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00311 (30365) covalent geometry : angle 0.52557 (41329) SS BOND : bond 0.00126 ( 44) SS BOND : angle 0.50492 ( 88) hydrogen bonds : bond 0.14024 ( 800) hydrogen bonds : angle 6.13493 ( 2136) link_NAG-ASN : bond 0.00816 ( 23) link_NAG-ASN : angle 3.06291 ( 69) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 628 time to evaluate : 0.843 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 58 PHE cc_start: 0.7238 (m-10) cc_final: 0.6991 (m-10) REVERT: A 223 LEU cc_start: 0.7206 (mp) cc_final: 0.6896 (mp) REVERT: A 300 LYS cc_start: 0.8346 (mtmt) cc_final: 0.7997 (mttm) REVERT: A 307 THR cc_start: 0.7835 (m) cc_final: 0.7490 (p) REVERT: A 364 ASP cc_start: 0.8201 (t0) cc_final: 0.7814 (t0) REVERT: A 396 TYR cc_start: 0.5889 (m-80) cc_final: 0.5033 (m-80) REVERT: A 516 GLU cc_start: 0.5249 (pt0) cc_final: 0.4204 (pt0) REVERT: A 546 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8297 (tt) REVERT: A 556 ASN cc_start: 0.8009 (p0) cc_final: 0.7404 (p0) REVERT: A 562 PHE cc_start: 0.7058 (p90) cc_final: 0.6634 (p90) REVERT: A 592 PHE cc_start: 0.6818 (p90) cc_final: 0.6200 (p90) REVERT: A 602 THR cc_start: 0.7836 (m) cc_final: 0.7160 (p) REVERT: A 615 VAL cc_start: 0.8413 (t) cc_final: 0.8108 (m) REVERT: A 732 THR cc_start: 0.8977 (OUTLIER) cc_final: 0.8530 (p) REVERT: A 737 ASP cc_start: 0.7069 (t0) cc_final: 0.6217 (t0) REVERT: A 776 LYS cc_start: 0.8282 (tmmt) cc_final: 0.7870 (tptp) REVERT: A 821 LEU cc_start: 0.8392 (tp) cc_final: 0.8037 (mt) REVERT: A 864 LEU cc_start: 0.8707 (tp) cc_final: 0.8418 (tt) REVERT: A 914 ASN cc_start: 0.7830 (p0) cc_final: 0.7602 (p0) REVERT: A 921 LYS cc_start: 0.8254 (mmmt) cc_final: 0.7767 (mmmt) REVERT: A 954 HIS cc_start: 0.6810 (m-70) cc_final: 0.6534 (m170) REVERT: A 960 ASN cc_start: 0.7426 (m-40) cc_final: 0.7129 (m-40) REVERT: A 964 LYS cc_start: 0.8511 (tmtm) cc_final: 0.8216 (tppt) REVERT: A 969 LYS cc_start: 0.7874 (mtmm) cc_final: 0.7616 (mppt) REVERT: A 980 ILE cc_start: 0.8796 (mt) cc_final: 0.8537 (pt) REVERT: A 984 LEU cc_start: 0.8961 (mt) cc_final: 0.8137 (mt) REVERT: A 988 GLU cc_start: 0.7638 (tp30) cc_final: 0.6757 (tp30) REVERT: A 1002 GLN cc_start: 0.7056 (tp-100) cc_final: 0.6609 (tp-100) REVERT: A 1057 PRO cc_start: 0.8968 (Cg_exo) cc_final: 0.8690 (Cg_endo) REVERT: A 1081 ILE cc_start: 0.8517 (pt) cc_final: 0.8066 (mm) REVERT: A 1111 GLU cc_start: 0.6842 (tt0) cc_final: 0.6595 (tt0) REVERT: B 33 THR cc_start: 0.9150 (OUTLIER) cc_final: 0.8927 (p) REVERT: B 41 LYS cc_start: 0.7527 (OUTLIER) cc_final: 0.7303 (mttt) REVERT: B 44 ARG cc_start: 0.8044 (mtt90) cc_final: 0.7667 (mtt180) REVERT: B 132 GLU cc_start: 0.3624 (pt0) cc_final: 0.3310 (pm20) REVERT: B 177 MET cc_start: 0.5805 (mtt) cc_final: 0.5309 (mtt) REVERT: B 186 ASN cc_start: 0.6148 (p0) cc_final: 0.5428 (p0) REVERT: B 188 ARG cc_start: 0.7213 (mtt-85) cc_final: 0.6549 (mtm-85) REVERT: B 189 GLU cc_start: 0.7069 (pm20) cc_final: 0.6469 (pm20) REVERT: B 193 LYS cc_start: 0.8050 (ttpt) cc_final: 0.7780 (ttmt) REVERT: B 200 LYS cc_start: 0.8562 (mttt) cc_final: 0.8269 (mptt) REVERT: B 267 VAL cc_start: 0.8310 (OUTLIER) cc_final: 0.8074 (p) REVERT: B 275 PHE cc_start: 0.7866 (m-80) cc_final: 0.7608 (m-10) REVERT: B 278 LYS cc_start: 0.8359 (ttmp) cc_final: 0.8157 (ttmm) REVERT: B 286 THR cc_start: 0.7724 (p) cc_final: 0.7488 (p) REVERT: B 307 THR cc_start: 0.7885 (m) cc_final: 0.7488 (p) REVERT: B 329 PHE cc_start: 0.5966 (m-10) cc_final: 0.5620 (m-10) REVERT: B 403 ARG cc_start: 0.5596 (mtm-85) cc_final: 0.5039 (ttm170) REVERT: B 524 VAL cc_start: -0.0245 (OUTLIER) cc_final: -0.1091 (t) REVERT: B 698 SER cc_start: 0.8138 (t) cc_final: 0.7800 (p) REVERT: B 759 PHE cc_start: 0.7276 (t80) cc_final: 0.6740 (t80) REVERT: B 768 THR cc_start: 0.8457 (m) cc_final: 0.8236 (p) REVERT: B 776 LYS cc_start: 0.8122 (ttpm) cc_final: 0.7801 (ttpp) REVERT: B 821 LEU cc_start: 0.8883 (tt) cc_final: 0.8641 (tp) REVERT: B 851 CYS cc_start: 0.7973 (t) cc_final: 0.7490 (p) REVERT: B 856 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8641 (tppp) REVERT: B 914 ASN cc_start: 0.8005 (p0) cc_final: 0.7569 (p0) REVERT: B 965 GLN cc_start: 0.6910 (mt0) cc_final: 0.6618 (mm110) REVERT: B 979 ASP cc_start: 0.8106 (m-30) cc_final: 0.7851 (m-30) REVERT: B 1019 ARG cc_start: 0.7717 (ttm110) cc_final: 0.7412 (ttm170) REVERT: B 1141 LEU cc_start: 0.7646 (tp) cc_final: 0.7109 (mm) REVERT: C 28 TYR cc_start: 0.7470 (m-80) cc_final: 0.6850 (m-10) REVERT: C 92 PHE cc_start: 0.7450 (t80) cc_final: 0.7185 (t80) REVERT: C 118 LEU cc_start: 0.8597 (mp) cc_final: 0.8181 (mm) REVERT: C 129 LYS cc_start: 0.8297 (ttmt) cc_final: 0.7613 (tptt) REVERT: C 188 ARG cc_start: 0.6198 (OUTLIER) cc_final: 0.5598 (tpp80) REVERT: C 560 LEU cc_start: 0.8477 (mt) cc_final: 0.8173 (mm) REVERT: C 602 THR cc_start: 0.8612 (m) cc_final: 0.8408 (m) REVERT: C 616 ASN cc_start: 0.5482 (t0) cc_final: 0.5081 (t0) REVERT: C 707 TYR cc_start: 0.7943 (t80) cc_final: 0.7315 (t80) REVERT: C 759 PHE cc_start: 0.6811 (m-80) cc_final: 0.6468 (m-80) REVERT: C 816 SER cc_start: 0.8284 (p) cc_final: 0.8077 (p) REVERT: C 819 GLU cc_start: 0.7300 (mt-10) cc_final: 0.7045 (mt-10) REVERT: C 850 ILE cc_start: 0.8807 (mm) cc_final: 0.8602 (tp) REVERT: C 851 CYS cc_start: 0.8041 (t) cc_final: 0.7532 (p) REVERT: C 914 ASN cc_start: 0.7751 (p0) cc_final: 0.7119 (p0) REVERT: C 922 LEU cc_start: 0.7954 (tp) cc_final: 0.7714 (tp) REVERT: C 950 ASP cc_start: 0.7005 (t70) cc_final: 0.6591 (t0) REVERT: C 953 ASN cc_start: 0.8247 (m-40) cc_final: 0.8035 (m-40) REVERT: C 978 ASN cc_start: 0.8284 (m-40) cc_final: 0.7958 (m-40) REVERT: C 985 ASP cc_start: 0.7750 (p0) cc_final: 0.7548 (p0) REVERT: C 991 VAL cc_start: 0.8827 (t) cc_final: 0.7893 (p) REVERT: C 1031 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7308 (mt-10) REVERT: C 1097 SER cc_start: 0.9166 (t) cc_final: 0.8678 (p) REVERT: C 1136 THR cc_start: 0.8852 (OUTLIER) cc_final: 0.8576 (p) REVERT: D 6 GLN cc_start: -0.0341 (OUTLIER) cc_final: -0.1229 (tp-100) REVERT: D 35 VAL cc_start: 0.2300 (OUTLIER) cc_final: 0.2005 (p) REVERT: D 111 LEU cc_start: 0.5380 (OUTLIER) cc_final: 0.4980 (tm) REVERT: D 144 LEU cc_start: 0.5959 (OUTLIER) cc_final: 0.5695 (tm) REVERT: D 193 PHE cc_start: -0.1356 (OUTLIER) cc_final: -0.1611 (p90) REVERT: E 174 VAL cc_start: 0.4147 (OUTLIER) cc_final: 0.3883 (t) REVERT: F 128 VAL cc_start: -0.3221 (OUTLIER) cc_final: -0.3630 (p) REVERT: F 160 MET cc_start: -0.0689 (ptp) cc_final: -0.1814 (mmm) outliers start: 173 outliers final: 60 residues processed: 773 average time/residue: 0.1896 time to fit residues: 231.3828 Evaluate side-chains 562 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 486 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 856 LYS Chi-restraints excluded: chain B residue 957 GLN 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 1138 TYR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 35 VAL 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 144 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 193 PHE Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 32 TYR Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 205 TYR Chi-restraints excluded: chain F residue 226 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 87 ASN A 173 GLN ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 ASN A 394 ASN A 409 GLN A 414 GLN A 422 ASN A 540 ASN A 564 GLN A 613 GLN A 690 GLN A 784 GLN A 853 GLN A 901 GLN A1002 GLN A1005 GLN A1011 GLN A1048 HIS A1101 HIS B 173 GLN B 181 GLN B 245 HIS B 321 GLN B 354 ASN B 370 ASN B 388 ASN B 448 ASN B 477 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN B 607 GLN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN B 901 GLN B 914 ASN B 926 GLN B 957 GLN B1010 GLN B1048 HIS B1054 GLN B1101 HIS B1119 ASN C 49 HIS C 99 ASN C 164 ASN C 205 HIS C 218 GLN C 271 GLN C 321 GLN C 354 ASN C 370 ASN C 388 ASN C 409 GLN C 422 ASN C 448 ASN C 477 ASN C 487 ASN C 540 ASN C 580 GLN C 613 GLN C 641 ASN C 784 GLN C 853 GLN C 895 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C 914 ASN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1048 HIS C1119 ASN C1125 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN D 39 GLN D 40 GLN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 GLN D 202 ASN E 80 GLN E 97 ASN E 137 GLN E 201 ASN E 206 GLN F 33 ASN F 39 GLN F 40 GLN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 165 GLN F 202 ASN F 207 GLN Total number of N/Q/H flips: 84 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.200994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.148344 restraints weight = 54614.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.150689 restraints weight = 25878.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.153234 restraints weight = 14387.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.155188 restraints weight = 8927.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.155244 restraints weight = 7241.993| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 30432 Z= 0.223 Angle : 0.682 14.004 41486 Z= 0.336 Chirality : 0.048 0.536 4711 Planarity : 0.005 0.106 5333 Dihedral : 7.255 80.110 4735 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 4.91 % Allowed : 13.28 % Favored : 81.82 % 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: -3.40 (0.12), residues: 3739 helix: 0.19 (0.20), residues: 672 sheet: -2.10 (0.19), residues: 658 loop : -3.26 (0.10), residues: 2409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 34 TYR 0.028 0.001 TYR B1067 PHE 0.027 0.002 PHE A 55 TRP 0.018 0.001 TRP A 64 HIS 0.008 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00487 (30365) covalent geometry : angle 0.66099 (41329) SS BOND : bond 0.00844 ( 44) SS BOND : angle 2.42404 ( 88) hydrogen bonds : bond 0.03958 ( 800) hydrogen bonds : angle 4.94578 ( 2136) link_NAG-ASN : bond 0.01485 ( 23) link_NAG-ASN : angle 3.17651 ( 69) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 521 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8140 (p0) cc_final: 0.7915 (p0) REVERT: A 64 TRP cc_start: 0.7787 (t60) cc_final: 0.7578 (t-100) REVERT: A 106 PHE cc_start: 0.7445 (m-80) cc_final: 0.6858 (m-80) REVERT: A 223 LEU cc_start: 0.7533 (mp) cc_final: 0.6734 (mp) REVERT: A 300 LYS cc_start: 0.8372 (mtmt) cc_final: 0.8088 (mtmm) REVERT: A 307 THR cc_start: 0.8043 (m) cc_final: 0.7736 (p) REVERT: A 396 TYR cc_start: 0.5983 (m-80) cc_final: 0.5334 (m-80) REVERT: A 516 GLU cc_start: 0.5853 (pt0) cc_final: 0.4924 (pt0) REVERT: A 546 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8309 (tt) REVERT: A 556 ASN cc_start: 0.8047 (p0) cc_final: 0.7677 (t0) REVERT: A 562 PHE cc_start: 0.7285 (p90) cc_final: 0.6971 (p90) REVERT: A 596 SER cc_start: 0.8825 (m) cc_final: 0.8576 (p) REVERT: A 602 THR cc_start: 0.8022 (m) cc_final: 0.7501 (p) REVERT: A 604 THR cc_start: 0.7062 (t) cc_final: 0.6412 (m) REVERT: A 615 VAL cc_start: 0.8577 (t) cc_final: 0.8337 (m) REVERT: A 674 TYR cc_start: 0.8188 (t80) cc_final: 0.7959 (t80) REVERT: A 737 ASP cc_start: 0.7038 (t0) cc_final: 0.6611 (t70) REVERT: A 790 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8181 (ptpp) REVERT: A 820 ASP cc_start: 0.8024 (m-30) cc_final: 0.7723 (t0) REVERT: A 856 LYS cc_start: 0.8015 (tppt) cc_final: 0.7776 (tppt) REVERT: A 864 LEU cc_start: 0.8609 (tp) cc_final: 0.8390 (tt) REVERT: A 921 LYS cc_start: 0.8433 (mmmt) cc_final: 0.7820 (mmmt) REVERT: A 950 ASP cc_start: 0.7203 (t70) cc_final: 0.6352 (t70) REVERT: A 954 HIS cc_start: 0.7134 (m-70) cc_final: 0.6729 (m170) REVERT: A 955 ASN cc_start: 0.8430 (t0) cc_final: 0.7950 (t0) REVERT: A 959 LEU cc_start: 0.8666 (mt) cc_final: 0.8374 (tp) REVERT: A 964 LYS cc_start: 0.8717 (tmtm) cc_final: 0.8516 (tppt) REVERT: A 984 LEU cc_start: 0.8837 (mt) cc_final: 0.8514 (mt) REVERT: A 988 GLU cc_start: 0.7667 (tp30) cc_final: 0.7104 (tp30) REVERT: A 1057 PRO cc_start: 0.8920 (Cg_exo) cc_final: 0.8612 (Cg_endo) REVERT: A 1081 ILE cc_start: 0.8524 (pt) cc_final: 0.8296 (mm) REVERT: B 41 LYS cc_start: 0.7570 (OUTLIER) cc_final: 0.7255 (mttt) REVERT: B 62 VAL cc_start: 0.8198 (t) cc_final: 0.7925 (m) REVERT: B 104 TRP cc_start: 0.7156 (m-90) cc_final: 0.6511 (m-90) REVERT: B 105 ILE cc_start: 0.8381 (mm) cc_final: 0.7810 (tp) REVERT: B 106 PHE cc_start: 0.7173 (m-80) cc_final: 0.6954 (m-80) REVERT: B 186 ASN cc_start: 0.6707 (p0) cc_final: 0.5626 (p0) REVERT: B 188 ARG cc_start: 0.7588 (mtt-85) cc_final: 0.7059 (mtt-85) REVERT: B 193 LYS cc_start: 0.8181 (ttpt) cc_final: 0.7814 (ttmm) REVERT: B 200 LYS cc_start: 0.8621 (mttt) cc_final: 0.8266 (mttt) REVERT: B 267 VAL cc_start: 0.8476 (OUTLIER) cc_final: 0.8209 (p) REVERT: B 307 THR cc_start: 0.8048 (m) cc_final: 0.7617 (p) REVERT: B 329 PHE cc_start: 0.6036 (m-10) cc_final: 0.5768 (m-10) REVERT: B 403 ARG cc_start: 0.6283 (mtm-85) cc_final: 0.5651 (ttm170) REVERT: B 563 GLN cc_start: 0.6874 (pt0) cc_final: 0.6600 (pt0) REVERT: B 592 PHE cc_start: 0.7467 (p90) cc_final: 0.5275 (p90) REVERT: B 602 THR cc_start: 0.8597 (OUTLIER) cc_final: 0.8236 (p) REVERT: B 698 SER cc_start: 0.8415 (t) cc_final: 0.7837 (p) REVERT: B 726 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8234 (mp) REVERT: B 776 LYS cc_start: 0.8305 (ttpm) cc_final: 0.7925 (ttpp) REVERT: B 780 GLU cc_start: 0.7467 (tp30) cc_final: 0.7060 (tp30) REVERT: B 851 CYS cc_start: 0.8252 (t) cc_final: 0.7747 (p) REVERT: B 856 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.8895 (tppp) REVERT: B 957 GLN cc_start: 0.7050 (tm-30) cc_final: 0.6706 (tm-30) REVERT: B 964 LYS cc_start: 0.8366 (tmmt) cc_final: 0.7594 (tmmt) REVERT: B 977 LEU cc_start: 0.8490 (mp) cc_final: 0.8268 (mt) REVERT: B 1019 ARG cc_start: 0.8006 (ttm110) cc_final: 0.7679 (ttp80) REVERT: C 55 PHE cc_start: 0.7111 (m-10) cc_final: 0.5466 (m-10) REVERT: C 104 TRP cc_start: 0.7063 (m-90) cc_final: 0.6775 (m-10) REVERT: C 106 PHE cc_start: 0.8013 (m-80) cc_final: 0.7767 (m-10) REVERT: C 118 LEU cc_start: 0.8667 (mp) cc_final: 0.8425 (mm) REVERT: C 129 LYS cc_start: 0.8309 (ttmt) cc_final: 0.7665 (tptt) REVERT: C 216 LEU cc_start: 0.8481 (mt) cc_final: 0.8206 (mm) REVERT: C 224 GLU cc_start: 0.6991 (pm20) cc_final: 0.6664 (pm20) REVERT: C 269 TYR cc_start: 0.6897 (m-10) cc_final: 0.6478 (m-80) REVERT: C 303 LEU cc_start: 0.8292 (tp) cc_final: 0.7916 (tp) REVERT: C 355 ARG cc_start: 0.6912 (OUTLIER) cc_final: 0.6711 (tmt90) REVERT: C 361 CYS cc_start: 0.6041 (OUTLIER) cc_final: 0.3079 (p) REVERT: C 362 VAL cc_start: 0.7533 (OUTLIER) cc_final: 0.7007 (m) REVERT: C 557 LYS cc_start: 0.8723 (mttm) cc_final: 0.8522 (mttm) REVERT: C 558 LYS cc_start: 0.8460 (mttt) cc_final: 0.8241 (mtmt) REVERT: C 707 TYR cc_start: 0.8106 (t80) cc_final: 0.7540 (t80) REVERT: C 718 PHE cc_start: 0.7824 (p90) cc_final: 0.7398 (p90) REVERT: C 754 LEU cc_start: 0.8659 (tp) cc_final: 0.8419 (tt) REVERT: C 776 LYS cc_start: 0.8394 (ttpp) cc_final: 0.8091 (ttpp) REVERT: C 820 ASP cc_start: 0.7636 (t70) cc_final: 0.7306 (t0) REVERT: C 821 LEU cc_start: 0.8921 (tp) cc_final: 0.8686 (tt) REVERT: C 851 CYS cc_start: 0.8019 (t) cc_final: 0.7688 (p) REVERT: C 854 LYS cc_start: 0.8279 (tmtt) cc_final: 0.8077 (tmtt) REVERT: C 868 GLU cc_start: 0.7505 (tp30) cc_final: 0.7293 (tp30) REVERT: C 914 ASN cc_start: 0.7767 (p0) cc_final: 0.7515 (p0) REVERT: C 950 ASP cc_start: 0.7355 (t70) cc_final: 0.6815 (t0) REVERT: C 978 ASN cc_start: 0.8563 (m-40) cc_final: 0.8218 (m-40) REVERT: C 1029 MET cc_start: 0.8541 (tpp) cc_final: 0.8211 (ttm) REVERT: C 1084 ASP cc_start: 0.7860 (t0) cc_final: 0.7566 (t0) REVERT: C 1086 LYS cc_start: 0.8419 (mmmt) cc_final: 0.8126 (mmmt) REVERT: C 1097 SER cc_start: 0.9001 (t) cc_final: 0.8414 (p) REVERT: C 1136 THR cc_start: 0.8886 (OUTLIER) cc_final: 0.8581 (p) REVERT: D 6 GLN cc_start: -0.0546 (OUTLIER) cc_final: -0.1342 (tp-100) REVERT: D 35 VAL cc_start: 0.2116 (OUTLIER) cc_final: 0.1803 (p) REVERT: D 90 CYS cc_start: 0.5907 (OUTLIER) cc_final: 0.5593 (t) REVERT: D 111 LEU cc_start: 0.5321 (OUTLIER) cc_final: 0.4914 (tm) REVERT: D 234 MET cc_start: -0.3852 (pmt) cc_final: -0.4444 (pmt) REVERT: F 160 MET cc_start: -0.0690 (ptp) cc_final: -0.1707 (mmm) outliers start: 159 outliers final: 85 residues processed: 646 average time/residue: 0.1788 time to fit residues: 186.0053 Evaluate side-chains 575 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 475 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 856 LYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 980 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 1130 ILE Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 35 VAL 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 90 CYS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 193 PHE Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 32 TYR Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain F residue 205 TYR Chi-restraints excluded: chain F residue 226 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 102 optimal weight: 0.9990 chunk 188 optimal weight: 1.9990 chunk 132 optimal weight: 9.9990 chunk 31 optimal weight: 0.2980 chunk 358 optimal weight: 0.0870 chunk 237 optimal weight: 10.0000 chunk 334 optimal weight: 20.0000 chunk 82 optimal weight: 5.9990 chunk 375 optimal weight: 30.0000 chunk 119 optimal weight: 0.7980 chunk 225 optimal weight: 0.9980 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN A1005 GLN A1101 HIS B 563 GLN B 607 GLN B 804 GLN B 895 GLN B 926 GLN B 965 GLN C 542 ASN C 563 GLN C 613 GLN C 641 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN C1011 GLN D 6 GLN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.201629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.148859 restraints weight = 54917.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.152283 restraints weight = 26320.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.155103 restraints weight = 13655.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.155196 restraints weight = 9512.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.155181 restraints weight = 8008.950| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 30432 Z= 0.123 Angle : 0.605 14.929 41486 Z= 0.295 Chirality : 0.045 0.412 4711 Planarity : 0.005 0.094 5333 Dihedral : 6.777 80.371 4704 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 4.57 % Allowed : 15.28 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.05 (0.13), residues: 3739 helix: 0.68 (0.21), residues: 666 sheet: -1.91 (0.19), residues: 666 loop : -3.06 (0.11), residues: 2407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 765 TYR 0.027 0.001 TYR A 170 PHE 0.024 0.001 PHE B 92 TRP 0.016 0.001 TRP A 64 HIS 0.007 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00278 (30365) covalent geometry : angle 0.59130 (41329) SS BOND : bond 0.00247 ( 44) SS BOND : angle 1.82656 ( 88) hydrogen bonds : bond 0.03271 ( 800) hydrogen bonds : angle 4.77933 ( 2136) link_NAG-ASN : bond 0.00526 ( 23) link_NAG-ASN : angle 2.54991 ( 69) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 483 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.6952 (m-10) cc_final: 0.6651 (m-10) REVERT: A 64 TRP cc_start: 0.7840 (t60) cc_final: 0.7589 (t60) REVERT: A 106 PHE cc_start: 0.7444 (m-80) cc_final: 0.6773 (m-80) REVERT: A 118 LEU cc_start: 0.6342 (OUTLIER) cc_final: 0.6053 (pp) REVERT: A 223 LEU cc_start: 0.7390 (mp) cc_final: 0.6857 (mp) REVERT: A 300 LYS cc_start: 0.8301 (mtmt) cc_final: 0.8038 (mtmm) REVERT: A 307 THR cc_start: 0.7990 (m) cc_final: 0.7661 (p) REVERT: A 308 VAL cc_start: 0.8677 (p) cc_final: 0.8452 (m) REVERT: A 396 TYR cc_start: 0.6122 (m-80) cc_final: 0.5565 (m-80) REVERT: A 516 GLU cc_start: 0.5874 (pt0) cc_final: 0.5143 (pt0) REVERT: A 546 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8247 (tt) REVERT: A 556 ASN cc_start: 0.8036 (p0) cc_final: 0.7529 (t0) REVERT: A 560 LEU cc_start: 0.7930 (tp) cc_final: 0.7620 (tp) REVERT: A 562 PHE cc_start: 0.7270 (p90) cc_final: 0.6944 (p90) REVERT: A 596 SER cc_start: 0.8820 (m) cc_final: 0.8567 (p) REVERT: A 602 THR cc_start: 0.7904 (m) cc_final: 0.7388 (p) REVERT: A 615 VAL cc_start: 0.8470 (t) cc_final: 0.8207 (m) REVERT: A 765 ARG cc_start: 0.7774 (ttm110) cc_final: 0.7434 (ttm110) REVERT: A 790 LYS cc_start: 0.8474 (ptpp) cc_final: 0.8102 (ptpp) REVERT: A 820 ASP cc_start: 0.7939 (m-30) cc_final: 0.7684 (t0) REVERT: A 864 LEU cc_start: 0.8606 (tp) cc_final: 0.8299 (tt) REVERT: A 921 LYS cc_start: 0.8429 (mmmt) cc_final: 0.7828 (mmmt) REVERT: A 950 ASP cc_start: 0.7131 (t70) cc_final: 0.6270 (t70) REVERT: A 954 HIS cc_start: 0.7111 (m-70) cc_final: 0.6718 (m170) REVERT: A 955 ASN cc_start: 0.8422 (t0) cc_final: 0.7989 (t0) REVERT: A 959 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8394 (tp) REVERT: A 964 LYS cc_start: 0.8760 (tmtm) cc_final: 0.8517 (tppt) REVERT: A 984 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8476 (mt) REVERT: A 988 GLU cc_start: 0.7431 (tp30) cc_final: 0.6963 (tp30) REVERT: A 1057 PRO cc_start: 0.8886 (Cg_exo) cc_final: 0.8546 (Cg_endo) REVERT: A 1081 ILE cc_start: 0.8161 (pt) cc_final: 0.7932 (mt) REVERT: A 1111 GLU cc_start: 0.7031 (tt0) cc_final: 0.6810 (tt0) REVERT: B 62 VAL cc_start: 0.8249 (t) cc_final: 0.7969 (p) REVERT: B 68 ILE cc_start: 0.7404 (OUTLIER) cc_final: 0.7189 (tp) REVERT: B 105 ILE cc_start: 0.8452 (mm) cc_final: 0.8025 (tp) REVERT: B 186 ASN cc_start: 0.6613 (p0) cc_final: 0.5598 (p0) REVERT: B 188 ARG cc_start: 0.7548 (mtt-85) cc_final: 0.6975 (mtt-85) REVERT: B 193 LYS cc_start: 0.8100 (ttpt) cc_final: 0.7773 (ttmm) REVERT: B 200 LYS cc_start: 0.8613 (mttt) cc_final: 0.8161 (mttp) REVERT: B 201 ILE cc_start: 0.9020 (mp) cc_final: 0.8767 (pt) REVERT: B 204 LYS cc_start: 0.7803 (tppp) cc_final: 0.7517 (tptt) REVERT: B 220 PHE cc_start: 0.7530 (t80) cc_final: 0.7241 (t80) REVERT: B 271 GLN cc_start: 0.7976 (tm-30) cc_final: 0.7527 (tm-30) REVERT: B 307 THR cc_start: 0.7931 (m) cc_final: 0.7562 (p) REVERT: B 329 PHE cc_start: 0.6005 (m-10) cc_final: 0.5723 (m-10) REVERT: B 403 ARG cc_start: 0.6186 (mtm-85) cc_final: 0.5633 (ttm170) REVERT: B 592 PHE cc_start: 0.7317 (p90) cc_final: 0.7109 (p90) REVERT: B 602 THR cc_start: 0.8525 (OUTLIER) cc_final: 0.8145 (p) REVERT: B 698 SER cc_start: 0.8300 (t) cc_final: 0.7795 (p) REVERT: B 759 PHE cc_start: 0.7254 (t80) cc_final: 0.6902 (t80) REVERT: B 773 GLU cc_start: 0.7288 (tp30) cc_final: 0.6686 (tp30) REVERT: B 776 LYS cc_start: 0.8155 (ttpm) cc_final: 0.7699 (ttpp) REVERT: B 780 GLU cc_start: 0.7504 (tp30) cc_final: 0.6943 (tp30) REVERT: B 803 SER cc_start: 0.8409 (m) cc_final: 0.8005 (p) REVERT: B 811 LYS cc_start: 0.7986 (tptp) cc_final: 0.7728 (tptp) REVERT: B 851 CYS cc_start: 0.8263 (t) cc_final: 0.7732 (p) REVERT: B 856 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8969 (tppp) REVERT: B 957 GLN cc_start: 0.7064 (tm-30) cc_final: 0.6630 (tm-30) REVERT: B 964 LYS cc_start: 0.8362 (tmmt) cc_final: 0.8094 (tmmt) REVERT: B 965 GLN cc_start: 0.7585 (mm110) cc_final: 0.6678 (mm-40) REVERT: B 1019 ARG cc_start: 0.7944 (ttm110) cc_final: 0.7595 (ttp80) REVERT: C 80 ASP cc_start: 0.6899 (t0) cc_final: 0.6693 (t0) REVERT: C 104 TRP cc_start: 0.7155 (m-90) cc_final: 0.6874 (m-10) REVERT: C 106 PHE cc_start: 0.8115 (m-80) cc_final: 0.7707 (m-80) REVERT: C 118 LEU cc_start: 0.8801 (mp) cc_final: 0.8511 (mm) REVERT: C 129 LYS cc_start: 0.8254 (ttmt) cc_final: 0.7679 (tptt) REVERT: C 229 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7463 (pp) REVERT: C 237 ARG cc_start: 0.7420 (mtp85) cc_final: 0.7034 (mtp85) REVERT: C 273 ARG cc_start: 0.6875 (mtt180) cc_final: 0.6557 (mtt180) REVERT: C 303 LEU cc_start: 0.8312 (tp) cc_final: 0.7890 (tp) REVERT: C 361 CYS cc_start: 0.5698 (OUTLIER) cc_final: 0.3436 (p) REVERT: C 362 VAL cc_start: 0.7465 (OUTLIER) cc_final: 0.7041 (m) REVERT: C 557 LYS cc_start: 0.8722 (mttm) cc_final: 0.8477 (mttm) REVERT: C 558 LYS cc_start: 0.8543 (mttt) cc_final: 0.8206 (mtmt) REVERT: C 563 GLN cc_start: 0.7255 (OUTLIER) cc_final: 0.7030 (pt0) REVERT: C 707 TYR cc_start: 0.8087 (t80) cc_final: 0.7520 (t80) REVERT: C 718 PHE cc_start: 0.7810 (p90) cc_final: 0.7315 (p90) REVERT: C 754 LEU cc_start: 0.8564 (tp) cc_final: 0.8355 (tt) REVERT: C 821 LEU cc_start: 0.8939 (tp) cc_final: 0.8677 (tt) REVERT: C 868 GLU cc_start: 0.7419 (tp30) cc_final: 0.7207 (tp30) REVERT: C 914 ASN cc_start: 0.7774 (p0) cc_final: 0.7520 (p0) REVERT: C 1029 MET cc_start: 0.8379 (tpp) cc_final: 0.8078 (ttm) REVERT: C 1050 MET cc_start: 0.7657 (mtm) cc_final: 0.7448 (mtp) REVERT: C 1084 ASP cc_start: 0.7898 (t0) cc_final: 0.7496 (t0) REVERT: C 1086 LYS cc_start: 0.8415 (mmmt) cc_final: 0.8005 (mmmt) REVERT: C 1097 SER cc_start: 0.8985 (t) cc_final: 0.8490 (p) REVERT: C 1136 THR cc_start: 0.8827 (OUTLIER) cc_final: 0.8492 (p) REVERT: D 35 VAL cc_start: 0.2170 (OUTLIER) cc_final: 0.1847 (p) REVERT: D 90 CYS cc_start: 0.5924 (OUTLIER) cc_final: 0.5485 (t) REVERT: D 111 LEU cc_start: 0.5181 (OUTLIER) cc_final: 0.4802 (tm) REVERT: D 208 MET cc_start: 0.2796 (tmm) cc_final: 0.2418 (tmm) REVERT: D 234 MET cc_start: -0.3715 (pmt) cc_final: -0.4282 (pmt) REVERT: E 174 VAL cc_start: 0.5139 (OUTLIER) cc_final: 0.4874 (t) REVERT: F 160 MET cc_start: -0.1046 (ptp) cc_final: -0.1881 (mmm) outliers start: 148 outliers final: 87 residues processed: 595 average time/residue: 0.1849 time to fit residues: 175.8229 Evaluate side-chains 557 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 454 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 LYS Chi-restraints excluded: chain B residue 975 SER 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 1116 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 955 ASN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 35 VAL 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 90 CYS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 193 PHE Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 32 TYR Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain F residue 205 TYR Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 226 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 54 optimal weight: 0.7980 chunk 154 optimal weight: 9.9990 chunk 310 optimal weight: 5.9990 chunk 249 optimal weight: 30.0000 chunk 267 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 272 optimal weight: 0.3980 chunk 82 optimal weight: 0.9990 chunk 358 optimal weight: 8.9990 chunk 124 optimal weight: 0.6980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN A1101 HIS B 334 ASN B 422 ASN B 607 GLN B 644 GLN B 690 GLN B1002 GLN C 448 ASN C 563 GLN C 613 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 GLN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.199189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.147965 restraints weight = 54555.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.148508 restraints weight = 29327.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.151248 restraints weight = 16204.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.151253 restraints weight = 11400.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.151476 restraints weight = 10850.908| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 30432 Z= 0.169 Angle : 0.614 10.154 41486 Z= 0.302 Chirality : 0.046 0.391 4711 Planarity : 0.004 0.066 5333 Dihedral : 6.789 80.361 4696 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 4.85 % Allowed : 15.93 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.86 (0.13), residues: 3739 helix: 0.75 (0.21), residues: 668 sheet: -1.78 (0.19), residues: 666 loop : -2.92 (0.11), residues: 2405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 34 TYR 0.025 0.001 TYR A 655 PHE 0.027 0.002 PHE B 106 TRP 0.027 0.001 TRP B 64 HIS 0.007 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00380 (30365) covalent geometry : angle 0.60153 (41329) SS BOND : bond 0.00368 ( 44) SS BOND : angle 1.76981 ( 88) hydrogen bonds : bond 0.03526 ( 800) hydrogen bonds : angle 4.84598 ( 2136) link_NAG-ASN : bond 0.00413 ( 23) link_NAG-ASN : angle 2.42631 ( 69) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 474 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.6970 (m-10) cc_final: 0.6614 (m-10) REVERT: A 64 TRP cc_start: 0.7786 (t60) cc_final: 0.7570 (t60) REVERT: A 106 PHE cc_start: 0.7434 (m-80) cc_final: 0.6735 (m-80) REVERT: A 118 LEU cc_start: 0.6479 (OUTLIER) cc_final: 0.6234 (pp) REVERT: A 223 LEU cc_start: 0.7552 (mp) cc_final: 0.6934 (mp) REVERT: A 300 LYS cc_start: 0.8361 (mtmt) cc_final: 0.8073 (mtmm) REVERT: A 307 THR cc_start: 0.8071 (m) cc_final: 0.7780 (p) REVERT: A 308 VAL cc_start: 0.8741 (p) cc_final: 0.8510 (m) REVERT: A 396 TYR cc_start: 0.6281 (m-80) cc_final: 0.5738 (m-80) REVERT: A 516 GLU cc_start: 0.5965 (pt0) cc_final: 0.5261 (pt0) REVERT: A 546 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8290 (tt) REVERT: A 556 ASN cc_start: 0.8035 (p0) cc_final: 0.7784 (t0) REVERT: A 560 LEU cc_start: 0.8150 (tp) cc_final: 0.7712 (tp) REVERT: A 562 PHE cc_start: 0.7369 (p90) cc_final: 0.7021 (p90) REVERT: A 596 SER cc_start: 0.8894 (m) cc_final: 0.8597 (p) REVERT: A 602 THR cc_start: 0.8036 (OUTLIER) cc_final: 0.7552 (p) REVERT: A 615 VAL cc_start: 0.8547 (t) cc_final: 0.8285 (m) REVERT: A 754 LEU cc_start: 0.8305 (mt) cc_final: 0.8098 (mt) REVERT: A 790 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8118 (ptpp) REVERT: A 820 ASP cc_start: 0.8081 (m-30) cc_final: 0.7825 (t0) REVERT: A 921 LYS cc_start: 0.8443 (mmmt) cc_final: 0.7842 (mmmt) REVERT: A 950 ASP cc_start: 0.7442 (t70) cc_final: 0.6104 (t0) REVERT: A 954 HIS cc_start: 0.7168 (m-70) cc_final: 0.6433 (m170) REVERT: A 955 ASN cc_start: 0.8409 (t0) cc_final: 0.8017 (t0) REVERT: A 964 LYS cc_start: 0.8817 (tmtm) cc_final: 0.8523 (tppt) REVERT: A 969 LYS cc_start: 0.7645 (mppt) cc_final: 0.7237 (mmtp) REVERT: A 984 LEU cc_start: 0.8739 (mt) cc_final: 0.8373 (mt) REVERT: A 988 GLU cc_start: 0.7585 (tp30) cc_final: 0.7168 (tp30) REVERT: A 1057 PRO cc_start: 0.8932 (Cg_exo) cc_final: 0.8604 (Cg_endo) REVERT: A 1081 ILE cc_start: 0.8268 (pt) cc_final: 0.8034 (mm) REVERT: B 105 ILE cc_start: 0.8484 (mm) cc_final: 0.8109 (tp) REVERT: B 106 PHE cc_start: 0.7127 (m-80) cc_final: 0.6895 (m-80) REVERT: B 189 GLU cc_start: 0.6822 (OUTLIER) cc_final: 0.6563 (mp0) REVERT: B 193 LYS cc_start: 0.8077 (ttpt) cc_final: 0.7753 (ttmt) REVERT: B 200 LYS cc_start: 0.8677 (mttt) cc_final: 0.8183 (mttp) REVERT: B 201 ILE cc_start: 0.9060 (mp) cc_final: 0.8713 (pt) REVERT: B 226 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7651 (tp) REVERT: B 227 VAL cc_start: 0.8755 (m) cc_final: 0.8396 (p) REVERT: B 271 GLN cc_start: 0.8038 (tm-30) cc_final: 0.7451 (tm-30) REVERT: B 281 GLU cc_start: 0.7588 (tp30) cc_final: 0.7099 (tp30) REVERT: B 307 THR cc_start: 0.7984 (m) cc_final: 0.7589 (p) REVERT: B 329 PHE cc_start: 0.6277 (m-10) cc_final: 0.6019 (m-10) REVERT: B 403 ARG cc_start: 0.6435 (mtm-85) cc_final: 0.5897 (ttm170) REVERT: B 602 THR cc_start: 0.8562 (OUTLIER) cc_final: 0.8204 (p) REVERT: B 654 GLU cc_start: 0.7511 (pm20) cc_final: 0.7297 (pm20) REVERT: B 725 GLU cc_start: 0.7114 (tm-30) cc_final: 0.6873 (tm-30) REVERT: B 726 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8285 (mt) REVERT: B 773 GLU cc_start: 0.7327 (tp30) cc_final: 0.7049 (tp30) REVERT: B 780 GLU cc_start: 0.7611 (tp30) cc_final: 0.7263 (tp30) REVERT: B 803 SER cc_start: 0.8523 (m) cc_final: 0.8120 (p) REVERT: B 851 CYS cc_start: 0.8411 (t) cc_final: 0.7792 (p) REVERT: B 856 LYS cc_start: 0.9253 (OUTLIER) cc_final: 0.8997 (tppp) REVERT: B 933 LYS cc_start: 0.8015 (mtmt) cc_final: 0.7774 (mtmt) REVERT: B 957 GLN cc_start: 0.7089 (tm-30) cc_final: 0.6651 (tm-30) REVERT: B 964 LYS cc_start: 0.8372 (tmmt) cc_final: 0.7977 (tmmt) REVERT: B 965 GLN cc_start: 0.7634 (mm110) cc_final: 0.6551 (mm-40) REVERT: B 1002 GLN cc_start: 0.8081 (tp-100) cc_final: 0.7552 (mm-40) REVERT: B 1019 ARG cc_start: 0.8063 (ttm110) cc_final: 0.7689 (ttp80) REVERT: C 53 ASP cc_start: 0.7580 (p0) cc_final: 0.7357 (p0) REVERT: C 80 ASP cc_start: 0.6927 (t0) cc_final: 0.6720 (t0) REVERT: C 104 TRP cc_start: 0.7265 (m-90) cc_final: 0.6919 (m-10) REVERT: C 106 PHE cc_start: 0.8202 (m-80) cc_final: 0.7687 (m-80) REVERT: C 129 LYS cc_start: 0.8370 (ttmt) cc_final: 0.7797 (tptt) REVERT: C 190 PHE cc_start: 0.7329 (m-80) cc_final: 0.6965 (m-80) REVERT: C 229 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7383 (pp) REVERT: C 273 ARG cc_start: 0.6958 (mtt180) cc_final: 0.6631 (mtt180) REVERT: C 303 LEU cc_start: 0.8317 (tp) cc_final: 0.7899 (tp) REVERT: C 361 CYS cc_start: 0.5321 (OUTLIER) cc_final: 0.3858 (p) REVERT: C 557 LYS cc_start: 0.8749 (mttm) cc_final: 0.8545 (mttm) REVERT: C 558 LYS cc_start: 0.8575 (mttt) cc_final: 0.8290 (mtmt) REVERT: C 564 GLN cc_start: 0.7852 (mt0) cc_final: 0.7581 (mt0) REVERT: C 707 TYR cc_start: 0.8074 (t80) cc_final: 0.7560 (t80) REVERT: C 763 LEU cc_start: 0.8279 (mt) cc_final: 0.8064 (mp) REVERT: C 821 LEU cc_start: 0.8951 (tp) cc_final: 0.8569 (tt) REVERT: C 914 ASN cc_start: 0.7887 (p0) cc_final: 0.7640 (p0) REVERT: C 994 ASP cc_start: 0.7356 (p0) cc_final: 0.7121 (p0) REVERT: C 1002 GLN cc_start: 0.7336 (tp40) cc_final: 0.6887 (tp40) REVERT: C 1029 MET cc_start: 0.8509 (tpp) cc_final: 0.8122 (ttm) REVERT: C 1031 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7672 (mt-10) REVERT: C 1076 THR cc_start: 0.9049 (m) cc_final: 0.8844 (p) REVERT: C 1084 ASP cc_start: 0.8020 (t0) cc_final: 0.7599 (t0) REVERT: C 1086 LYS cc_start: 0.8540 (mmmt) cc_final: 0.8195 (mmmt) REVERT: C 1136 THR cc_start: 0.8836 (OUTLIER) cc_final: 0.8493 (p) REVERT: D 35 VAL cc_start: 0.2310 (OUTLIER) cc_final: 0.1978 (p) REVERT: D 90 CYS cc_start: 0.5833 (OUTLIER) cc_final: 0.5405 (t) REVERT: D 111 LEU cc_start: 0.5250 (OUTLIER) cc_final: 0.4856 (tm) REVERT: D 234 MET cc_start: -0.3719 (pmt) cc_final: -0.4271 (pmt) REVERT: E 174 VAL cc_start: 0.5080 (OUTLIER) cc_final: 0.4874 (t) REVERT: F 160 MET cc_start: -0.1027 (ptp) cc_final: -0.1878 (mmm) outliers start: 157 outliers final: 100 residues processed: 592 average time/residue: 0.1846 time to fit residues: 175.1812 Evaluate side-chains 560 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 444 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 LYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 954 HIS Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 955 ASN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 35 VAL 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 90 CYS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 32 TYR Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 226 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 128 optimal weight: 2.9990 chunk 229 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 342 optimal weight: 7.9990 chunk 325 optimal weight: 20.0000 chunk 162 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 238 optimal weight: 0.2980 chunk 351 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 ASN A 935 GLN A1101 HIS B 607 GLN B 641 ASN B 762 GLN C 81 ASN C 183 ASN C 448 ASN C 613 GLN C 675 GLN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 ASN ** F 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 = 0.4423 r_free = 0.4423 target = 0.198299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.145978 restraints weight = 54457.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.147939 restraints weight = 26620.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.150875 restraints weight = 14292.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.151649 restraints weight = 9032.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.151969 restraints weight = 8446.490| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 30432 Z= 0.192 Angle : 0.626 13.297 41486 Z= 0.309 Chirality : 0.046 0.400 4711 Planarity : 0.005 0.083 5333 Dihedral : 6.676 80.228 4685 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 5.19 % Allowed : 16.70 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.80 (0.13), residues: 3739 helix: 0.76 (0.21), residues: 668 sheet: -1.80 (0.19), residues: 681 loop : -2.84 (0.11), residues: 2390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 34 TYR 0.023 0.001 TYR B1067 PHE 0.020 0.002 PHE B 92 TRP 0.031 0.001 TRP B 64 HIS 0.008 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00429 (30365) covalent geometry : angle 0.61472 (41329) SS BOND : bond 0.00451 ( 44) SS BOND : angle 1.73181 ( 88) hydrogen bonds : bond 0.03670 ( 800) hydrogen bonds : angle 4.93134 ( 2136) link_NAG-ASN : bond 0.00381 ( 23) link_NAG-ASN : angle 2.40093 ( 69) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 462 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.6979 (m-10) cc_final: 0.6629 (m-10) REVERT: A 106 PHE cc_start: 0.7460 (m-80) cc_final: 0.6993 (m-80) REVERT: A 223 LEU cc_start: 0.7395 (mp) cc_final: 0.6860 (mp) REVERT: A 300 LYS cc_start: 0.8415 (mtmt) cc_final: 0.8027 (mttp) REVERT: A 307 THR cc_start: 0.8153 (m) cc_final: 0.7890 (p) REVERT: A 308 VAL cc_start: 0.8807 (p) cc_final: 0.8530 (m) REVERT: A 396 TYR cc_start: 0.6363 (m-80) cc_final: 0.5739 (m-80) REVERT: A 516 GLU cc_start: 0.6072 (pt0) cc_final: 0.5478 (pt0) REVERT: A 546 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8477 (tt) REVERT: A 556 ASN cc_start: 0.8004 (p0) cc_final: 0.7773 (t0) REVERT: A 560 LEU cc_start: 0.8170 (tp) cc_final: 0.7862 (tp) REVERT: A 562 PHE cc_start: 0.7328 (p90) cc_final: 0.6969 (p90) REVERT: A 596 SER cc_start: 0.8960 (m) cc_final: 0.8573 (p) REVERT: A 602 THR cc_start: 0.8059 (m) cc_final: 0.7547 (p) REVERT: A 675 GLN cc_start: 0.7455 (pp30) cc_final: 0.7204 (pp30) REVERT: A 743 CYS cc_start: 0.6526 (OUTLIER) cc_final: 0.5550 (t) REVERT: A 765 ARG cc_start: 0.7911 (ttm110) cc_final: 0.7509 (mtp85) REVERT: A 820 ASP cc_start: 0.8018 (m-30) cc_final: 0.7730 (t0) REVERT: A 921 LYS cc_start: 0.8497 (mmmt) cc_final: 0.7911 (mmmt) REVERT: A 950 ASP cc_start: 0.7426 (t70) cc_final: 0.6058 (t0) REVERT: A 954 HIS cc_start: 0.7126 (m-70) cc_final: 0.6393 (m170) REVERT: A 955 ASN cc_start: 0.8415 (t0) cc_final: 0.8075 (t0) REVERT: A 964 LYS cc_start: 0.8810 (tmtm) cc_final: 0.8579 (tppt) REVERT: A 969 LYS cc_start: 0.7731 (mppt) cc_final: 0.7343 (mmtp) REVERT: A 984 LEU cc_start: 0.8650 (mt) cc_final: 0.8297 (mt) REVERT: A 988 GLU cc_start: 0.7529 (tp30) cc_final: 0.7122 (tp30) REVERT: A 1005 GLN cc_start: 0.7955 (mm-40) cc_final: 0.7712 (tp40) REVERT: A 1057 PRO cc_start: 0.8917 (Cg_exo) cc_final: 0.8597 (Cg_endo) REVERT: A 1081 ILE cc_start: 0.8321 (pt) cc_final: 0.8023 (mm) REVERT: B 106 PHE cc_start: 0.7153 (m-80) cc_final: 0.6916 (m-80) REVERT: B 188 ARG cc_start: 0.7529 (mtt-85) cc_final: 0.6828 (mtm-85) REVERT: B 189 GLU cc_start: 0.6723 (OUTLIER) cc_final: 0.6487 (mp0) REVERT: B 193 LYS cc_start: 0.8104 (ttpt) cc_final: 0.7752 (ttmt) REVERT: B 200 LYS cc_start: 0.8680 (mttt) cc_final: 0.8222 (mttp) REVERT: B 201 ILE cc_start: 0.9013 (mp) cc_final: 0.8707 (pt) REVERT: B 226 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7780 (tp) REVERT: B 227 VAL cc_start: 0.8868 (m) cc_final: 0.8640 (m) REVERT: B 271 GLN cc_start: 0.8086 (tm-30) cc_final: 0.7509 (tm-30) REVERT: B 281 GLU cc_start: 0.7552 (tp30) cc_final: 0.7161 (tp30) REVERT: B 307 THR cc_start: 0.8059 (m) cc_final: 0.7683 (p) REVERT: B 329 PHE cc_start: 0.6538 (m-10) cc_final: 0.6318 (m-10) REVERT: B 403 ARG cc_start: 0.6591 (mtm-85) cc_final: 0.6058 (ttm170) REVERT: B 602 THR cc_start: 0.8593 (OUTLIER) cc_final: 0.8255 (p) REVERT: B 644 GLN cc_start: 0.8280 (tp-100) cc_final: 0.7799 (tp40) REVERT: B 726 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8125 (mt) REVERT: B 773 GLU cc_start: 0.7389 (tp30) cc_final: 0.6890 (tp30) REVERT: B 780 GLU cc_start: 0.7743 (tp30) cc_final: 0.7394 (tp30) REVERT: B 803 SER cc_start: 0.8587 (m) cc_final: 0.8229 (p) REVERT: B 851 CYS cc_start: 0.8340 (t) cc_final: 0.7757 (p) REVERT: B 856 LYS cc_start: 0.9205 (OUTLIER) cc_final: 0.8938 (tppp) REVERT: B 933 LYS cc_start: 0.8090 (mtmt) cc_final: 0.7859 (mtmt) REVERT: B 957 GLN cc_start: 0.7079 (tm-30) cc_final: 0.6641 (tm-30) REVERT: B 1002 GLN cc_start: 0.8144 (tp-100) cc_final: 0.7800 (mm-40) REVERT: B 1019 ARG cc_start: 0.8081 (ttm110) cc_final: 0.7709 (ttp80) REVERT: B 1130 ILE cc_start: 0.8701 (OUTLIER) cc_final: 0.8447 (tp) REVERT: C 34 ARG cc_start: 0.7107 (mtp85) cc_final: 0.6680 (mtt-85) REVERT: C 129 LYS cc_start: 0.8381 (ttmt) cc_final: 0.7801 (tptt) REVERT: C 229 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7377 (pp) REVERT: C 273 ARG cc_start: 0.7163 (mtt180) cc_final: 0.6743 (mmm-85) REVERT: C 274 THR cc_start: 0.8541 (p) cc_final: 0.8250 (m) REVERT: C 303 LEU cc_start: 0.8288 (tp) cc_final: 0.7906 (tp) REVERT: C 355 ARG cc_start: 0.6896 (OUTLIER) cc_final: 0.6452 (tmt90) REVERT: C 361 CYS cc_start: 0.5279 (OUTLIER) cc_final: 0.4035 (p) REVERT: C 558 LYS cc_start: 0.8546 (mttt) cc_final: 0.8275 (mttt) REVERT: C 559 PHE cc_start: 0.7843 (m-80) cc_final: 0.7565 (m-80) REVERT: C 564 GLN cc_start: 0.8044 (mt0) cc_final: 0.7831 (mt0) REVERT: C 707 TYR cc_start: 0.8097 (t80) cc_final: 0.7579 (t80) REVERT: C 763 LEU cc_start: 0.8312 (mt) cc_final: 0.8088 (mp) REVERT: C 773 GLU cc_start: 0.7044 (tm-30) cc_final: 0.6183 (tm-30) REVERT: C 869 MET cc_start: 0.7941 (mmm) cc_final: 0.7711 (mtp) REVERT: C 1002 GLN cc_start: 0.7406 (tp40) cc_final: 0.7161 (tp40) REVERT: C 1029 MET cc_start: 0.8539 (tpp) cc_final: 0.8130 (ttm) REVERT: C 1084 ASP cc_start: 0.8046 (t0) cc_final: 0.7592 (t0) REVERT: C 1086 LYS cc_start: 0.8518 (mmmt) cc_final: 0.8304 (mmmt) REVERT: C 1097 SER cc_start: 0.8963 (t) cc_final: 0.8431 (p) REVERT: C 1136 THR cc_start: 0.8830 (OUTLIER) cc_final: 0.8482 (p) REVERT: D 85 GLU cc_start: 0.2911 (OUTLIER) cc_final: 0.2539 (pm20) REVERT: D 111 LEU cc_start: 0.5362 (OUTLIER) cc_final: 0.4944 (tm) REVERT: D 208 MET cc_start: 0.2685 (tmm) cc_final: 0.2319 (tmm) REVERT: D 234 MET cc_start: -0.3651 (pmt) cc_final: -0.4123 (pmt) REVERT: F 160 MET cc_start: -0.0987 (ptp) cc_final: -0.1879 (mmm) outliers start: 168 outliers final: 108 residues processed: 591 average time/residue: 0.1966 time to fit residues: 184.8815 Evaluate side-chains 574 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 452 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 LYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 954 HIS Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 955 ASN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU 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 85 GLU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 201 ASN Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 226 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 281 optimal weight: 0.9990 chunk 6 optimal weight: 10.0000 chunk 218 optimal weight: 0.1980 chunk 33 optimal weight: 0.0020 chunk 225 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 157 optimal weight: 0.9980 chunk 356 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 89 optimal weight: 0.5980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN A 641 ASN A 935 GLN A1002 GLN B 607 GLN B 641 ASN B 955 ASN B 965 GLN C 448 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.199299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.148111 restraints weight = 54674.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.148985 restraints weight = 27663.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.151648 restraints weight = 16653.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.152120 restraints weight = 10379.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.152245 restraints weight = 10652.789| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 30432 Z= 0.118 Angle : 0.600 9.840 41486 Z= 0.294 Chirality : 0.045 0.394 4711 Planarity : 0.004 0.052 5333 Dihedral : 6.509 80.126 4682 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 4.72 % Allowed : 17.41 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.60 (0.13), residues: 3739 helix: 0.92 (0.21), residues: 677 sheet: -1.69 (0.19), residues: 708 loop : -2.72 (0.12), residues: 2354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1014 TYR 0.017 0.001 TYR B1067 PHE 0.032 0.001 PHE A 329 TRP 0.027 0.001 TRP C 104 HIS 0.007 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00272 (30365) covalent geometry : angle 0.58956 (41329) SS BOND : bond 0.00294 ( 44) SS BOND : angle 1.55887 ( 88) hydrogen bonds : bond 0.03216 ( 800) hydrogen bonds : angle 4.81504 ( 2136) link_NAG-ASN : bond 0.00394 ( 23) link_NAG-ASN : angle 2.19309 ( 69) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 450 time to evaluate : 0.950 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 58 PHE cc_start: 0.6952 (m-10) cc_final: 0.6568 (m-10) REVERT: A 106 PHE cc_start: 0.7497 (m-80) cc_final: 0.7079 (m-80) REVERT: A 177 MET cc_start: 0.3839 (tpp) cc_final: 0.3435 (tpp) REVERT: A 190 PHE cc_start: 0.7384 (m-80) cc_final: 0.7048 (m-10) REVERT: A 223 LEU cc_start: 0.7487 (mp) cc_final: 0.6811 (mp) REVERT: A 300 LYS cc_start: 0.8350 (mtmt) cc_final: 0.7931 (mttp) REVERT: A 307 THR cc_start: 0.8038 (m) cc_final: 0.7774 (p) REVERT: A 308 VAL cc_start: 0.8762 (p) cc_final: 0.8500 (m) REVERT: A 396 TYR cc_start: 0.6363 (m-80) cc_final: 0.5737 (m-80) REVERT: A 516 GLU cc_start: 0.6069 (pt0) cc_final: 0.5488 (pt0) REVERT: A 556 ASN cc_start: 0.8033 (p0) cc_final: 0.7656 (t0) REVERT: A 562 PHE cc_start: 0.7452 (p90) cc_final: 0.7079 (p90) REVERT: A 596 SER cc_start: 0.8905 (m) cc_final: 0.8569 (p) REVERT: A 602 THR cc_start: 0.8016 (OUTLIER) cc_final: 0.7499 (p) REVERT: A 644 GLN cc_start: 0.7755 (tp40) cc_final: 0.7390 (tp40) REVERT: A 675 GLN cc_start: 0.7410 (pp30) cc_final: 0.7116 (pp30) REVERT: A 743 CYS cc_start: 0.6551 (OUTLIER) cc_final: 0.5466 (t) REVERT: A 790 LYS cc_start: 0.8583 (ptpp) cc_final: 0.8224 (ptpp) REVERT: A 820 ASP cc_start: 0.7971 (m-30) cc_final: 0.7687 (t0) REVERT: A 921 LYS cc_start: 0.8475 (mmmt) cc_final: 0.7875 (mmmt) REVERT: A 950 ASP cc_start: 0.7398 (t70) cc_final: 0.6654 (t0) REVERT: A 954 HIS cc_start: 0.7095 (m-70) cc_final: 0.6700 (m170) REVERT: A 955 ASN cc_start: 0.8382 (t0) cc_final: 0.8031 (t0) REVERT: A 964 LYS cc_start: 0.8871 (tmtm) cc_final: 0.8592 (tppt) REVERT: A 984 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8384 (mt) REVERT: A 988 GLU cc_start: 0.7525 (tp30) cc_final: 0.7102 (tp30) REVERT: A 1002 GLN cc_start: 0.7379 (tp-100) cc_final: 0.6812 (tp-100) REVERT: A 1057 PRO cc_start: 0.8884 (Cg_exo) cc_final: 0.8532 (Cg_endo) REVERT: B 106 PHE cc_start: 0.7167 (m-80) cc_final: 0.6902 (m-80) REVERT: B 193 LYS cc_start: 0.8091 (ttpt) cc_final: 0.7722 (ttmt) REVERT: B 200 LYS cc_start: 0.8703 (mttt) cc_final: 0.8275 (mptp) REVERT: B 201 ILE cc_start: 0.9046 (mp) cc_final: 0.8731 (pt) REVERT: B 226 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7675 (tp) REVERT: B 227 VAL cc_start: 0.8801 (m) cc_final: 0.8372 (p) REVERT: B 271 GLN cc_start: 0.8055 (tm-30) cc_final: 0.7499 (tm-30) REVERT: B 281 GLU cc_start: 0.7574 (tp30) cc_final: 0.7155 (tp30) REVERT: B 307 THR cc_start: 0.8001 (m) cc_final: 0.7639 (p) REVERT: B 329 PHE cc_start: 0.6627 (m-10) cc_final: 0.6395 (m-10) REVERT: B 403 ARG cc_start: 0.6448 (mtm-85) cc_final: 0.5911 (ttm170) REVERT: B 602 THR cc_start: 0.8501 (OUTLIER) cc_final: 0.8162 (p) REVERT: B 644 GLN cc_start: 0.8334 (tp-100) cc_final: 0.8016 (tp40) REVERT: B 726 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.7979 (mt) REVERT: B 773 GLU cc_start: 0.7431 (tp30) cc_final: 0.6700 (tp30) REVERT: B 776 LYS cc_start: 0.8201 (ttpp) cc_final: 0.7759 (ttpp) REVERT: B 803 SER cc_start: 0.8504 (m) cc_final: 0.8206 (p) REVERT: B 851 CYS cc_start: 0.8352 (t) cc_final: 0.7780 (p) REVERT: B 856 LYS cc_start: 0.9168 (OUTLIER) cc_final: 0.8937 (tppp) REVERT: B 957 GLN cc_start: 0.7108 (tm-30) cc_final: 0.6615 (tm-30) REVERT: B 965 GLN cc_start: 0.7548 (mm110) cc_final: 0.7192 (mp10) REVERT: B 970 PHE cc_start: 0.7415 (m-80) cc_final: 0.6985 (m-80) REVERT: B 1002 GLN cc_start: 0.8076 (tp-100) cc_final: 0.7354 (mm-40) REVERT: B 1019 ARG cc_start: 0.8032 (ttm110) cc_final: 0.7723 (ttp80) REVERT: C 34 ARG cc_start: 0.7052 (mtp85) cc_final: 0.6589 (mtt-85) REVERT: C 129 LYS cc_start: 0.8378 (ttmt) cc_final: 0.7764 (tptt) REVERT: C 190 PHE cc_start: 0.7425 (m-80) cc_final: 0.7020 (m-10) REVERT: C 229 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7373 (pp) REVERT: C 273 ARG cc_start: 0.6920 (mtt180) cc_final: 0.6685 (mmm-85) REVERT: C 303 LEU cc_start: 0.8269 (tp) cc_final: 0.7886 (tp) REVERT: C 355 ARG cc_start: 0.6950 (OUTLIER) cc_final: 0.6380 (tmt90) REVERT: C 361 CYS cc_start: 0.5006 (OUTLIER) cc_final: 0.3849 (p) REVERT: C 564 GLN cc_start: 0.7998 (mt0) cc_final: 0.7634 (mt0) REVERT: C 675 GLN cc_start: 0.7745 (mm110) cc_final: 0.7528 (mm110) REVERT: C 707 TYR cc_start: 0.8093 (t80) cc_final: 0.7550 (t80) REVERT: C 763 LEU cc_start: 0.8204 (mt) cc_final: 0.7947 (mp) REVERT: C 1002 GLN cc_start: 0.7281 (tp40) cc_final: 0.6686 (tp40) REVERT: C 1029 MET cc_start: 0.8410 (tpp) cc_final: 0.8070 (ttm) REVERT: C 1136 THR cc_start: 0.8815 (OUTLIER) cc_final: 0.8485 (p) REVERT: D 85 GLU cc_start: 0.3070 (OUTLIER) cc_final: 0.2742 (pm20) REVERT: D 90 CYS cc_start: 0.6004 (OUTLIER) cc_final: 0.5527 (t) REVERT: D 111 LEU cc_start: 0.5212 (OUTLIER) cc_final: 0.4825 (tm) REVERT: D 234 MET cc_start: -0.3977 (pmt) cc_final: -0.4200 (pmt) REVERT: F 160 MET cc_start: -0.1046 (ptp) cc_final: -0.1869 (mmm) outliers start: 153 outliers final: 103 residues processed: 563 average time/residue: 0.1926 time to fit residues: 173.3550 Evaluate side-chains 553 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 436 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 LYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 954 HIS Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 955 ASN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU 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 85 GLU Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 32 TYR Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 226 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 98 optimal weight: 0.9990 chunk 300 optimal weight: 0.6980 chunk 253 optimal weight: 0.9990 chunk 188 optimal weight: 3.9990 chunk 149 optimal weight: 0.9980 chunk 150 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 335 optimal weight: 8.9990 chunk 18 optimal weight: 0.5980 chunk 126 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 ASN A 935 GLN A1005 GLN ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN B 641 ASN C 448 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 159 HIS ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.198867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.148137 restraints weight = 54537.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.149805 restraints weight = 25772.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.150476 restraints weight = 14873.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.150992 restraints weight = 13928.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.151065 restraints weight = 11706.449| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 30432 Z= 0.135 Angle : 0.613 16.241 41486 Z= 0.299 Chirality : 0.045 0.394 4711 Planarity : 0.004 0.063 5333 Dihedral : 6.494 79.966 4673 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 4.35 % Allowed : 18.43 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.13), residues: 3739 helix: 1.05 (0.21), residues: 660 sheet: -1.61 (0.19), residues: 712 loop : -2.64 (0.12), residues: 2367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 188 TYR 0.022 0.001 TYR C 655 PHE 0.037 0.001 PHE C 65 TRP 0.042 0.001 TRP C 104 HIS 0.006 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00310 (30365) covalent geometry : angle 0.60244 (41329) SS BOND : bond 0.00388 ( 44) SS BOND : angle 1.73979 ( 88) hydrogen bonds : bond 0.03233 ( 800) hydrogen bonds : angle 4.80718 ( 2136) link_NAG-ASN : bond 0.00356 ( 23) link_NAG-ASN : angle 2.18059 ( 69) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 444 time to evaluate : 0.965 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 106 PHE cc_start: 0.7444 (m-80) cc_final: 0.6993 (m-80) REVERT: A 177 MET cc_start: 0.3862 (tpp) cc_final: 0.3491 (tpp) REVERT: A 190 PHE cc_start: 0.7387 (m-80) cc_final: 0.6986 (m-10) REVERT: A 223 LEU cc_start: 0.7419 (mp) cc_final: 0.6906 (mp) REVERT: A 296 LEU cc_start: 0.8453 (tp) cc_final: 0.7305 (tp) REVERT: A 300 LYS cc_start: 0.8373 (mtmt) cc_final: 0.7769 (mttp) REVERT: A 307 THR cc_start: 0.8060 (m) cc_final: 0.7803 (p) REVERT: A 308 VAL cc_start: 0.8773 (p) cc_final: 0.8492 (m) REVERT: A 329 PHE cc_start: 0.7194 (m-80) cc_final: 0.6876 (t80) REVERT: A 396 TYR cc_start: 0.6384 (m-80) cc_final: 0.5763 (m-80) REVERT: A 516 GLU cc_start: 0.6221 (pt0) cc_final: 0.5524 (pt0) REVERT: A 556 ASN cc_start: 0.8041 (p0) cc_final: 0.7655 (t0) REVERT: A 562 PHE cc_start: 0.7606 (p90) cc_final: 0.7405 (p90) REVERT: A 596 SER cc_start: 0.8923 (m) cc_final: 0.8534 (p) REVERT: A 602 THR cc_start: 0.8074 (OUTLIER) cc_final: 0.7513 (p) REVERT: A 675 GLN cc_start: 0.7350 (pp30) cc_final: 0.7064 (pp30) REVERT: A 743 CYS cc_start: 0.6570 (OUTLIER) cc_final: 0.5550 (t) REVERT: A 790 LYS cc_start: 0.8596 (ptpp) cc_final: 0.8228 (ptpp) REVERT: A 820 ASP cc_start: 0.8016 (m-30) cc_final: 0.7709 (t0) REVERT: A 921 LYS cc_start: 0.8491 (mmmt) cc_final: 0.7876 (mmmt) REVERT: A 950 ASP cc_start: 0.7400 (t70) cc_final: 0.6931 (t0) REVERT: A 955 ASN cc_start: 0.8392 (t0) cc_final: 0.8051 (t0) REVERT: A 964 LYS cc_start: 0.8859 (tmtm) cc_final: 0.8615 (tppt) REVERT: A 969 LYS cc_start: 0.7573 (mppt) cc_final: 0.7236 (mmtm) REVERT: A 984 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8165 (mt) REVERT: A 988 GLU cc_start: 0.7569 (tp30) cc_final: 0.7129 (tp30) REVERT: A 1002 GLN cc_start: 0.7419 (tp-100) cc_final: 0.6953 (tp-100) REVERT: A 1057 PRO cc_start: 0.8911 (Cg_exo) cc_final: 0.8579 (Cg_endo) REVERT: B 106 PHE cc_start: 0.7230 (m-80) cc_final: 0.6989 (m-80) REVERT: B 189 GLU cc_start: 0.6506 (mp0) cc_final: 0.6262 (mp0) REVERT: B 193 LYS cc_start: 0.8052 (ttpt) cc_final: 0.7752 (ttmt) REVERT: B 200 LYS cc_start: 0.8690 (mttt) cc_final: 0.8319 (mptp) REVERT: B 201 ILE cc_start: 0.9138 (mp) cc_final: 0.8767 (pt) REVERT: B 226 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7532 (tp) REVERT: B 227 VAL cc_start: 0.8743 (m) cc_final: 0.8478 (m) REVERT: B 271 GLN cc_start: 0.8078 (tm-30) cc_final: 0.7577 (tm-30) REVERT: B 281 GLU cc_start: 0.7548 (tp30) cc_final: 0.7137 (tp30) REVERT: B 307 THR cc_start: 0.8094 (m) cc_final: 0.7735 (p) REVERT: B 329 PHE cc_start: 0.6784 (m-10) cc_final: 0.6548 (m-10) REVERT: B 403 ARG cc_start: 0.6437 (mtm-85) cc_final: 0.5908 (ttm170) REVERT: B 602 THR cc_start: 0.8524 (OUTLIER) cc_final: 0.8185 (p) REVERT: B 644 GLN cc_start: 0.8283 (tp-100) cc_final: 0.7934 (tp40) REVERT: B 726 ILE cc_start: 0.8607 (OUTLIER) cc_final: 0.8252 (mt) REVERT: B 773 GLU cc_start: 0.7474 (tp30) cc_final: 0.6906 (tp30) REVERT: B 803 SER cc_start: 0.8513 (m) cc_final: 0.8203 (p) REVERT: B 851 CYS cc_start: 0.8383 (t) cc_final: 0.7799 (p) REVERT: B 856 LYS cc_start: 0.9160 (OUTLIER) cc_final: 0.8933 (tppp) REVERT: B 933 LYS cc_start: 0.8129 (mtmt) cc_final: 0.7803 (mtmt) REVERT: B 957 GLN cc_start: 0.7131 (tm-30) cc_final: 0.6620 (tm-30) REVERT: B 965 GLN cc_start: 0.7604 (mm110) cc_final: 0.7304 (mp10) REVERT: B 970 PHE cc_start: 0.7463 (m-80) cc_final: 0.7008 (m-80) REVERT: B 1002 GLN cc_start: 0.8045 (tp-100) cc_final: 0.7400 (mm-40) REVERT: B 1019 ARG cc_start: 0.8022 (ttm110) cc_final: 0.7716 (ttp80) REVERT: C 34 ARG cc_start: 0.7099 (mtp85) cc_final: 0.6631 (mmt-90) REVERT: C 129 LYS cc_start: 0.8369 (ttmt) cc_final: 0.7779 (tptp) REVERT: C 190 PHE cc_start: 0.7436 (m-80) cc_final: 0.7152 (m-80) REVERT: C 229 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7369 (pp) REVERT: C 269 TYR cc_start: 0.6898 (m-10) cc_final: 0.6493 (m-10) REVERT: C 355 ARG cc_start: 0.6984 (OUTLIER) cc_final: 0.6367 (tmt90) REVERT: C 558 LYS cc_start: 0.8453 (mtmt) cc_final: 0.8161 (mttt) REVERT: C 564 GLN cc_start: 0.8047 (mt0) cc_final: 0.7655 (mt0) REVERT: C 643 PHE cc_start: 0.7754 (t80) cc_final: 0.7311 (t80) REVERT: C 675 GLN cc_start: 0.7798 (mm110) cc_final: 0.7497 (mm110) REVERT: C 707 TYR cc_start: 0.8099 (t80) cc_final: 0.7563 (t80) REVERT: C 1002 GLN cc_start: 0.7197 (tp40) cc_final: 0.6586 (tp40) REVERT: C 1029 MET cc_start: 0.8437 (tpp) cc_final: 0.8159 (ttm) REVERT: C 1136 THR cc_start: 0.8800 (OUTLIER) cc_final: 0.8460 (p) REVERT: D 85 GLU cc_start: 0.3019 (OUTLIER) cc_final: 0.2675 (pm20) REVERT: D 111 LEU cc_start: 0.5248 (OUTLIER) cc_final: 0.4852 (tm) REVERT: D 234 MET cc_start: -0.4018 (pmt) cc_final: -0.4269 (pmt) REVERT: F 160 MET cc_start: -0.1017 (ptp) cc_final: -0.1900 (mmm) outliers start: 141 outliers final: 109 residues processed: 550 average time/residue: 0.1913 time to fit residues: 167.7203 Evaluate side-chains 560 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 439 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 LYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 954 HIS Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 955 ASN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU 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 85 GLU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 226 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 13 optimal weight: 10.0000 chunk 183 optimal weight: 0.9990 chunk 342 optimal weight: 0.0170 chunk 179 optimal weight: 0.9990 chunk 166 optimal weight: 0.1980 chunk 339 optimal weight: 50.0000 chunk 309 optimal weight: 6.9990 chunk 175 optimal weight: 0.9990 chunk 118 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 overall best weight: 0.6222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN A1005 GLN A1113 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN C 448 ASN C 542 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 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 = 0.4456 r_free = 0.4456 target = 0.199235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.148073 restraints weight = 54664.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.148947 restraints weight = 28047.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.151518 restraints weight = 16080.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.152150 restraints weight = 10669.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.152375 restraints weight = 9860.806| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 30432 Z= 0.123 Angle : 0.616 16.397 41486 Z= 0.300 Chirality : 0.045 0.391 4711 Planarity : 0.004 0.058 5333 Dihedral : 6.421 79.854 4668 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 4.08 % Allowed : 18.77 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.13), residues: 3739 helix: 1.01 (0.21), residues: 671 sheet: -1.56 (0.19), residues: 702 loop : -2.57 (0.12), residues: 2366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 995 TYR 0.023 0.001 TYR A 170 PHE 0.033 0.001 PHE C 562 TRP 0.047 0.001 TRP C 104 HIS 0.007 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00284 (30365) covalent geometry : angle 0.60667 (41329) SS BOND : bond 0.00317 ( 44) SS BOND : angle 1.69680 ( 88) hydrogen bonds : bond 0.03154 ( 800) hydrogen bonds : angle 4.81286 ( 2136) link_NAG-ASN : bond 0.00352 ( 23) link_NAG-ASN : angle 2.09454 ( 69) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 439 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 PHE cc_start: 0.7392 (m-80) cc_final: 0.6983 (m-80) REVERT: A 177 MET cc_start: 0.4070 (tpp) cc_final: 0.3721 (tpp) REVERT: A 190 PHE cc_start: 0.7347 (m-80) cc_final: 0.6965 (m-10) REVERT: A 223 LEU cc_start: 0.7452 (mp) cc_final: 0.6904 (mp) REVERT: A 296 LEU cc_start: 0.8479 (tp) cc_final: 0.8238 (tp) REVERT: A 307 THR cc_start: 0.8014 (m) cc_final: 0.7721 (p) REVERT: A 308 VAL cc_start: 0.8720 (p) cc_final: 0.8432 (m) REVERT: A 329 PHE cc_start: 0.7170 (m-80) cc_final: 0.6335 (t80) REVERT: A 396 TYR cc_start: 0.6209 (m-80) cc_final: 0.5617 (m-80) REVERT: A 516 GLU cc_start: 0.6126 (pt0) cc_final: 0.5461 (pt0) REVERT: A 556 ASN cc_start: 0.8016 (p0) cc_final: 0.7684 (t0) REVERT: A 596 SER cc_start: 0.8903 (m) cc_final: 0.8548 (p) REVERT: A 602 THR cc_start: 0.8089 (OUTLIER) cc_final: 0.7570 (p) REVERT: A 644 GLN cc_start: 0.7727 (tp40) cc_final: 0.7468 (tp40) REVERT: A 675 GLN cc_start: 0.7309 (OUTLIER) cc_final: 0.7009 (pp30) REVERT: A 743 CYS cc_start: 0.6617 (OUTLIER) cc_final: 0.5585 (t) REVERT: A 790 LYS cc_start: 0.8578 (ptpp) cc_final: 0.8225 (ptpp) REVERT: A 820 ASP cc_start: 0.7976 (m-30) cc_final: 0.7631 (t0) REVERT: A 921 LYS cc_start: 0.8491 (mmmt) cc_final: 0.8025 (mmmt) REVERT: A 950 ASP cc_start: 0.7367 (t70) cc_final: 0.6615 (t0) REVERT: A 954 HIS cc_start: 0.7072 (m-70) cc_final: 0.6649 (m170) REVERT: A 955 ASN cc_start: 0.8421 (t0) cc_final: 0.8048 (t0) REVERT: A 964 LYS cc_start: 0.8873 (tmtm) cc_final: 0.8579 (tppt) REVERT: A 969 LYS cc_start: 0.7519 (mppt) cc_final: 0.7198 (mmtm) REVERT: A 981 PHE cc_start: 0.7602 (m-10) cc_final: 0.7289 (m-10) REVERT: A 984 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8218 (mt) REVERT: A 988 GLU cc_start: 0.7476 (tp30) cc_final: 0.7053 (tp30) REVERT: A 1002 GLN cc_start: 0.7375 (tp-100) cc_final: 0.6924 (tp-100) REVERT: A 1057 PRO cc_start: 0.8885 (Cg_exo) cc_final: 0.8558 (Cg_endo) REVERT: B 106 PHE cc_start: 0.7179 (m-80) cc_final: 0.6915 (m-80) REVERT: B 188 ARG cc_start: 0.7795 (mpt-90) cc_final: 0.7549 (mpt-90) REVERT: B 193 LYS cc_start: 0.8075 (ttpt) cc_final: 0.7819 (ttmt) REVERT: B 200 LYS cc_start: 0.8690 (mttt) cc_final: 0.8305 (mptp) REVERT: B 201 ILE cc_start: 0.9119 (mp) cc_final: 0.8763 (pt) REVERT: B 205 HIS cc_start: 0.7462 (t-90) cc_final: 0.7218 (t-90) REVERT: B 226 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7547 (tp) REVERT: B 227 VAL cc_start: 0.8731 (m) cc_final: 0.8473 (m) REVERT: B 271 GLN cc_start: 0.8065 (tm-30) cc_final: 0.7545 (tm-30) REVERT: B 281 GLU cc_start: 0.7572 (tp30) cc_final: 0.7161 (tp30) REVERT: B 307 THR cc_start: 0.8112 (m) cc_final: 0.7749 (p) REVERT: B 329 PHE cc_start: 0.6813 (m-10) cc_final: 0.6585 (m-10) REVERT: B 403 ARG cc_start: 0.6430 (mtm-85) cc_final: 0.5900 (ttm170) REVERT: B 602 THR cc_start: 0.8496 (OUTLIER) cc_final: 0.8142 (p) REVERT: B 644 GLN cc_start: 0.8241 (tp-100) cc_final: 0.7906 (tp40) REVERT: B 726 ILE cc_start: 0.8570 (OUTLIER) cc_final: 0.8246 (mt) REVERT: B 773 GLU cc_start: 0.7443 (tp30) cc_final: 0.6860 (tp30) REVERT: B 803 SER cc_start: 0.8558 (m) cc_final: 0.8244 (p) REVERT: B 851 CYS cc_start: 0.8312 (t) cc_final: 0.7780 (p) REVERT: B 856 LYS cc_start: 0.9120 (OUTLIER) cc_final: 0.8900 (tppp) REVERT: B 933 LYS cc_start: 0.8120 (mtmt) cc_final: 0.7806 (mtmt) REVERT: B 957 GLN cc_start: 0.7099 (tm-30) cc_final: 0.6606 (tm-30) REVERT: B 965 GLN cc_start: 0.7612 (mm110) cc_final: 0.7276 (mp10) REVERT: B 970 PHE cc_start: 0.7475 (m-80) cc_final: 0.7111 (m-80) REVERT: B 1002 GLN cc_start: 0.8057 (tp-100) cc_final: 0.7783 (mm-40) REVERT: B 1019 ARG cc_start: 0.8030 (ttm110) cc_final: 0.7615 (ttp80) REVERT: C 34 ARG cc_start: 0.7102 (mtp85) cc_final: 0.6549 (mmt-90) REVERT: C 129 LYS cc_start: 0.8369 (ttmt) cc_final: 0.7814 (tptt) REVERT: C 169 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7776 (tm-30) REVERT: C 190 PHE cc_start: 0.7432 (m-80) cc_final: 0.7162 (m-80) REVERT: C 193 LYS cc_start: 0.7195 (ptpp) cc_final: 0.6975 (ptpt) REVERT: C 229 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7348 (pp) REVERT: C 269 TYR cc_start: 0.6917 (m-10) cc_final: 0.6569 (m-80) REVERT: C 355 ARG cc_start: 0.6957 (OUTLIER) cc_final: 0.6323 (tmt90) REVERT: C 536 ASN cc_start: 0.8949 (m-40) cc_final: 0.8656 (t0) REVERT: C 558 LYS cc_start: 0.8438 (mtmt) cc_final: 0.8161 (mttt) REVERT: C 564 GLN cc_start: 0.7994 (mt0) cc_final: 0.7595 (mt0) REVERT: C 643 PHE cc_start: 0.7773 (t80) cc_final: 0.7369 (t80) REVERT: C 663 ASP cc_start: 0.7537 (t0) cc_final: 0.7219 (t0) REVERT: C 675 GLN cc_start: 0.7739 (mm110) cc_final: 0.7479 (mm110) REVERT: C 707 TYR cc_start: 0.8102 (t80) cc_final: 0.7550 (t80) REVERT: C 1005 GLN cc_start: 0.8077 (tp40) cc_final: 0.7660 (mm-40) REVERT: C 1029 MET cc_start: 0.8425 (tpp) cc_final: 0.8111 (ttm) REVERT: C 1136 THR cc_start: 0.8808 (OUTLIER) cc_final: 0.8472 (p) REVERT: D 85 GLU cc_start: 0.3030 (OUTLIER) cc_final: 0.2699 (pm20) REVERT: D 111 LEU cc_start: 0.5287 (OUTLIER) cc_final: 0.4889 (tm) REVERT: D 234 MET cc_start: -0.3980 (pmt) cc_final: -0.4240 (pmt) REVERT: F 160 MET cc_start: -0.1054 (ptp) cc_final: -0.1889 (mmm) outliers start: 132 outliers final: 103 residues processed: 537 average time/residue: 0.1913 time to fit residues: 163.5352 Evaluate side-chains 546 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 430 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 LYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 954 HIS Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 955 ASN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU 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 85 GLU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 226 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 277 optimal weight: 0.5980 chunk 359 optimal weight: 6.9990 chunk 157 optimal weight: 3.9990 chunk 176 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 chunk 169 optimal weight: 3.9990 chunk 276 optimal weight: 0.5980 chunk 215 optimal weight: 0.9980 chunk 310 optimal weight: 0.1980 chunk 351 optimal weight: 9.9990 chunk 140 optimal weight: 0.0980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN B 641 ASN B 644 GLN B 762 GLN B 935 GLN C 448 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.199843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.148444 restraints weight = 54885.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.150474 restraints weight = 27019.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.152269 restraints weight = 14660.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.152536 restraints weight = 11732.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.152747 restraints weight = 10358.422| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30432 Z= 0.112 Angle : 0.617 17.252 41486 Z= 0.300 Chirality : 0.045 0.360 4711 Planarity : 0.004 0.066 5333 Dihedral : 6.311 79.697 4666 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 3.89 % Allowed : 19.02 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z 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: -2.31 (0.13), residues: 3739 helix: 1.05 (0.21), residues: 668 sheet: -1.49 (0.19), residues: 703 loop : -2.47 (0.12), residues: 2368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 995 TYR 0.015 0.001 TYR C 655 PHE 0.032 0.001 PHE B 238 TRP 0.047 0.001 TRP C 104 HIS 0.007 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00257 (30365) covalent geometry : angle 0.60738 (41329) SS BOND : bond 0.00407 ( 44) SS BOND : angle 1.71984 ( 88) hydrogen bonds : bond 0.03065 ( 800) hydrogen bonds : angle 4.77247 ( 2136) link_NAG-ASN : bond 0.00348 ( 23) link_NAG-ASN : angle 1.98161 ( 69) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 436 time to evaluate : 1.083 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: A 106 PHE cc_start: 0.7496 (m-80) cc_final: 0.7085 (m-80) REVERT: A 177 MET cc_start: 0.3997 (tpp) cc_final: 0.3637 (tpp) REVERT: A 190 PHE cc_start: 0.7316 (m-80) cc_final: 0.6877 (m-10) REVERT: A 223 LEU cc_start: 0.7508 (mp) cc_final: 0.6902 (mp) REVERT: A 296 LEU cc_start: 0.8478 (tp) cc_final: 0.8043 (tp) REVERT: A 300 LYS cc_start: 0.8367 (mtmt) cc_final: 0.7996 (mttp) REVERT: A 307 THR cc_start: 0.7972 (m) cc_final: 0.7728 (p) REVERT: A 396 TYR cc_start: 0.6249 (m-80) cc_final: 0.5978 (m-80) REVERT: A 556 ASN cc_start: 0.7995 (p0) cc_final: 0.7690 (t0) REVERT: A 596 SER cc_start: 0.8921 (m) cc_final: 0.8554 (p) REVERT: A 602 THR cc_start: 0.8060 (OUTLIER) cc_final: 0.7482 (p) REVERT: A 644 GLN cc_start: 0.7778 (tp40) cc_final: 0.7571 (tp40) REVERT: A 675 GLN cc_start: 0.7278 (OUTLIER) cc_final: 0.6990 (pp30) REVERT: A 743 CYS cc_start: 0.6632 (OUTLIER) cc_final: 0.5591 (t) REVERT: A 751 ASN cc_start: 0.7490 (OUTLIER) cc_final: 0.6956 (t0) REVERT: A 790 LYS cc_start: 0.8593 (ptpp) cc_final: 0.8231 (ptpp) REVERT: A 820 ASP cc_start: 0.7975 (m-30) cc_final: 0.7626 (t0) REVERT: A 950 ASP cc_start: 0.7319 (t70) cc_final: 0.6586 (t0) REVERT: A 954 HIS cc_start: 0.7058 (m-70) cc_final: 0.6641 (m170) REVERT: A 955 ASN cc_start: 0.8427 (t0) cc_final: 0.8038 (t0) REVERT: A 964 LYS cc_start: 0.8892 (tmtm) cc_final: 0.8589 (tppt) REVERT: A 984 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8311 (mt) REVERT: A 988 GLU cc_start: 0.7519 (tp30) cc_final: 0.7106 (tp30) REVERT: A 1002 GLN cc_start: 0.7360 (tp-100) cc_final: 0.6940 (tp-100) REVERT: A 1057 PRO cc_start: 0.8909 (Cg_exo) cc_final: 0.8580 (Cg_endo) REVERT: B 105 ILE cc_start: 0.8502 (mm) cc_final: 0.8247 (pt) REVERT: B 188 ARG cc_start: 0.7836 (mpt-90) cc_final: 0.7364 (mtm-85) REVERT: B 193 LYS cc_start: 0.8070 (ttpt) cc_final: 0.7814 (ttmt) REVERT: B 200 LYS cc_start: 0.8713 (mttt) cc_final: 0.8309 (mptp) REVERT: B 226 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7422 (tp) REVERT: B 227 VAL cc_start: 0.8734 (m) cc_final: 0.8420 (m) REVERT: B 271 GLN cc_start: 0.8054 (tm-30) cc_final: 0.7512 (tm-30) REVERT: B 281 GLU cc_start: 0.7582 (tp30) cc_final: 0.7161 (tp30) REVERT: B 307 THR cc_start: 0.8109 (m) cc_final: 0.7772 (p) REVERT: B 329 PHE cc_start: 0.6829 (m-10) cc_final: 0.6562 (m-10) REVERT: B 403 ARG cc_start: 0.6468 (mtm-85) cc_final: 0.5928 (ttm170) REVERT: B 602 THR cc_start: 0.8482 (OUTLIER) cc_final: 0.8110 (p) REVERT: B 726 ILE cc_start: 0.8517 (OUTLIER) cc_final: 0.8215 (mt) REVERT: B 751 ASN cc_start: 0.8209 (m-40) cc_final: 0.7930 (m110) REVERT: B 773 GLU cc_start: 0.7402 (tp30) cc_final: 0.6821 (tp30) REVERT: B 803 SER cc_start: 0.8536 (m) cc_final: 0.8258 (p) REVERT: B 851 CYS cc_start: 0.8333 (t) cc_final: 0.7756 (p) REVERT: B 856 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8840 (tppp) REVERT: B 957 GLN cc_start: 0.7107 (tm-30) cc_final: 0.6574 (tm-30) REVERT: B 965 GLN cc_start: 0.7574 (mm110) cc_final: 0.7231 (mp10) REVERT: B 970 PHE cc_start: 0.7483 (m-80) cc_final: 0.6837 (m-80) REVERT: B 1002 GLN cc_start: 0.8027 (tp-100) cc_final: 0.7810 (mm-40) REVERT: B 1019 ARG cc_start: 0.8034 (ttm110) cc_final: 0.7618 (ttp80) REVERT: C 34 ARG cc_start: 0.7105 (mtp85) cc_final: 0.6474 (mmt-90) REVERT: C 41 LYS cc_start: 0.8300 (mtmt) cc_final: 0.7737 (ttmm) REVERT: C 129 LYS cc_start: 0.8326 (ttmt) cc_final: 0.7938 (tptt) REVERT: C 169 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7310 (tm-30) REVERT: C 229 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7409 (pp) REVERT: C 269 TYR cc_start: 0.6926 (m-10) cc_final: 0.6590 (m-80) REVERT: C 274 THR cc_start: 0.8433 (p) cc_final: 0.7943 (m) REVERT: C 275 PHE cc_start: 0.7648 (m-80) cc_final: 0.7328 (m-80) REVERT: C 355 ARG cc_start: 0.7034 (OUTLIER) cc_final: 0.6485 (tmt90) REVERT: C 536 ASN cc_start: 0.8906 (m-40) cc_final: 0.8643 (t0) REVERT: C 552 LEU cc_start: 0.8233 (mt) cc_final: 0.8021 (mp) REVERT: C 558 LYS cc_start: 0.8461 (mtmt) cc_final: 0.8200 (mttt) REVERT: C 564 GLN cc_start: 0.7975 (mt0) cc_final: 0.7569 (mt0) REVERT: C 643 PHE cc_start: 0.7793 (t80) cc_final: 0.7361 (t80) REVERT: C 663 ASP cc_start: 0.7530 (t0) cc_final: 0.7185 (t0) REVERT: C 675 GLN cc_start: 0.7761 (mm110) cc_final: 0.7460 (mm110) REVERT: C 707 TYR cc_start: 0.8106 (t80) cc_final: 0.7539 (t80) REVERT: C 820 ASP cc_start: 0.7534 (t70) cc_final: 0.7152 (t0) REVERT: C 1005 GLN cc_start: 0.8033 (tp40) cc_final: 0.7730 (mm-40) REVERT: C 1029 MET cc_start: 0.8375 (tpp) cc_final: 0.8118 (ttm) REVERT: C 1136 THR cc_start: 0.8822 (OUTLIER) cc_final: 0.8483 (p) REVERT: D 111 LEU cc_start: 0.5164 (OUTLIER) cc_final: 0.4790 (tm) REVERT: D 234 MET cc_start: -0.3738 (pmt) cc_final: -0.4152 (pmt) REVERT: F 160 MET cc_start: -0.1173 (ptp) cc_final: -0.1909 (mmm) outliers start: 126 outliers final: 104 residues processed: 529 average time/residue: 0.1933 time to fit residues: 163.8310 Evaluate side-chains 548 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 431 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 LYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 954 HIS Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU 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 177 ILE Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 32 TYR Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 226 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 203 optimal weight: 1.9990 chunk 255 optimal weight: 0.8980 chunk 342 optimal weight: 50.0000 chunk 17 optimal weight: 9.9990 chunk 180 optimal weight: 0.0570 chunk 281 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 189 optimal weight: 1.9990 chunk 266 optimal weight: 0.0980 chunk 136 optimal weight: 1.9990 chunk 86 optimal weight: 0.0470 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN B 641 ASN B1010 GLN C 448 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.199364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.148804 restraints weight = 54459.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.150424 restraints weight = 24756.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.151912 restraints weight = 14175.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.152038 restraints weight = 12819.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.152171 restraints weight = 10789.722| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 30432 Z= 0.124 Angle : 0.631 16.194 41486 Z= 0.308 Chirality : 0.046 0.345 4711 Planarity : 0.005 0.071 5333 Dihedral : 6.261 79.610 4663 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 3.89 % Allowed : 19.14 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.13), residues: 3739 helix: 1.10 (0.21), residues: 662 sheet: -1.41 (0.19), residues: 721 loop : -2.47 (0.12), residues: 2356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 995 TYR 0.020 0.001 TYR A 170 PHE 0.036 0.001 PHE B 238 TRP 0.071 0.002 TRP C 104 HIS 0.007 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00287 (30365) covalent geometry : angle 0.62183 (41329) SS BOND : bond 0.00369 ( 44) SS BOND : angle 1.77260 ( 88) hydrogen bonds : bond 0.03140 ( 800) hydrogen bonds : angle 4.81523 ( 2136) link_NAG-ASN : bond 0.00326 ( 23) link_NAG-ASN : angle 1.93561 ( 69) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 439 time to evaluate : 0.989 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: A 106 PHE cc_start: 0.7401 (m-80) cc_final: 0.6979 (m-80) REVERT: A 177 MET cc_start: 0.4181 (tpp) cc_final: 0.3941 (tpp) REVERT: A 190 PHE cc_start: 0.7364 (m-80) cc_final: 0.6871 (m-80) REVERT: A 223 LEU cc_start: 0.7467 (mp) cc_final: 0.6921 (mp) REVERT: A 296 LEU cc_start: 0.8537 (tp) cc_final: 0.8153 (tp) REVERT: A 307 THR cc_start: 0.8069 (m) cc_final: 0.7848 (p) REVERT: A 396 TYR cc_start: 0.6318 (m-80) cc_final: 0.6048 (m-80) REVERT: A 556 ASN cc_start: 0.8001 (p0) cc_final: 0.7799 (t0) REVERT: A 596 SER cc_start: 0.8940 (m) cc_final: 0.8595 (p) REVERT: A 602 THR cc_start: 0.8285 (m) cc_final: 0.7775 (p) REVERT: A 644 GLN cc_start: 0.7569 (tp40) cc_final: 0.7303 (tp40) REVERT: A 675 GLN cc_start: 0.7273 (OUTLIER) cc_final: 0.6981 (pp30) REVERT: A 737 ASP cc_start: 0.7364 (m-30) cc_final: 0.6848 (p0) REVERT: A 743 CYS cc_start: 0.6701 (OUTLIER) cc_final: 0.5724 (t) REVERT: A 751 ASN cc_start: 0.7464 (OUTLIER) cc_final: 0.6904 (t0) REVERT: A 790 LYS cc_start: 0.8587 (ptpp) cc_final: 0.8229 (ptpp) REVERT: A 819 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7492 (mt-10) REVERT: A 820 ASP cc_start: 0.7973 (m-30) cc_final: 0.7638 (t0) REVERT: A 825 LYS cc_start: 0.8835 (mtpp) cc_final: 0.8514 (tttt) REVERT: A 950 ASP cc_start: 0.7344 (t70) cc_final: 0.6603 (t0) REVERT: A 954 HIS cc_start: 0.7029 (m-70) cc_final: 0.6611 (m170) REVERT: A 955 ASN cc_start: 0.8393 (t0) cc_final: 0.8020 (t0) REVERT: A 964 LYS cc_start: 0.8839 (tmtm) cc_final: 0.8625 (tppt) REVERT: A 969 LYS cc_start: 0.7514 (mppt) cc_final: 0.7146 (mmtm) REVERT: A 984 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8281 (mt) REVERT: A 988 GLU cc_start: 0.7485 (tp30) cc_final: 0.7059 (tp30) REVERT: A 1002 GLN cc_start: 0.7348 (tp-100) cc_final: 0.6932 (tp-100) REVERT: A 1057 PRO cc_start: 0.8899 (Cg_exo) cc_final: 0.8573 (Cg_endo) REVERT: B 105 ILE cc_start: 0.8510 (mm) cc_final: 0.8270 (pt) REVERT: B 193 LYS cc_start: 0.8062 (ttpt) cc_final: 0.7822 (ttmt) REVERT: B 200 LYS cc_start: 0.8735 (mttt) cc_final: 0.8383 (mptp) REVERT: B 226 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7489 (tp) REVERT: B 227 VAL cc_start: 0.8722 (m) cc_final: 0.8343 (m) REVERT: B 271 GLN cc_start: 0.8055 (tm-30) cc_final: 0.7514 (tm-30) REVERT: B 307 THR cc_start: 0.8128 (m) cc_final: 0.7780 (p) REVERT: B 329 PHE cc_start: 0.6853 (m-10) cc_final: 0.6607 (m-10) REVERT: B 403 ARG cc_start: 0.6383 (mtm-85) cc_final: 0.5916 (ttm170) REVERT: B 602 THR cc_start: 0.8488 (OUTLIER) cc_final: 0.8131 (p) REVERT: B 726 ILE cc_start: 0.8509 (OUTLIER) cc_final: 0.8270 (mt) REVERT: B 751 ASN cc_start: 0.8209 (m-40) cc_final: 0.7927 (m110) REVERT: B 773 GLU cc_start: 0.7475 (tp30) cc_final: 0.6889 (tp30) REVERT: B 803 SER cc_start: 0.8596 (m) cc_final: 0.8313 (p) REVERT: B 851 CYS cc_start: 0.8323 (t) cc_final: 0.7754 (p) REVERT: B 957 GLN cc_start: 0.7079 (tm-30) cc_final: 0.6583 (tm-30) REVERT: B 965 GLN cc_start: 0.7598 (mm110) cc_final: 0.7247 (mp10) REVERT: B 970 PHE cc_start: 0.7489 (m-80) cc_final: 0.6951 (m-80) REVERT: B 1002 GLN cc_start: 0.8077 (tp-100) cc_final: 0.7781 (mm-40) REVERT: B 1019 ARG cc_start: 0.7996 (ttm110) cc_final: 0.7758 (ttm-80) REVERT: C 34 ARG cc_start: 0.7076 (mtp85) cc_final: 0.6435 (mmt-90) REVERT: C 129 LYS cc_start: 0.8403 (ttmt) cc_final: 0.7964 (tptt) REVERT: C 169 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7314 (tm-30) REVERT: C 229 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7393 (pp) REVERT: C 269 TYR cc_start: 0.6957 (m-10) cc_final: 0.6621 (m-80) REVERT: C 274 THR cc_start: 0.8455 (p) cc_final: 0.7963 (m) REVERT: C 275 PHE cc_start: 0.7657 (m-80) cc_final: 0.7278 (m-80) REVERT: C 310 LYS cc_start: 0.8394 (ttpp) cc_final: 0.8185 (tttp) REVERT: C 355 ARG cc_start: 0.7001 (OUTLIER) cc_final: 0.6455 (tmt90) REVERT: C 552 LEU cc_start: 0.8227 (mt) cc_final: 0.8014 (mp) REVERT: C 558 LYS cc_start: 0.8527 (mtmt) cc_final: 0.8245 (mttt) REVERT: C 564 GLN cc_start: 0.7950 (mt0) cc_final: 0.7556 (mt0) REVERT: C 643 PHE cc_start: 0.7829 (t80) cc_final: 0.7405 (t80) REVERT: C 663 ASP cc_start: 0.7494 (t0) cc_final: 0.7266 (t0) REVERT: C 707 TYR cc_start: 0.8097 (t80) cc_final: 0.7545 (t80) REVERT: C 820 ASP cc_start: 0.7562 (t70) cc_final: 0.7174 (t0) REVERT: C 1029 MET cc_start: 0.8418 (tpp) cc_final: 0.8145 (ttm) REVERT: C 1086 LYS cc_start: 0.8237 (mmmt) cc_final: 0.7986 (mmmt) REVERT: C 1136 THR cc_start: 0.8829 (OUTLIER) cc_final: 0.8487 (p) REVERT: D 111 LEU cc_start: 0.5264 (OUTLIER) cc_final: 0.4861 (tm) REVERT: D 234 MET cc_start: -0.3702 (pmt) cc_final: -0.4137 (pmt) REVERT: F 160 MET cc_start: -0.1120 (ptp) cc_final: -0.1930 (mmm) outliers start: 126 outliers final: 102 residues processed: 532 average time/residue: 0.1927 time to fit residues: 164.0485 Evaluate side-chains 553 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 440 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 954 HIS Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 657 ASN Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU 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 177 ILE Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 32 TYR Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 226 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 260 optimal weight: 0.4980 chunk 120 optimal weight: 0.9980 chunk 233 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 199 optimal weight: 0.9990 chunk 184 optimal weight: 3.9990 chunk 232 optimal weight: 0.9980 chunk 181 optimal weight: 0.7980 chunk 173 optimal weight: 0.2980 chunk 163 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN A 394 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN B 641 ASN C 448 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.199193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.149171 restraints weight = 54733.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.149090 restraints weight = 29914.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.150675 restraints weight = 18121.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.152504 restraints weight = 12993.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.152353 restraints weight = 11132.624| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 30432 Z= 0.128 Angle : 0.638 15.636 41486 Z= 0.313 Chirality : 0.046 0.363 4711 Planarity : 0.004 0.069 5333 Dihedral : 6.252 79.552 4659 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 3.86 % Allowed : 19.42 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.13), residues: 3739 helix: 1.05 (0.21), residues: 663 sheet: -1.38 (0.19), residues: 722 loop : -2.44 (0.12), residues: 2354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1014 TYR 0.016 0.001 TYR B1067 PHE 0.036 0.001 PHE C 190 TRP 0.068 0.002 TRP C 104 HIS 0.007 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00297 (30365) covalent geometry : angle 0.62865 (41329) SS BOND : bond 0.00376 ( 44) SS BOND : angle 1.78585 ( 88) hydrogen bonds : bond 0.03159 ( 800) hydrogen bonds : angle 4.82900 ( 2136) link_NAG-ASN : bond 0.00335 ( 23) link_NAG-ASN : angle 1.90651 ( 69) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5652.72 seconds wall clock time: 98 minutes 24.05 seconds (5904.05 seconds total)