Starting phenix.real_space_refine on Sun Jul 5 18:44:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wor_32656/07_2026/7wor_32656.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wor_32656/07_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_32656/07_2026/7wor_32656.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wor_32656/07_2026/7wor_32656.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7wor_32656/07_2026/7wor_32656.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wor_32656/07_2026/7wor_32656.cif" model { file = "/net/cci-nas-00/data/ceres_data/7wor_32656/07_2026/7wor_32656.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wor_32656/07_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-6108/lib/python3.11/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 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 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 chiralities: 8 Time building chain proxies: 6.78, per 1000 atoms: 0.23 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: 2.47 Conformation dependent library (CDL) restraints added in 1.4 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: 0.95 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: 6.56 Time building geometry restraints manager: 3.39 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: 17010 16.86 - 33.72: 686 33.72 - 50.58: 114 50.58 - 67.45: 29 67.45 - 84.31: 4 Dihedral angle restraints: 17843 sinusoidal: 6852 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 17840 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: 3.090 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: 0.030 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 28.040 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.060 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 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 : 9.190 84.306 10673 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/Z covalent geometry : bond 0.00311 / 0.20 (30365) covalent geometry : angle 0.52557 / 0.29 (41329) SS BOND : bond 0.00126 / 0.08 ( 44) SS BOND : angle 0.50492 / 0.34 ( 88) hydrogen bonds : bond 0.14024 / 9.10 ( 800) hydrogen bonds : angle 6.13493 / 4.18 ( 2136) link_NAG-ASN : bond 0.00816 / 0.49 ( 23) link_NAG-ASN : angle 3.06291 / 1.93 ( 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 : 0.768 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: 0.1851 time to fit residues: 226.6544 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 : 1.056 ------------------------------------------------------------------------------- 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... A 49 HIS A 87 ASN A 173 GLN ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 B1005 GLN B1010 GLN B1048 HIS B1054 GLN 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 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 127 GLN 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: 85 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.201619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.148992 restraints weight = 54733.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.151339 restraints weight = 25916.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.153914 restraints weight = 14342.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.156018 restraints weight = 8957.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.155816 restraints weight = 7560.505| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 30432 Z= 0.219 Angle : 0.672 13.356 41486 Z= 0.330 Chirality : 0.048 0.639 4711 Planarity : 0.005 0.117 5333 Dihedral : 6.173 80.089 4252 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 4.88 % Allowed : 13.28 % Favored : 81.85 % 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: -3.42 (0.12), residues: 3739 helix: 0.18 (0.20), residues: 675 sheet: -2.09 (0.19), residues: 657 loop : -3.28 (0.10), residues: 2407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 34 TYR 0.027 0.001 TYR B1067 PHE 0.027 0.002 PHE A 55 TRP 0.017 0.001 TRP A 64 HIS 0.007 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.22 (30365) covalent geometry : angle 0.64823 / 0.32 (41329) SS BOND : bond 0.00439 / 0.26 ( 44) SS BOND : angle 2.63173 / 1.65 ( 88) hydrogen bonds : bond 0.03987 / 2.58 ( 800) hydrogen bonds : angle 4.92333 / 3.37 ( 2136) link_NAG-ASN : bond 0.00838 / 0.34 ( 23) link_NAG-ASN : angle 3.34609 / 2.00 ( 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 670 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 512 time to evaluate : 0.869 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: 0.8097 (p0) cc_final: 0.7885 (p0) REVERT: A 88 ASP cc_start: 0.5526 (p0) cc_final: 0.5087 (p0) REVERT: A 223 LEU cc_start: 0.7616 (mp) cc_final: 0.6785 (mp) REVERT: A 300 LYS cc_start: 0.8379 (mtmt) cc_final: 0.8070 (mtmm) REVERT: A 307 THR cc_start: 0.8023 (m) cc_final: 0.7712 (p) REVERT: A 396 TYR cc_start: 0.5965 (m-80) cc_final: 0.5266 (m-80) REVERT: A 516 GLU cc_start: 0.5758 (pt0) cc_final: 0.4813 (pt0) REVERT: A 546 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8313 (tt) REVERT: A 556 ASN cc_start: 0.8041 (p0) cc_final: 0.7638 (t0) REVERT: A 562 PHE cc_start: 0.7252 (p90) cc_final: 0.6901 (p90) REVERT: A 596 SER cc_start: 0.8810 (m) cc_final: 0.8558 (p) REVERT: A 602 THR cc_start: 0.7963 (m) cc_final: 0.7467 (p) REVERT: A 604 THR cc_start: 0.6916 (t) cc_final: 0.6253 (m) REVERT: A 615 VAL cc_start: 0.8551 (t) cc_final: 0.8307 (m) REVERT: A 737 ASP cc_start: 0.7013 (t0) cc_final: 0.6690 (t0) REVERT: A 790 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8184 (ptpp) REVERT: A 820 ASP cc_start: 0.7972 (m-30) cc_final: 0.7692 (t0) REVERT: A 864 LEU cc_start: 0.8615 (tp) cc_final: 0.8365 (tt) REVERT: A 921 LYS cc_start: 0.8433 (mmmt) cc_final: 0.7818 (mmmt) REVERT: A 950 ASP cc_start: 0.7169 (t70) cc_final: 0.6365 (t70) REVERT: A 954 HIS cc_start: 0.7131 (m-70) cc_final: 0.6760 (m170) REVERT: A 955 ASN cc_start: 0.8440 (t0) cc_final: 0.8061 (t0) REVERT: A 964 LYS cc_start: 0.8712 (tmtm) cc_final: 0.8493 (tppt) REVERT: A 984 LEU cc_start: 0.8856 (mt) cc_final: 0.8526 (mt) REVERT: A 988 GLU cc_start: 0.7664 (tp30) cc_final: 0.7106 (tp30) REVERT: A 1057 PRO cc_start: 0.8929 (Cg_exo) cc_final: 0.8617 (Cg_endo) REVERT: A 1081 ILE cc_start: 0.8516 (pt) cc_final: 0.8312 (mm) REVERT: B 41 LYS cc_start: 0.7569 (OUTLIER) cc_final: 0.7269 (mtpt) REVERT: B 62 VAL cc_start: 0.8163 (t) cc_final: 0.7881 (m) REVERT: B 105 ILE cc_start: 0.8382 (mm) cc_final: 0.7809 (tp) REVERT: B 106 PHE cc_start: 0.7164 (m-80) cc_final: 0.6915 (m-80) REVERT: B 186 ASN cc_start: 0.6661 (p0) cc_final: 0.5562 (p0) REVERT: B 188 ARG cc_start: 0.7582 (mtt-85) cc_final: 0.7027 (mtt-85) REVERT: B 193 LYS cc_start: 0.8176 (ttpt) cc_final: 0.7913 (ttpt) REVERT: B 200 LYS cc_start: 0.8614 (mttt) cc_final: 0.8241 (mttt) REVERT: B 201 ILE cc_start: 0.8907 (mt) cc_final: 0.8672 (pt) REVERT: B 267 VAL cc_start: 0.8471 (OUTLIER) cc_final: 0.8217 (p) REVERT: B 307 THR cc_start: 0.8053 (m) cc_final: 0.7608 (p) REVERT: B 329 PHE cc_start: 0.6003 (m-10) cc_final: 0.5737 (m-10) REVERT: B 403 ARG cc_start: 0.6234 (mtm-85) cc_final: 0.5637 (ttm170) REVERT: B 563 GLN cc_start: 0.6685 (pt0) cc_final: 0.6414 (pt0) REVERT: B 592 PHE cc_start: 0.7479 (p90) cc_final: 0.5242 (p90) REVERT: B 602 THR cc_start: 0.8591 (OUTLIER) cc_final: 0.8211 (p) REVERT: B 698 SER cc_start: 0.8415 (t) cc_final: 0.7864 (p) REVERT: B 726 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8215 (mp) REVERT: B 776 LYS cc_start: 0.8292 (ttpm) cc_final: 0.7824 (ttpp) REVERT: B 780 GLU cc_start: 0.7425 (tp30) cc_final: 0.7027 (tp30) REVERT: B 851 CYS cc_start: 0.8261 (t) cc_final: 0.7744 (p) REVERT: B 856 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8882 (tppp) REVERT: B 957 GLN cc_start: 0.7087 (tm-30) cc_final: 0.6725 (tm-30) REVERT: B 1019 ARG cc_start: 0.7988 (ttm110) cc_final: 0.7644 (ttp80) REVERT: C 55 PHE cc_start: 0.7156 (m-10) cc_final: 0.5324 (m-10) REVERT: C 102 ARG cc_start: 0.5905 (tpp-160) cc_final: 0.5565 (tpp-160) REVERT: C 104 TRP cc_start: 0.7055 (m-90) cc_final: 0.6811 (m-10) REVERT: C 106 PHE cc_start: 0.8012 (m-80) cc_final: 0.7726 (m-10) REVERT: C 118 LEU cc_start: 0.8645 (mp) cc_final: 0.8399 (mm) REVERT: C 129 LYS cc_start: 0.8307 (ttmt) cc_final: 0.7661 (tptt) REVERT: C 216 LEU cc_start: 0.8467 (mt) cc_final: 0.8179 (mm) REVERT: C 224 GLU cc_start: 0.7000 (pm20) cc_final: 0.6677 (pm20) REVERT: C 303 LEU cc_start: 0.8288 (tp) cc_final: 0.7932 (tp) REVERT: C 355 ARG cc_start: 0.6890 (OUTLIER) cc_final: 0.6643 (tmt90) REVERT: C 361 CYS cc_start: 0.5976 (OUTLIER) cc_final: 0.2868 (p) REVERT: C 362 VAL cc_start: 0.7560 (OUTLIER) cc_final: 0.7045 (m) REVERT: C 537 LYS cc_start: 0.8046 (tttp) cc_final: 0.7832 (tptm) REVERT: C 557 LYS cc_start: 0.8723 (mttm) cc_final: 0.8507 (mttm) REVERT: C 558 LYS cc_start: 0.8472 (mttt) cc_final: 0.8228 (mtpt) REVERT: C 707 TYR cc_start: 0.8098 (t80) cc_final: 0.7545 (t80) REVERT: C 754 LEU cc_start: 0.8625 (tp) cc_final: 0.8371 (tt) REVERT: C 820 ASP cc_start: 0.7637 (t70) cc_final: 0.7302 (t0) REVERT: C 821 LEU cc_start: 0.8906 (tp) cc_final: 0.8675 (tt) REVERT: C 851 CYS cc_start: 0.8028 (t) cc_final: 0.7689 (p) REVERT: C 854 LYS cc_start: 0.8241 (tmtt) cc_final: 0.8040 (tmtt) REVERT: C 868 GLU cc_start: 0.7475 (tp30) cc_final: 0.7268 (tp30) REVERT: C 914 ASN cc_start: 0.7756 (p0) cc_final: 0.7521 (p0) REVERT: C 950 ASP cc_start: 0.7321 (t70) cc_final: 0.6794 (t0) REVERT: C 978 ASN cc_start: 0.8539 (m-40) cc_final: 0.8163 (m-40) REVERT: C 1029 MET cc_start: 0.8550 (tpp) cc_final: 0.8173 (ttm) REVERT: C 1084 ASP cc_start: 0.7761 (t0) cc_final: 0.7479 (t0) REVERT: C 1097 SER cc_start: 0.9032 (t) cc_final: 0.8461 (p) REVERT: C 1111 GLU cc_start: 0.7422 (tt0) cc_final: 0.7220 (tt0) REVERT: C 1136 THR cc_start: 0.8907 (OUTLIER) cc_final: 0.8602 (p) REVERT: D 6 GLN cc_start: -0.0541 (OUTLIER) cc_final: -0.1331 (tp-100) REVERT: D 35 VAL cc_start: 0.2087 (OUTLIER) cc_final: 0.1770 (p) REVERT: D 90 CYS cc_start: 0.6020 (OUTLIER) cc_final: 0.5679 (t) REVERT: D 111 LEU cc_start: 0.5326 (OUTLIER) cc_final: 0.4913 (tm) REVERT: D 234 MET cc_start: -0.3841 (pmt) cc_final: -0.4364 (pmt) REVERT: E 207 MET cc_start: 0.3237 (ptp) cc_final: 0.1415 (ppp) REVERT: F 160 MET cc_start: -0.0766 (ptp) cc_final: -0.1707 (mmm) outliers start: 158 outliers final: 85 residues processed: 640 average time/residue: 0.1730 time to fit residues: 178.0083 Evaluate side-chains 566 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 466 time to evaluate : 1.096 ------------------------------------------------------------------------------- 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 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 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 980 ILE Chi-restraints excluded: chain B residue 1005 GLN 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 705 VAL 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 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 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: 0.9980 chunk 188 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 358 optimal weight: 0.0000 chunk 237 optimal weight: 9.9990 chunk 334 optimal weight: 20.0000 chunk 82 optimal weight: 5.9990 chunk 375 optimal weight: 6.9990 chunk 119 optimal weight: 0.4980 chunk 225 optimal weight: 3.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN A1005 GLN A1101 HIS B 409 GLN B 563 GLN B 607 GLN B 644 GLN B 690 GLN B 804 GLN B 965 GLN B1101 HIS C 563 GLN C 613 GLN C 641 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 GLN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.197250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.145204 restraints weight = 54326.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.146762 restraints weight = 24972.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.148079 restraints weight = 14995.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.149283 restraints weight = 11697.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.149354 restraints weight = 10219.413| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 30432 Z= 0.252 Angle : 0.682 14.046 41486 Z= 0.337 Chirality : 0.048 0.455 4711 Planarity : 0.005 0.102 5333 Dihedral : 6.158 80.339 4222 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 4.85 % Allowed : 15.16 % Favored : 79.99 % 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: -3.18 (0.12), residues: 3739 helix: 0.50 (0.21), residues: 659 sheet: -2.03 (0.18), residues: 663 loop : -3.11 (0.11), residues: 2417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 102 TYR 0.031 0.001 TYR A 655 PHE 0.026 0.002 PHE C 32 TRP 0.028 0.001 TRP A 64 HIS 0.010 0.001 HIS A1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.25 (30365) covalent geometry : angle 0.66590 / 0.33 (41329) SS BOND : bond 0.00386 / 0.24 ( 44) SS BOND : angle 2.22791 / 1.53 ( 88) hydrogen bonds : bond 0.04087 / 2.69 ( 800) hydrogen bonds : angle 5.02621 / 3.44 ( 2136) link_NAG-ASN : bond 0.00490 / 0.29 ( 23) link_NAG-ASN : angle 2.76400 / 1.67 ( 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 651 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 494 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 TYR cc_start: 0.7962 (m-10) cc_final: 0.7761 (m-10) REVERT: A 58 PHE cc_start: 0.6888 (m-10) cc_final: 0.6621 (m-10) REVERT: A 64 TRP cc_start: 0.7926 (t60) cc_final: 0.7705 (t60) REVERT: A 65 PHE cc_start: 0.6190 (m-80) cc_final: 0.5933 (m-80) REVERT: A 106 PHE cc_start: 0.7434 (m-80) cc_final: 0.6794 (m-80) REVERT: A 118 LEU cc_start: 0.6542 (OUTLIER) cc_final: 0.6294 (pp) REVERT: A 177 MET cc_start: 0.4348 (tpp) cc_final: 0.3984 (tpp) REVERT: A 223 LEU cc_start: 0.7555 (mp) cc_final: 0.6970 (mp) REVERT: A 307 THR cc_start: 0.8213 (m) cc_final: 0.7919 (p) REVERT: A 308 VAL cc_start: 0.8823 (p) cc_final: 0.8579 (m) REVERT: A 396 TYR cc_start: 0.6186 (m-80) cc_final: 0.5651 (m-80) REVERT: A 516 GLU cc_start: 0.5987 (pt0) cc_final: 0.5247 (pt0) REVERT: A 546 LEU cc_start: 0.8690 (tm) cc_final: 0.8361 (tt) REVERT: A 556 ASN cc_start: 0.8031 (p0) cc_final: 0.7801 (t0) REVERT: A 560 LEU cc_start: 0.8255 (tp) cc_final: 0.7896 (tp) REVERT: A 562 PHE cc_start: 0.7371 (p90) cc_final: 0.7053 (p90) REVERT: A 596 SER cc_start: 0.8916 (m) cc_final: 0.8576 (p) REVERT: A 602 THR cc_start: 0.8077 (m) cc_final: 0.7565 (p) REVERT: A 615 VAL cc_start: 0.8625 (t) cc_final: 0.8383 (m) REVERT: A 790 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8121 (ptpp) REVERT: A 820 ASP cc_start: 0.8007 (m-30) cc_final: 0.7754 (t0) REVERT: A 864 LEU cc_start: 0.8557 (tp) cc_final: 0.8242 (tt) REVERT: A 921 LYS cc_start: 0.8464 (mmmt) cc_final: 0.7871 (mmmt) REVERT: A 950 ASP cc_start: 0.7498 (t70) cc_final: 0.6249 (t0) REVERT: A 954 HIS cc_start: 0.7151 (m-70) cc_final: 0.6459 (m170) REVERT: A 955 ASN cc_start: 0.8388 (t0) cc_final: 0.8007 (t0) REVERT: A 969 LYS cc_start: 0.7679 (mppt) cc_final: 0.7298 (mmtp) REVERT: A 984 LEU cc_start: 0.8772 (mt) cc_final: 0.8465 (mt) REVERT: A 988 GLU cc_start: 0.7629 (tp30) cc_final: 0.7201 (tp30) REVERT: A 1057 PRO cc_start: 0.8932 (Cg_exo) cc_final: 0.8628 (Cg_endo) REVERT: B 62 VAL cc_start: 0.8342 (t) cc_final: 0.8109 (p) REVERT: B 64 TRP cc_start: 0.7823 (t60) cc_final: 0.7565 (t60) REVERT: B 105 ILE cc_start: 0.8542 (mm) cc_final: 0.8290 (tp) REVERT: B 186 ASN cc_start: 0.6737 (p0) cc_final: 0.6317 (p0) REVERT: B 193 LYS cc_start: 0.8136 (ttpt) cc_final: 0.7804 (ttmt) REVERT: B 200 LYS cc_start: 0.8621 (mttt) cc_final: 0.8293 (mttt) REVERT: B 201 ILE cc_start: 0.8939 (mt) cc_final: 0.8623 (pt) REVERT: B 204 LYS cc_start: 0.7816 (tppp) cc_final: 0.7444 (tppp) REVERT: B 205 HIS cc_start: 0.6864 (t-170) cc_final: 0.6569 (t-170) REVERT: B 224 GLU cc_start: 0.6971 (mm-30) cc_final: 0.6705 (mp0) REVERT: B 226 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7907 (tp) REVERT: B 267 VAL cc_start: 0.8404 (OUTLIER) cc_final: 0.8202 (p) REVERT: B 271 GLN cc_start: 0.8112 (tm-30) cc_final: 0.7548 (tm-30) REVERT: B 307 THR cc_start: 0.8025 (m) cc_final: 0.7634 (p) REVERT: B 329 PHE cc_start: 0.6301 (m-10) cc_final: 0.6080 (m-10) REVERT: B 403 ARG cc_start: 0.6682 (mtm-85) cc_final: 0.6114 (ttm170) REVERT: B 592 PHE cc_start: 0.7418 (p90) cc_final: 0.7197 (p90) REVERT: B 602 THR cc_start: 0.8628 (OUTLIER) cc_final: 0.8315 (p) REVERT: B 726 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8097 (mt) REVERT: B 773 GLU cc_start: 0.7478 (tp30) cc_final: 0.7030 (tp30) REVERT: B 776 LYS cc_start: 0.8194 (ttpm) cc_final: 0.7881 (ttpp) REVERT: B 780 GLU cc_start: 0.7650 (tp30) cc_final: 0.7426 (tp30) REVERT: B 803 SER cc_start: 0.8584 (m) cc_final: 0.8166 (p) REVERT: B 811 LYS cc_start: 0.8032 (tptp) cc_final: 0.7783 (tptp) REVERT: B 851 CYS cc_start: 0.8309 (t) cc_final: 0.7749 (p) REVERT: B 856 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8926 (tppp) REVERT: B 933 LYS cc_start: 0.8159 (mtmt) cc_final: 0.7934 (mtmt) REVERT: B 957 GLN cc_start: 0.7121 (tm-30) cc_final: 0.6669 (tm-30) REVERT: B 964 LYS cc_start: 0.8271 (tmmt) cc_final: 0.7466 (tmmt) REVERT: B 965 GLN cc_start: 0.7658 (mm110) cc_final: 0.6809 (mp10) REVERT: B 1019 ARG cc_start: 0.8055 (ttm110) cc_final: 0.7665 (ttp80) REVERT: B 1130 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8438 (tp) REVERT: C 55 PHE cc_start: 0.6926 (m-10) cc_final: 0.6599 (m-10) REVERT: C 80 ASP cc_start: 0.6933 (t0) cc_final: 0.6680 (t0) REVERT: C 104 TRP cc_start: 0.7235 (m-90) cc_final: 0.7028 (m-10) REVERT: C 106 PHE cc_start: 0.8108 (m-80) cc_final: 0.7647 (m-80) REVERT: C 118 LEU cc_start: 0.8796 (mp) cc_final: 0.8514 (mm) REVERT: C 129 LYS cc_start: 0.8340 (ttmt) cc_final: 0.7799 (tptt) REVERT: C 188 ARG cc_start: 0.5891 (OUTLIER) cc_final: 0.5552 (tpp80) REVERT: C 229 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7487 (pp) REVERT: C 269 TYR cc_start: 0.6843 (m-10) cc_final: 0.6524 (m-80) REVERT: C 303 LEU cc_start: 0.8318 (tp) cc_final: 0.7940 (tp) REVERT: C 361 CYS cc_start: 0.5666 (OUTLIER) cc_final: 0.3643 (p) REVERT: C 362 VAL cc_start: 0.7469 (OUTLIER) cc_final: 0.7102 (m) REVERT: C 557 LYS cc_start: 0.8770 (mttm) cc_final: 0.8559 (mttm) REVERT: C 558 LYS cc_start: 0.8626 (mttt) cc_final: 0.8345 (mtmt) REVERT: C 663 ASP cc_start: 0.7311 (t0) cc_final: 0.6935 (t0) REVERT: C 707 TYR cc_start: 0.8131 (t80) cc_final: 0.7600 (t80) REVERT: C 773 GLU cc_start: 0.7088 (tm-30) cc_final: 0.6402 (tm-30) REVERT: C 821 LEU cc_start: 0.8949 (tp) cc_final: 0.8601 (tt) REVERT: C 859 THR cc_start: 0.8338 (OUTLIER) cc_final: 0.8110 (p) REVERT: C 869 MET cc_start: 0.7813 (OUTLIER) cc_final: 0.7586 (mmm) REVERT: C 914 ASN cc_start: 0.7863 (p0) cc_final: 0.7474 (p0) REVERT: C 1031 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7730 (mt-10) REVERT: C 1084 ASP cc_start: 0.7981 (t0) cc_final: 0.7588 (t0) REVERT: C 1086 LYS cc_start: 0.8531 (mmmt) cc_final: 0.8307 (mmmt) REVERT: C 1097 SER cc_start: 0.8977 (t) cc_final: 0.8491 (p) REVERT: C 1111 GLU cc_start: 0.7504 (tt0) cc_final: 0.7281 (tt0) REVERT: C 1136 THR cc_start: 0.8833 (OUTLIER) cc_final: 0.8470 (p) REVERT: D 6 GLN cc_start: -0.0622 (OUTLIER) cc_final: -0.1309 (tp-100) REVERT: D 35 VAL cc_start: 0.2235 (OUTLIER) cc_final: 0.1908 (p) REVERT: D 90 CYS cc_start: 0.5768 (OUTLIER) cc_final: 0.5296 (t) REVERT: D 111 LEU cc_start: 0.5425 (OUTLIER) cc_final: 0.5013 (tm) REVERT: D 234 MET cc_start: -0.3629 (pmt) cc_final: -0.4238 (pmt) REVERT: E 174 VAL cc_start: 0.5084 (OUTLIER) cc_final: 0.4811 (t) REVERT: F 160 MET cc_start: -0.0907 (ptp) cc_final: -0.1836 (mmm) outliers start: 157 outliers final: 94 residues processed: 610 average time/residue: 0.1752 time to fit residues: 171.6456 Evaluate side-chains 569 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 455 time to evaluate : 1.004 ------------------------------------------------------------------------------- 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 130 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 538 CYS 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 790 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 991 VAL 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 118 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 267 VAL 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 726 ILE Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 772 VAL 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 954 HIS Chi-restraints excluded: chain B residue 975 SER 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 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 51 THR Chi-restraints excluded: chain C residue 54 LEU 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 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 705 VAL 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 826 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 869 MET 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 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 E residue 174 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 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 205 TYR 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: 4.9990 chunk 249 optimal weight: 40.0000 chunk 267 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 272 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 chunk 358 optimal weight: 0.0270 chunk 124 optimal weight: 0.8980 overall best weight: 0.9440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN A1005 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN B 641 ASN B 926 GLN B1002 GLN B1010 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 675 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN ** 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.199212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.145864 restraints weight = 54271.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.149088 restraints weight = 25201.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.151337 restraints weight = 13669.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.153201 restraints weight = 9245.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.153024 restraints weight = 8065.237| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 30432 Z= 0.151 Angle : 0.616 10.831 41486 Z= 0.302 Chirality : 0.046 0.414 4711 Planarity : 0.005 0.081 5333 Dihedral : 5.871 80.487 4210 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 5.03 % Allowed : 15.84 % Favored : 79.13 % 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: -2.95 (0.13), residues: 3739 helix: 0.65 (0.21), residues: 673 sheet: -1.85 (0.18), residues: 674 loop : -2.97 (0.11), residues: 2392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 34 TYR 0.024 0.001 TYR A 655 PHE 0.025 0.002 PHE B 759 TRP 0.022 0.001 TRP C 104 HIS 0.007 0.001 HIS A1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (30365) covalent geometry : angle 0.60288 / 0.30 (41329) SS BOND : bond 0.00350 / 0.25 ( 44) SS BOND : angle 1.91320 / 1.31 ( 88) hydrogen bonds : bond 0.03500 / 2.31 ( 800) hydrogen bonds : angle 4.89920 / 3.39 ( 2136) link_NAG-ASN : bond 0.00421 / 0.28 ( 23) link_NAG-ASN : angle 2.43814 / 1.46 ( 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 628 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 465 time to evaluate : 1.027 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 38 TYR cc_start: 0.7987 (m-10) cc_final: 0.7786 (m-10) REVERT: A 58 PHE cc_start: 0.6967 (m-10) cc_final: 0.6626 (m-10) REVERT: A 65 PHE cc_start: 0.6223 (m-80) cc_final: 0.5865 (m-80) REVERT: A 106 PHE cc_start: 0.7474 (m-80) cc_final: 0.7021 (m-80) REVERT: A 118 LEU cc_start: 0.6544 (OUTLIER) cc_final: 0.6324 (pp) REVERT: A 223 LEU cc_start: 0.7467 (mp) cc_final: 0.7035 (mp) REVERT: A 307 THR cc_start: 0.8203 (m) cc_final: 0.7927 (p) REVERT: A 308 VAL cc_start: 0.8803 (p) cc_final: 0.8542 (m) REVERT: A 396 TYR cc_start: 0.6236 (m-80) cc_final: 0.5716 (m-80) REVERT: A 516 GLU cc_start: 0.5988 (pt0) cc_final: 0.5305 (pt0) REVERT: A 546 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8446 (tt) REVERT: A 560 LEU cc_start: 0.8209 (tp) cc_final: 0.7848 (tp) REVERT: A 562 PHE cc_start: 0.7429 (p90) cc_final: 0.7056 (p90) REVERT: A 596 SER cc_start: 0.8902 (m) cc_final: 0.8560 (p) REVERT: A 602 THR cc_start: 0.7969 (OUTLIER) cc_final: 0.7471 (p) REVERT: A 743 CYS cc_start: 0.6306 (OUTLIER) cc_final: 0.5443 (t) REVERT: A 765 ARG cc_start: 0.7847 (ttm110) cc_final: 0.7489 (mtp-110) REVERT: A 790 LYS cc_start: 0.8584 (ptpp) cc_final: 0.8173 (ptpp) REVERT: A 820 ASP cc_start: 0.7977 (m-30) cc_final: 0.7724 (t0) REVERT: A 921 LYS cc_start: 0.8474 (mmmt) cc_final: 0.7883 (mmmt) REVERT: A 950 ASP cc_start: 0.7379 (t70) cc_final: 0.6044 (t0) REVERT: A 954 HIS cc_start: 0.7132 (m-70) cc_final: 0.6411 (m170) REVERT: A 955 ASN cc_start: 0.8380 (t0) cc_final: 0.7977 (t0) REVERT: A 969 LYS cc_start: 0.7663 (mppt) cc_final: 0.7311 (mmtm) REVERT: A 984 LEU cc_start: 0.8746 (mt) cc_final: 0.8481 (mt) REVERT: A 988 GLU cc_start: 0.7518 (tp30) cc_final: 0.7095 (tp30) REVERT: A 1057 PRO cc_start: 0.8896 (Cg_exo) cc_final: 0.8572 (Cg_endo) REVERT: B 62 VAL cc_start: 0.8363 (t) cc_final: 0.8110 (p) REVERT: B 193 LYS cc_start: 0.8130 (ttpt) cc_final: 0.7745 (ttmt) REVERT: B 200 LYS cc_start: 0.8649 (mttt) cc_final: 0.8282 (mttt) REVERT: B 205 HIS cc_start: 0.6916 (t-170) cc_final: 0.6563 (t-170) REVERT: B 224 GLU cc_start: 0.7032 (mm-30) cc_final: 0.6647 (mp0) REVERT: B 226 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7959 (tp) REVERT: B 227 VAL cc_start: 0.8964 (m) cc_final: 0.8656 (t) REVERT: B 271 GLN cc_start: 0.8059 (tm-30) cc_final: 0.7397 (tm-30) REVERT: B 281 GLU cc_start: 0.7683 (tp30) cc_final: 0.7228 (tp30) REVERT: B 307 THR cc_start: 0.8003 (m) cc_final: 0.7642 (p) REVERT: B 329 PHE cc_start: 0.6485 (m-10) cc_final: 0.6273 (m-10) REVERT: B 602 THR cc_start: 0.8570 (OUTLIER) cc_final: 0.8231 (p) REVERT: B 725 GLU cc_start: 0.7026 (tp30) cc_final: 0.6753 (tm-30) REVERT: B 726 ILE cc_start: 0.8664 (OUTLIER) cc_final: 0.8102 (mt) REVERT: B 773 GLU cc_start: 0.7449 (tp30) cc_final: 0.7132 (tp30) REVERT: B 780 GLU cc_start: 0.7675 (tp30) cc_final: 0.7307 (tp30) REVERT: B 803 SER cc_start: 0.8537 (m) cc_final: 0.8203 (p) REVERT: B 851 CYS cc_start: 0.8303 (t) cc_final: 0.7762 (p) REVERT: B 856 LYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8921 (tppp) REVERT: B 933 LYS cc_start: 0.8088 (mtmt) cc_final: 0.7865 (mtmt) REVERT: B 955 ASN cc_start: 0.8311 (m-40) cc_final: 0.7930 (m110) REVERT: B 957 GLN cc_start: 0.7059 (tm-30) cc_final: 0.6563 (tm-30) REVERT: B 964 LYS cc_start: 0.8319 (tmmt) cc_final: 0.7681 (tmmt) REVERT: B 965 GLN cc_start: 0.7619 (mm110) cc_final: 0.6532 (mm-40) REVERT: B 1019 ARG cc_start: 0.8079 (ttm110) cc_final: 0.7727 (ttp80) REVERT: C 34 ARG cc_start: 0.7069 (mtp85) cc_final: 0.6553 (mtt-85) REVERT: C 80 ASP cc_start: 0.6942 (t0) cc_final: 0.6630 (t0) REVERT: C 106 PHE cc_start: 0.8078 (m-80) cc_final: 0.7626 (m-80) REVERT: C 118 LEU cc_start: 0.8792 (mp) cc_final: 0.8511 (mm) REVERT: C 129 LYS cc_start: 0.8316 (ttmt) cc_final: 0.7775 (tptt) REVERT: C 190 PHE cc_start: 0.7387 (m-80) cc_final: 0.7079 (m-10) REVERT: C 229 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7437 (pp) REVERT: C 269 TYR cc_start: 0.6861 (m-10) cc_final: 0.6539 (m-80) REVERT: C 303 LEU cc_start: 0.8318 (tp) cc_final: 0.7933 (tp) REVERT: C 310 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8237 (ttpp) REVERT: C 361 CYS cc_start: 0.5341 (OUTLIER) cc_final: 0.3965 (p) REVERT: C 362 VAL cc_start: 0.7505 (OUTLIER) cc_final: 0.7180 (m) REVERT: C 537 LYS cc_start: 0.8339 (tttp) cc_final: 0.8079 (tptm) REVERT: C 558 LYS cc_start: 0.8584 (mttt) cc_final: 0.8091 (mttt) REVERT: C 564 GLN cc_start: 0.7982 (mt0) cc_final: 0.7623 (mt0) REVERT: C 663 ASP cc_start: 0.7334 (t0) cc_final: 0.6784 (t0) REVERT: C 707 TYR cc_start: 0.8118 (t80) cc_final: 0.7578 (t80) REVERT: C 820 ASP cc_start: 0.7667 (t70) cc_final: 0.7351 (t0) REVERT: C 869 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.7649 (mmm) REVERT: C 914 ASN cc_start: 0.7724 (p0) cc_final: 0.7513 (p0) REVERT: C 950 ASP cc_start: 0.7621 (m-30) cc_final: 0.7095 (m-30) REVERT: C 1029 MET cc_start: 0.8521 (tpp) cc_final: 0.8137 (ttm) REVERT: C 1076 THR cc_start: 0.9059 (m) cc_final: 0.8829 (p) REVERT: C 1086 LYS cc_start: 0.8477 (mmmt) cc_final: 0.8276 (mmmt) REVERT: C 1111 GLU cc_start: 0.7527 (tt0) cc_final: 0.7320 (tt0) REVERT: C 1136 THR cc_start: 0.8851 (OUTLIER) cc_final: 0.8518 (p) REVERT: D 35 VAL cc_start: 0.2468 (OUTLIER) cc_final: 0.2147 (p) REVERT: D 90 CYS cc_start: 0.5728 (OUTLIER) cc_final: 0.5307 (t) REVERT: D 111 LEU cc_start: 0.5397 (OUTLIER) cc_final: 0.4984 (tm) REVERT: D 208 MET cc_start: 0.2794 (tmm) cc_final: 0.2412 (tmm) REVERT: D 234 MET cc_start: -0.3666 (pmt) cc_final: -0.4271 (pmt) REVERT: E 236 TYR cc_start: 0.5647 (p90) cc_final: 0.5382 (p90) REVERT: F 160 MET cc_start: -0.0967 (ptp) cc_final: -0.1857 (mmm) outliers start: 163 outliers final: 97 residues processed: 588 average time/residue: 0.1718 time to fit residues: 162.2968 Evaluate side-chains 560 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 446 time to evaluate : 0.997 ------------------------------------------------------------------------------- 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 354 ASN 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 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 978 ASN 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 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 564 GLN 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 750 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 LYS 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 1104 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 191 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 312 ILE 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 776 LYS Chi-restraints excluded: chain C residue 869 MET 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 1072 GLU 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 247 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 205 TYR 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: 4.9990 chunk 229 optimal weight: 0.1980 chunk 75 optimal weight: 0.9980 chunk 342 optimal weight: 50.0000 chunk 325 optimal weight: 8.9990 chunk 162 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 238 optimal weight: 3.9990 chunk 351 optimal weight: 3.9990 chunk 155 optimal weight: 0.4980 chunk 151 optimal weight: 6.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.196167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.144650 restraints weight = 54414.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.146081 restraints weight = 27263.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.148075 restraints weight = 15180.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.148275 restraints weight = 12290.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.148308 restraints weight = 10284.874| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 30432 Z= 0.232 Angle : 0.655 10.435 41486 Z= 0.325 Chirality : 0.047 0.393 4711 Planarity : 0.005 0.063 5333 Dihedral : 5.832 80.310 4196 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.95 % Favored : 90.05 % Rotamer: Outliers : 4.97 % Allowed : 16.95 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z 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: -2.90 (0.13), residues: 3739 helix: 0.66 (0.21), residues: 664 sheet: -1.84 (0.18), residues: 680 loop : -2.91 (0.11), residues: 2395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 188 TYR 0.029 0.001 TYR A 655 PHE 0.032 0.002 PHE A 329 TRP 0.037 0.002 TRP C 104 HIS 0.009 0.001 HIS A1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.23 (30365) covalent geometry : angle 0.64232 / 0.32 (41329) SS BOND : bond 0.00384 / 0.25 ( 44) SS BOND : angle 1.94908 / 1.32 ( 88) hydrogen bonds : bond 0.03951 / 2.60 ( 800) hydrogen bonds : angle 5.04257 / 3.49 ( 2136) link_NAG-ASN : bond 0.00382 / 0.23 ( 23) link_NAG-ASN : angle 2.48845 / 1.51 ( 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 626 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 465 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 TYR cc_start: 0.8173 (m-10) cc_final: 0.7924 (m-10) REVERT: A 58 PHE cc_start: 0.7114 (m-10) cc_final: 0.6737 (m-10) REVERT: A 106 PHE cc_start: 0.7578 (m-80) cc_final: 0.7112 (m-80) REVERT: A 177 MET cc_start: 0.4117 (tpp) cc_final: 0.3825 (tpp) REVERT: A 190 PHE cc_start: 0.7520 (m-80) cc_final: 0.7107 (m-80) REVERT: A 223 LEU cc_start: 0.7479 (mp) cc_final: 0.6895 (mp) REVERT: A 265 TYR cc_start: 0.5869 (p90) cc_final: 0.5623 (p90) REVERT: A 300 LYS cc_start: 0.8433 (mttp) cc_final: 0.8124 (mttm) REVERT: A 307 THR cc_start: 0.8328 (m) cc_final: 0.8086 (p) REVERT: A 308 VAL cc_start: 0.8826 (p) cc_final: 0.8554 (m) REVERT: A 396 TYR cc_start: 0.6347 (m-80) cc_final: 0.5681 (m-80) REVERT: A 516 GLU cc_start: 0.5960 (pt0) cc_final: 0.5422 (pt0) REVERT: A 546 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8490 (tt) REVERT: A 560 LEU cc_start: 0.8237 (tp) cc_final: 0.8021 (tp) REVERT: A 562 PHE cc_start: 0.7505 (p90) cc_final: 0.7010 (p90) REVERT: A 596 SER cc_start: 0.8914 (m) cc_final: 0.8556 (p) REVERT: A 602 THR cc_start: 0.8116 (OUTLIER) cc_final: 0.7622 (p) REVERT: A 743 CYS cc_start: 0.6585 (OUTLIER) cc_final: 0.5692 (t) REVERT: A 790 LYS cc_start: 0.8562 (ptpp) cc_final: 0.8151 (ptpp) REVERT: A 820 ASP cc_start: 0.8093 (m-30) cc_final: 0.7819 (t0) REVERT: A 921 LYS cc_start: 0.8496 (mmmt) cc_final: 0.7897 (mmmt) REVERT: A 950 ASP cc_start: 0.7540 (t70) cc_final: 0.6816 (t0) REVERT: A 954 HIS cc_start: 0.7128 (m-70) cc_final: 0.6761 (m170) REVERT: A 955 ASN cc_start: 0.8434 (t0) cc_final: 0.8095 (t0) REVERT: A 969 LYS cc_start: 0.7817 (mppt) cc_final: 0.7457 (mmtm) REVERT: A 983 ARG cc_start: 0.7997 (ttp80) cc_final: 0.7716 (ttp80) REVERT: A 984 LEU cc_start: 0.8636 (tt) cc_final: 0.8160 (mt) REVERT: A 988 GLU cc_start: 0.7580 (tp30) cc_final: 0.7221 (tp30) REVERT: A 1057 PRO cc_start: 0.8968 (Cg_exo) cc_final: 0.8654 (Cg_endo) REVERT: B 64 TRP cc_start: 0.7699 (t60) cc_final: 0.7495 (t-100) REVERT: B 189 GLU cc_start: 0.6768 (mp0) cc_final: 0.6545 (mp0) REVERT: B 193 LYS cc_start: 0.8133 (ttpt) cc_final: 0.7818 (ttmt) REVERT: B 200 LYS cc_start: 0.8670 (mttt) cc_final: 0.8205 (mttp) REVERT: B 201 ILE cc_start: 0.9058 (mp) cc_final: 0.8730 (pt) REVERT: B 205 HIS cc_start: 0.7080 (t-170) cc_final: 0.6821 (t-170) REVERT: B 224 GLU cc_start: 0.7088 (mm-30) cc_final: 0.6764 (mp0) REVERT: B 226 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7801 (tp) REVERT: B 227 VAL cc_start: 0.8919 (m) cc_final: 0.8715 (m) REVERT: B 271 GLN cc_start: 0.8137 (tm-30) cc_final: 0.7547 (tm-30) REVERT: B 307 THR cc_start: 0.8192 (m) cc_final: 0.7834 (p) REVERT: B 403 ARG cc_start: 0.6856 (mtm-85) cc_final: 0.6285 (ttm170) REVERT: B 602 THR cc_start: 0.8645 (OUTLIER) cc_final: 0.8332 (p) REVERT: B 644 GLN cc_start: 0.8252 (tp-100) cc_final: 0.7809 (tp40) REVERT: B 697 MET cc_start: 0.7232 (OUTLIER) cc_final: 0.6981 (mtm) REVERT: B 726 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8171 (mt) REVERT: B 773 GLU cc_start: 0.7357 (tp30) cc_final: 0.6945 (tp30) REVERT: B 803 SER cc_start: 0.8625 (m) cc_final: 0.8269 (p) REVERT: B 851 CYS cc_start: 0.8386 (t) cc_final: 0.7788 (p) REVERT: B 856 LYS cc_start: 0.9216 (OUTLIER) cc_final: 0.8941 (tppp) REVERT: B 933 LYS cc_start: 0.8148 (mtmt) cc_final: 0.7854 (mtmt) REVERT: B 957 GLN cc_start: 0.7110 (tm-30) cc_final: 0.6609 (tm-30) REVERT: B 964 LYS cc_start: 0.8377 (tmmt) cc_final: 0.7853 (tmmt) REVERT: B 965 GLN cc_start: 0.7708 (mm110) cc_final: 0.6705 (mm-40) REVERT: B 1002 GLN cc_start: 0.8242 (mm-40) cc_final: 0.7821 (mm-40) REVERT: B 1014 ARG cc_start: 0.7446 (ttp-110) cc_final: 0.7218 (ttp-170) REVERT: B 1019 ARG cc_start: 0.8117 (ttm110) cc_final: 0.7762 (ttp80) REVERT: C 34 ARG cc_start: 0.7026 (mtp85) cc_final: 0.6496 (mtt-85) REVERT: C 41 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7973 (mtmt) REVERT: C 104 TRP cc_start: 0.7571 (m-10) cc_final: 0.7335 (m-10) REVERT: C 106 PHE cc_start: 0.8242 (m-80) cc_final: 0.7608 (m-80) REVERT: C 118 LEU cc_start: 0.8822 (mp) cc_final: 0.8543 (mm) REVERT: C 129 LYS cc_start: 0.8381 (ttmt) cc_final: 0.7826 (tptt) REVERT: C 169 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7955 (tm-30) REVERT: C 190 PHE cc_start: 0.7545 (m-80) cc_final: 0.7307 (m-10) REVERT: C 229 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7506 (pp) REVERT: C 269 TYR cc_start: 0.6959 (m-10) cc_final: 0.6605 (m-80) REVERT: C 303 LEU cc_start: 0.8270 (tp) cc_final: 0.7886 (tp) REVERT: C 361 CYS cc_start: 0.5397 (OUTLIER) cc_final: 0.4203 (p) REVERT: C 362 VAL cc_start: 0.7583 (OUTLIER) cc_final: 0.7344 (m) REVERT: C 537 LYS cc_start: 0.8507 (tttp) cc_final: 0.8222 (tptt) REVERT: C 558 LYS cc_start: 0.8557 (mttt) cc_final: 0.8273 (mttt) REVERT: C 564 GLN cc_start: 0.8132 (mt0) cc_final: 0.7751 (mt0) REVERT: C 663 ASP cc_start: 0.7422 (t0) cc_final: 0.7038 (t0) REVERT: C 707 TYR cc_start: 0.8127 (t80) cc_final: 0.7555 (t80) REVERT: C 773 GLU cc_start: 0.7194 (tm-30) cc_final: 0.6377 (tm-30) REVERT: C 1002 GLN cc_start: 0.7230 (tp40) cc_final: 0.6770 (tp40) REVERT: C 1086 LYS cc_start: 0.8553 (mmmt) cc_final: 0.8320 (mmmt) REVERT: C 1136 THR cc_start: 0.8859 (OUTLIER) cc_final: 0.8499 (p) REVERT: D 35 VAL cc_start: 0.2480 (OUTLIER) cc_final: 0.2144 (p) REVERT: D 90 CYS cc_start: 0.5962 (OUTLIER) cc_final: 0.5430 (t) REVERT: D 111 LEU cc_start: 0.5163 (OUTLIER) cc_final: 0.4789 (tm) REVERT: D 234 MET cc_start: -0.3749 (pmt) cc_final: -0.4184 (pmt) REVERT: E 236 TYR cc_start: 0.5576 (p90) cc_final: 0.5365 (p90) REVERT: F 160 MET cc_start: -0.1054 (ptp) cc_final: -0.1868 (mmm) outliers start: 161 outliers final: 107 residues processed: 588 average time/residue: 0.1744 time to fit residues: 165.1279 Evaluate side-chains 568 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 445 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 602 THR Chi-restraints excluded: chain A residue 616 ASN 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 1001 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 A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 120 VAL 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 564 GLN 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 697 MET Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 726 ILE 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 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 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 572 THR Chi-restraints excluded: chain C residue 587 ILE 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 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 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 201 ASN Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 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 205 TYR 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: 0.5980 chunk 6 optimal weight: 6.9990 chunk 218 optimal weight: 3.9990 chunk 33 optimal weight: 0.0670 chunk 225 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 157 optimal weight: 1.9990 chunk 356 optimal weight: 0.0020 chunk 118 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 89 optimal weight: 0.7980 overall best weight: 0.6928 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN A 935 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN C 81 ASN C 183 ASN C 205 HIS ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.198129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.145737 restraints weight = 54504.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.148329 restraints weight = 26843.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.150950 restraints weight = 14258.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.151170 restraints weight = 10083.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.151034 restraints weight = 8580.259| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.3929 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= 0.127 Angle : 0.611 9.764 41486 Z= 0.302 Chirality : 0.046 0.373 4711 Planarity : 0.004 0.053 5333 Dihedral : 5.653 80.200 4194 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 4.54 % Allowed : 17.75 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z 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: -2.67 (0.13), residues: 3739 helix: 0.89 (0.21), residues: 670 sheet: -1.63 (0.19), residues: 681 loop : -2.80 (0.11), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 63 TYR 0.029 0.001 TYR A 655 PHE 0.024 0.001 PHE A 643 TRP 0.023 0.001 TRP C 104 HIS 0.006 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (30365) covalent geometry : angle 0.60061 / 0.30 (41329) SS BOND : bond 0.00361 / 0.28 ( 44) SS BOND : angle 1.62853 / 1.08 ( 88) hydrogen bonds : bond 0.03375 / 2.24 ( 800) hydrogen bonds : angle 4.94989 / 3.44 ( 2136) link_NAG-ASN : bond 0.00395 / 0.26 ( 23) link_NAG-ASN : angle 2.27239 / 1.35 ( 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 608 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 461 time to evaluate : 0.985 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 38 TYR cc_start: 0.8078 (m-10) cc_final: 0.7842 (m-10) REVERT: A 58 PHE cc_start: 0.6995 (m-10) cc_final: 0.6607 (m-10) REVERT: A 106 PHE cc_start: 0.7557 (m-80) cc_final: 0.7174 (m-80) REVERT: A 177 MET cc_start: 0.4249 (tpp) cc_final: 0.3964 (tpp) REVERT: A 190 PHE cc_start: 0.7444 (m-80) cc_final: 0.7024 (m-80) REVERT: A 223 LEU cc_start: 0.7442 (mp) cc_final: 0.6924 (mp) REVERT: A 300 LYS cc_start: 0.8433 (mttp) cc_final: 0.7993 (mttm) REVERT: A 307 THR cc_start: 0.8158 (m) cc_final: 0.7895 (p) REVERT: A 308 VAL cc_start: 0.8801 (p) cc_final: 0.8497 (m) REVERT: A 329 PHE cc_start: 0.7083 (m-80) cc_final: 0.6822 (t80) REVERT: A 396 TYR cc_start: 0.6315 (m-80) cc_final: 0.5725 (m-80) REVERT: A 516 GLU cc_start: 0.5994 (pt0) cc_final: 0.5437 (pt0) REVERT: A 560 LEU cc_start: 0.8160 (tp) cc_final: 0.7937 (tp) REVERT: A 562 PHE cc_start: 0.7506 (p90) cc_final: 0.6996 (p90) REVERT: A 596 SER cc_start: 0.8917 (m) cc_final: 0.8542 (p) REVERT: A 602 THR cc_start: 0.7976 (OUTLIER) cc_final: 0.7448 (p) REVERT: A 643 PHE cc_start: 0.6796 (t80) cc_final: 0.6514 (t80) REVERT: A 743 CYS cc_start: 0.6665 (OUTLIER) cc_final: 0.5474 (t) REVERT: A 790 LYS cc_start: 0.8565 (ptpp) cc_final: 0.8185 (ptpp) REVERT: A 820 ASP cc_start: 0.7960 (m-30) cc_final: 0.7652 (t0) REVERT: A 868 GLU cc_start: 0.7252 (mm-30) cc_final: 0.6931 (mm-30) REVERT: A 921 LYS cc_start: 0.8467 (mmmt) cc_final: 0.7888 (mmmt) REVERT: A 950 ASP cc_start: 0.7390 (t70) cc_final: 0.6613 (t0) REVERT: A 954 HIS cc_start: 0.7041 (m-70) cc_final: 0.6614 (m170) REVERT: A 955 ASN cc_start: 0.8359 (t0) cc_final: 0.7983 (t0) REVERT: A 969 LYS cc_start: 0.7554 (mppt) cc_final: 0.7201 (mmtm) REVERT: A 983 ARG cc_start: 0.7984 (ttp80) cc_final: 0.7650 (ttp80) REVERT: A 984 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8083 (mt) REVERT: A 988 GLU cc_start: 0.7412 (tp30) cc_final: 0.7050 (tp30) REVERT: A 1057 PRO cc_start: 0.8929 (Cg_exo) cc_final: 0.8590 (Cg_endo) REVERT: B 193 LYS cc_start: 0.8090 (ttpt) cc_final: 0.7752 (ttmt) REVERT: B 200 LYS cc_start: 0.8666 (mttt) cc_final: 0.8266 (mptp) REVERT: B 201 ILE cc_start: 0.9129 (mp) cc_final: 0.8771 (pt) REVERT: B 204 LYS cc_start: 0.8189 (tppt) cc_final: 0.7976 (tptt) REVERT: B 205 HIS cc_start: 0.7044 (t-170) cc_final: 0.6771 (t-170) REVERT: B 224 GLU cc_start: 0.7112 (mm-30) cc_final: 0.6846 (mp0) REVERT: B 226 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7685 (tp) REVERT: B 227 VAL cc_start: 0.8779 (m) cc_final: 0.8431 (p) REVERT: B 271 GLN cc_start: 0.8101 (tm-30) cc_final: 0.7651 (tm-30) REVERT: B 307 THR cc_start: 0.8108 (m) cc_final: 0.7734 (p) REVERT: B 403 ARG cc_start: 0.6686 (mtm-85) cc_final: 0.6125 (ttm170) REVERT: B 602 THR cc_start: 0.8520 (OUTLIER) cc_final: 0.8171 (p) REVERT: B 644 GLN cc_start: 0.8249 (tp-100) cc_final: 0.7874 (tp40) REVERT: B 773 GLU cc_start: 0.7493 (tp30) cc_final: 0.6960 (tp30) REVERT: B 780 GLU cc_start: 0.7688 (tp30) cc_final: 0.7337 (tp30) REVERT: B 803 SER cc_start: 0.8550 (m) cc_final: 0.8272 (p) REVERT: B 851 CYS cc_start: 0.8326 (t) cc_final: 0.7746 (p) REVERT: B 856 LYS cc_start: 0.9113 (OUTLIER) cc_final: 0.8898 (tppp) REVERT: B 933 LYS cc_start: 0.8068 (mtmt) cc_final: 0.7517 (ttmm) REVERT: B 957 GLN cc_start: 0.7049 (tm-30) cc_final: 0.6575 (tm-30) REVERT: B 960 ASN cc_start: 0.8216 (m-40) cc_final: 0.7908 (t0) REVERT: B 965 GLN cc_start: 0.7660 (mm110) cc_final: 0.7424 (mm-40) REVERT: B 1019 ARG cc_start: 0.8053 (ttm110) cc_final: 0.7726 (ttp80) REVERT: C 34 ARG cc_start: 0.6955 (mtp85) cc_final: 0.6465 (mtt-85) REVERT: C 41 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7894 (mtmt) REVERT: C 104 TRP cc_start: 0.7476 (m-10) cc_final: 0.7258 (m-10) REVERT: C 106 PHE cc_start: 0.8215 (m-80) cc_final: 0.7606 (m-80) REVERT: C 129 LYS cc_start: 0.8370 (ttmt) cc_final: 0.7786 (tptt) REVERT: C 190 PHE cc_start: 0.7429 (m-80) cc_final: 0.7148 (m-10) REVERT: C 229 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7442 (pp) REVERT: C 269 TYR cc_start: 0.6934 (m-10) cc_final: 0.6626 (m-80) REVERT: C 303 LEU cc_start: 0.8268 (tp) cc_final: 0.7883 (tp) REVERT: C 361 CYS cc_start: 0.5161 (OUTLIER) cc_final: 0.4033 (p) REVERT: C 537 LYS cc_start: 0.8482 (tttp) cc_final: 0.8166 (tptt) REVERT: C 552 LEU cc_start: 0.8300 (mt) cc_final: 0.8056 (mp) REVERT: C 558 LYS cc_start: 0.8566 (mttt) cc_final: 0.8298 (mttt) REVERT: C 564 GLN cc_start: 0.7950 (mt0) cc_final: 0.7631 (mt0) REVERT: C 663 ASP cc_start: 0.7459 (t0) cc_final: 0.6956 (t0) REVERT: C 675 GLN cc_start: 0.7720 (mm110) cc_final: 0.7502 (mm110) REVERT: C 707 TYR cc_start: 0.8103 (t80) cc_final: 0.7509 (t80) REVERT: C 740 MET cc_start: 0.7545 (mtt) cc_final: 0.7339 (mtp) REVERT: C 1002 GLN cc_start: 0.7147 (tp40) cc_final: 0.6827 (tp40) REVERT: C 1029 MET cc_start: 0.8495 (tpp) cc_final: 0.8139 (ttm) REVERT: C 1031 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7617 (mt-10) REVERT: C 1086 LYS cc_start: 0.8400 (mmmt) cc_final: 0.8165 (mmmt) REVERT: C 1136 THR cc_start: 0.8848 (OUTLIER) cc_final: 0.8499 (p) REVERT: D 85 GLU cc_start: 0.3108 (OUTLIER) cc_final: 0.2767 (pm20) REVERT: D 111 LEU cc_start: 0.5084 (OUTLIER) cc_final: 0.4724 (tm) REVERT: D 208 MET cc_start: 0.2614 (tmm) cc_final: 0.2277 (tmm) REVERT: D 234 MET cc_start: -0.4046 (pmt) cc_final: -0.4308 (pmt) REVERT: F 160 MET cc_start: -0.1063 (ptp) cc_final: -0.1857 (mmm) outliers start: 147 outliers final: 101 residues processed: 570 average time/residue: 0.1716 time to fit residues: 157.1454 Evaluate side-chains 559 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 446 time to evaluate : 0.897 ------------------------------------------------------------------------------- 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 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 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 747 THR Chi-restraints excluded: chain A residue 751 ASN 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 B residue 50 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 120 VAL 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 318 PHE 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 535 LYS Chi-restraints excluded: chain B residue 564 GLN 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 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 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 191 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 241 LEU 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 572 THR Chi-restraints excluded: chain C residue 587 ILE 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 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 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 E residue 247 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 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: 0.4980 chunk 300 optimal weight: 0.9980 chunk 253 optimal weight: 0.6980 chunk 188 optimal weight: 0.6980 chunk 149 optimal weight: 0.9980 chunk 150 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 335 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 126 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN B 422 ASN B 641 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 233 ASN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.198128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.146996 restraints weight = 54426.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.147867 restraints weight = 27352.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.150062 restraints weight = 16027.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.151086 restraints weight = 10935.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.151139 restraints weight = 9850.514| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 30432 Z= 0.128 Angle : 0.607 9.700 41486 Z= 0.299 Chirality : 0.045 0.353 4711 Planarity : 0.004 0.051 5333 Dihedral : 5.574 79.997 4187 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 4.35 % Allowed : 18.03 % Favored : 77.62 % 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: -2.54 (0.13), residues: 3739 helix: 0.98 (0.21), residues: 667 sheet: -1.55 (0.19), residues: 682 loop : -2.70 (0.12), residues: 2390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 34 TYR 0.026 0.001 TYR A 655 PHE 0.024 0.001 PHE A 592 TRP 0.034 0.001 TRP B 64 HIS 0.005 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (30365) covalent geometry : angle 0.59672 / 0.30 (41329) SS BOND : bond 0.00322 / 0.23 ( 44) SS BOND : angle 1.64709 / 1.07 ( 88) hydrogen bonds : bond 0.03298 / 2.19 ( 800) hydrogen bonds : angle 4.88624 / 3.39 ( 2136) link_NAG-ASN : bond 0.00361 / 0.24 ( 23) link_NAG-ASN : angle 2.15230 / 1.27 ( 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 592 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 451 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 TYR cc_start: 0.8057 (m-10) cc_final: 0.7819 (m-10) REVERT: A 106 PHE cc_start: 0.7440 (m-80) cc_final: 0.7035 (m-80) REVERT: A 177 MET cc_start: 0.4436 (tpp) cc_final: 0.4187 (tpp) REVERT: A 190 PHE cc_start: 0.7515 (m-80) cc_final: 0.7112 (m-80) REVERT: A 223 LEU cc_start: 0.7375 (mp) cc_final: 0.6934 (mp) REVERT: A 300 LYS cc_start: 0.8420 (mttp) cc_final: 0.8139 (mttm) REVERT: A 307 THR cc_start: 0.8107 (m) cc_final: 0.7884 (p) REVERT: A 308 VAL cc_start: 0.8781 (p) cc_final: 0.8501 (m) REVERT: A 396 TYR cc_start: 0.6172 (m-80) cc_final: 0.5622 (m-80) REVERT: A 516 GLU cc_start: 0.6068 (pt0) cc_final: 0.5484 (pt0) REVERT: A 562 PHE cc_start: 0.7494 (p90) cc_final: 0.6977 (p90) REVERT: A 596 SER cc_start: 0.8963 (m) cc_final: 0.8528 (p) REVERT: A 602 THR cc_start: 0.8063 (OUTLIER) cc_final: 0.7534 (p) REVERT: A 675 GLN cc_start: 0.7204 (pp30) cc_final: 0.7001 (tm-30) REVERT: A 743 CYS cc_start: 0.6680 (OUTLIER) cc_final: 0.5497 (t) REVERT: A 790 LYS cc_start: 0.8552 (ptpp) cc_final: 0.8189 (ptpp) REVERT: A 820 ASP cc_start: 0.7992 (m-30) cc_final: 0.7662 (t0) REVERT: A 868 GLU cc_start: 0.7344 (mm-30) cc_final: 0.6961 (mm-30) REVERT: A 921 LYS cc_start: 0.8493 (mmmt) cc_final: 0.8030 (mmmt) REVERT: A 950 ASP cc_start: 0.7405 (t70) cc_final: 0.6630 (t0) REVERT: A 954 HIS cc_start: 0.7046 (m-70) cc_final: 0.6637 (m170) REVERT: A 955 ASN cc_start: 0.8378 (t0) cc_final: 0.8028 (t0) REVERT: A 969 LYS cc_start: 0.7631 (mppt) cc_final: 0.7276 (mmtm) REVERT: A 983 ARG cc_start: 0.7980 (ttp80) cc_final: 0.7599 (ttp80) REVERT: A 984 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.7948 (mt) REVERT: A 988 GLU cc_start: 0.7407 (tp30) cc_final: 0.7075 (tp30) REVERT: A 1005 GLN cc_start: 0.7979 (mm-40) cc_final: 0.7755 (tp40) REVERT: A 1057 PRO cc_start: 0.8903 (Cg_exo) cc_final: 0.8577 (Cg_endo) REVERT: B 105 ILE cc_start: 0.8536 (mm) cc_final: 0.8293 (pt) REVERT: B 188 ARG cc_start: 0.7766 (mtt-85) cc_final: 0.7408 (mtt-85) REVERT: B 193 LYS cc_start: 0.8096 (ttpt) cc_final: 0.7775 (ttmt) REVERT: B 200 LYS cc_start: 0.8684 (mttt) cc_final: 0.8302 (mptp) REVERT: B 201 ILE cc_start: 0.9128 (mp) cc_final: 0.8795 (pt) REVERT: B 224 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6826 (mp0) REVERT: B 226 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7554 (tp) REVERT: B 227 VAL cc_start: 0.8779 (m) cc_final: 0.8539 (m) REVERT: B 271 GLN cc_start: 0.8097 (tm-30) cc_final: 0.7541 (tm-30) REVERT: B 307 THR cc_start: 0.8103 (m) cc_final: 0.7750 (p) REVERT: B 403 ARG cc_start: 0.6486 (mtm-85) cc_final: 0.5973 (ttm170) REVERT: B 602 THR cc_start: 0.8542 (OUTLIER) cc_final: 0.8200 (p) REVERT: B 644 GLN cc_start: 0.8134 (tp-100) cc_final: 0.7761 (tp40) REVERT: B 773 GLU cc_start: 0.7472 (tp30) cc_final: 0.6896 (tp30) REVERT: B 780 GLU cc_start: 0.7686 (tp30) cc_final: 0.7332 (tp30) REVERT: B 803 SER cc_start: 0.8555 (m) cc_final: 0.8259 (p) REVERT: B 851 CYS cc_start: 0.8351 (t) cc_final: 0.7749 (p) REVERT: B 856 LYS cc_start: 0.9103 (OUTLIER) cc_final: 0.8873 (tppp) REVERT: B 933 LYS cc_start: 0.8112 (mtmt) cc_final: 0.7547 (ttmm) REVERT: B 957 GLN cc_start: 0.7069 (tm-30) cc_final: 0.6559 (tm-30) REVERT: B 960 ASN cc_start: 0.8219 (m-40) cc_final: 0.7905 (t0) REVERT: B 965 GLN cc_start: 0.7626 (mm110) cc_final: 0.7385 (mm-40) REVERT: B 1019 ARG cc_start: 0.8037 (ttm110) cc_final: 0.7710 (ttp80) REVERT: C 34 ARG cc_start: 0.6734 (mtp85) cc_final: 0.6327 (mtt-85) REVERT: C 41 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7921 (mtmt) REVERT: C 129 LYS cc_start: 0.8381 (ttmt) cc_final: 0.7823 (tptt) REVERT: C 169 GLU cc_start: 0.8087 (tm-30) cc_final: 0.7873 (tm-30) REVERT: C 190 PHE cc_start: 0.7415 (m-80) cc_final: 0.7200 (m-10) REVERT: C 229 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7456 (pp) REVERT: C 269 TYR cc_start: 0.6953 (m-10) cc_final: 0.6651 (m-80) REVERT: C 274 THR cc_start: 0.8535 (p) cc_final: 0.8187 (m) REVERT: C 303 LEU cc_start: 0.8248 (tp) cc_final: 0.8024 (tp) REVERT: C 361 CYS cc_start: 0.4986 (OUTLIER) cc_final: 0.3868 (p) REVERT: C 537 LYS cc_start: 0.8485 (tttp) cc_final: 0.8166 (tptt) REVERT: C 552 LEU cc_start: 0.8306 (mt) cc_final: 0.8072 (mp) REVERT: C 558 LYS cc_start: 0.8544 (mttt) cc_final: 0.8294 (mttt) REVERT: C 564 GLN cc_start: 0.8007 (mt0) cc_final: 0.7685 (mt0) REVERT: C 675 GLN cc_start: 0.7735 (mm110) cc_final: 0.7475 (mm110) REVERT: C 707 TYR cc_start: 0.8095 (t80) cc_final: 0.7497 (t80) REVERT: C 740 MET cc_start: 0.7500 (mtt) cc_final: 0.7298 (mtp) REVERT: C 1002 GLN cc_start: 0.7214 (tp40) cc_final: 0.6973 (tp40) REVERT: C 1005 GLN cc_start: 0.7992 (tp40) cc_final: 0.7785 (mm-40) REVERT: C 1029 MET cc_start: 0.8500 (tpp) cc_final: 0.8127 (ttm) REVERT: C 1086 LYS cc_start: 0.8378 (mmmt) cc_final: 0.8157 (mmmt) REVERT: C 1136 THR cc_start: 0.8854 (OUTLIER) cc_final: 0.8517 (p) REVERT: D 85 GLU cc_start: 0.2988 (OUTLIER) cc_final: 0.2626 (pm20) REVERT: D 90 CYS cc_start: 0.5981 (OUTLIER) cc_final: 0.5571 (t) REVERT: D 111 LEU cc_start: 0.5213 (OUTLIER) cc_final: 0.4823 (tm) REVERT: D 208 MET cc_start: 0.2724 (tmm) cc_final: 0.2343 (tmm) REVERT: D 234 MET cc_start: -0.4031 (pmt) cc_final: -0.4275 (pmt) REVERT: F 160 MET cc_start: -0.1012 (ptp) cc_final: -0.1878 (mmm) outliers start: 141 outliers final: 103 residues processed: 555 average time/residue: 0.1654 time to fit residues: 147.4576 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 : 0.830 ------------------------------------------------------------------------------- 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 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 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 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 B residue 50 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 318 PHE 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 535 LYS Chi-restraints excluded: chain B residue 564 GLN 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 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 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 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 191 VAL Chi-restraints excluded: chain C residue 229 LEU 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 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 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 1072 GLU 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 E residue 247 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 13 optimal weight: 7.9990 chunk 183 optimal weight: 1.9990 chunk 342 optimal weight: 50.0000 chunk 179 optimal weight: 0.5980 chunk 166 optimal weight: 0.6980 chunk 339 optimal weight: 50.0000 chunk 309 optimal weight: 6.9990 chunk 175 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN B 607 GLN B 644 GLN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 233 ASN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.196613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.144703 restraints weight = 54484.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.146463 restraints weight = 26718.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.147675 restraints weight = 15605.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.148430 restraints weight = 12430.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.148589 restraints weight = 10661.441| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 30432 Z= 0.179 Angle : 0.663 25.546 41486 Z= 0.326 Chirality : 0.047 0.403 4711 Planarity : 0.004 0.063 5333 Dihedral : 5.696 79.849 4187 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 4.20 % Allowed : 18.22 % Favored : 77.59 % 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: -2.50 (0.13), residues: 3739 helix: 0.94 (0.21), residues: 659 sheet: -1.54 (0.19), residues: 685 loop : -2.63 (0.12), residues: 2395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B1014 TYR 0.032 0.001 TYR A 655 PHE 0.033 0.002 PHE C 65 TRP 0.037 0.002 TRP B 64 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 (30365) covalent geometry : angle 0.65088 / 0.32 (41329) SS BOND : bond 0.00561 / 0.44 ( 44) SS BOND : angle 2.13589 / 1.42 ( 88) hydrogen bonds : bond 0.03593 / 2.37 ( 800) hydrogen bonds : angle 4.96251 / 3.43 ( 2136) link_NAG-ASN : bond 0.00335 / 0.21 ( 23) link_NAG-ASN : angle 2.20642 / 1.33 ( 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 597 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 461 time to evaluate : 1.029 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: A 38 TYR cc_start: 0.8129 (m-10) cc_final: 0.7911 (m-10) REVERT: A 106 PHE cc_start: 0.7541 (m-80) cc_final: 0.7099 (m-80) REVERT: A 177 MET cc_start: 0.4463 (tpp) cc_final: 0.4182 (tpp) REVERT: A 190 PHE cc_start: 0.7583 (m-80) cc_final: 0.7067 (m-80) REVERT: A 223 LEU cc_start: 0.7374 (mp) cc_final: 0.6904 (mp) REVERT: A 300 LYS cc_start: 0.8406 (mttp) cc_final: 0.8102 (mttm) REVERT: A 307 THR cc_start: 0.8195 (m) cc_final: 0.7978 (p) REVERT: A 396 TYR cc_start: 0.6287 (m-80) cc_final: 0.5973 (m-80) REVERT: A 429 PHE cc_start: 0.6929 (t80) cc_final: 0.5834 (t80) REVERT: A 528 LYS cc_start: 0.8212 (pttp) cc_final: 0.8010 (pttp) REVERT: A 562 PHE cc_start: 0.7558 (p90) cc_final: 0.7246 (p90) REVERT: A 596 SER cc_start: 0.9009 (m) cc_final: 0.8514 (p) REVERT: A 602 THR cc_start: 0.8192 (OUTLIER) cc_final: 0.7630 (p) REVERT: A 743 CYS cc_start: 0.6751 (OUTLIER) cc_final: 0.5671 (t) REVERT: A 790 LYS cc_start: 0.8554 (ptpp) cc_final: 0.8167 (ptpp) REVERT: A 820 ASP cc_start: 0.8027 (m-30) cc_final: 0.7660 (t0) REVERT: A 825 LYS cc_start: 0.8857 (mtpp) cc_final: 0.8592 (tttt) REVERT: A 868 GLU cc_start: 0.7309 (mm-30) cc_final: 0.6941 (mm-30) REVERT: A 921 LYS cc_start: 0.8514 (mmmt) cc_final: 0.8050 (mmmt) REVERT: A 950 ASP cc_start: 0.7443 (t70) cc_final: 0.6695 (t0) REVERT: A 954 HIS cc_start: 0.7056 (m-70) cc_final: 0.6595 (m170) REVERT: A 955 ASN cc_start: 0.8412 (t0) cc_final: 0.8088 (t0) REVERT: A 969 LYS cc_start: 0.7707 (mppt) cc_final: 0.7282 (mmtp) REVERT: A 983 ARG cc_start: 0.8030 (ttp80) cc_final: 0.7819 (ttp80) REVERT: A 984 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8198 (mt) REVERT: A 988 GLU cc_start: 0.7550 (tp30) cc_final: 0.7159 (tp30) REVERT: A 1005 GLN cc_start: 0.7975 (mm-40) cc_final: 0.7742 (tp40) REVERT: A 1057 PRO cc_start: 0.8903 (Cg_exo) cc_final: 0.8601 (Cg_endo) REVERT: B 105 ILE cc_start: 0.8605 (mm) cc_final: 0.8315 (pt) REVERT: B 188 ARG cc_start: 0.7769 (mtt-85) cc_final: 0.6782 (mtm-85) REVERT: B 193 LYS cc_start: 0.8094 (ttpt) cc_final: 0.7781 (ttmt) REVERT: B 200 LYS cc_start: 0.8699 (mttt) cc_final: 0.8317 (mptp) REVERT: B 201 ILE cc_start: 0.9129 (mp) cc_final: 0.8823 (pt) REVERT: B 224 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6864 (mp0) REVERT: B 226 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7656 (tp) REVERT: B 228 ASP cc_start: 0.7617 (t70) cc_final: 0.7390 (t0) REVERT: B 271 GLN cc_start: 0.8138 (tm-30) cc_final: 0.7553 (tm-30) REVERT: B 307 THR cc_start: 0.8246 (m) cc_final: 0.7881 (p) REVERT: B 403 ARG cc_start: 0.6843 (mtm-85) cc_final: 0.6207 (ttm170) REVERT: B 602 THR cc_start: 0.8563 (OUTLIER) cc_final: 0.8219 (p) REVERT: B 773 GLU cc_start: 0.7499 (tp30) cc_final: 0.6950 (tp30) REVERT: B 803 SER cc_start: 0.8669 (m) cc_final: 0.8372 (p) REVERT: B 819 GLU cc_start: 0.7347 (mm-30) cc_final: 0.7111 (mm-30) REVERT: B 851 CYS cc_start: 0.8387 (t) cc_final: 0.7773 (p) REVERT: B 856 LYS cc_start: 0.9131 (OUTLIER) cc_final: 0.8916 (tppp) REVERT: B 933 LYS cc_start: 0.8110 (mtmt) cc_final: 0.7823 (mtmt) REVERT: B 957 GLN cc_start: 0.7107 (tm-30) cc_final: 0.6631 (tm-30) REVERT: B 960 ASN cc_start: 0.8250 (m-40) cc_final: 0.7945 (t0) REVERT: B 965 GLN cc_start: 0.7699 (mm110) cc_final: 0.7464 (mm-40) REVERT: B 1019 ARG cc_start: 0.8073 (ttm110) cc_final: 0.7753 (ttp80) REVERT: C 34 ARG cc_start: 0.6849 (mtp85) cc_final: 0.6309 (mtt-85) REVERT: C 41 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7864 (mtmt) REVERT: C 129 LYS cc_start: 0.8381 (ttmt) cc_final: 0.7597 (tppt) REVERT: C 169 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7669 (tm-30) REVERT: C 229 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7491 (pp) REVERT: C 269 TYR cc_start: 0.6969 (m-10) cc_final: 0.6664 (m-80) REVERT: C 303 LEU cc_start: 0.8090 (tp) cc_final: 0.7761 (tp) REVERT: C 355 ARG cc_start: 0.7003 (OUTLIER) cc_final: 0.6403 (tmt90) REVERT: C 362 VAL cc_start: 0.7560 (OUTLIER) cc_final: 0.7325 (m) REVERT: C 489 TYR cc_start: 0.2454 (OUTLIER) cc_final: -0.0250 (m-80) REVERT: C 537 LYS cc_start: 0.8533 (tttp) cc_final: 0.8220 (tptm) REVERT: C 552 LEU cc_start: 0.8333 (mt) cc_final: 0.8091 (mp) REVERT: C 558 LYS cc_start: 0.8571 (mttt) cc_final: 0.8333 (mttt) REVERT: C 564 GLN cc_start: 0.8087 (mt0) cc_final: 0.7792 (mt0) REVERT: C 707 TYR cc_start: 0.8094 (t80) cc_final: 0.7534 (t80) REVERT: C 773 GLU cc_start: 0.7154 (tm-30) cc_final: 0.6390 (tm-30) REVERT: C 848 ASP cc_start: 0.8017 (t70) cc_final: 0.7769 (t0) REVERT: C 1002 GLN cc_start: 0.7221 (tp40) cc_final: 0.6955 (tp40) REVERT: C 1031 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7623 (mt-10) REVERT: C 1136 THR cc_start: 0.8858 (OUTLIER) cc_final: 0.8519 (p) REVERT: D 90 CYS cc_start: 0.6044 (OUTLIER) cc_final: 0.5535 (t) REVERT: D 111 LEU cc_start: 0.5207 (OUTLIER) cc_final: 0.4832 (tm) REVERT: D 234 MET cc_start: -0.4008 (pmt) cc_final: -0.4252 (pmt) REVERT: F 160 MET cc_start: -0.1184 (ptp) cc_final: -0.1944 (mmm) outliers start: 136 outliers final: 104 residues processed: 557 average time/residue: 0.1726 time to fit residues: 153.7127 Evaluate side-chains 570 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 451 time to evaluate : 1.558 ------------------------------------------------------------------------------- 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 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 549 THR 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 747 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 759 PHE 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 90 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 318 PHE 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 564 GLN 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 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 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 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 191 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 241 LEU 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 489 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 572 THR 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 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 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 E residue 247 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 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 155 VAL 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: 0.6980 chunk 359 optimal weight: 20.0000 chunk 157 optimal weight: 1.9990 chunk 176 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 169 optimal weight: 3.9990 chunk 276 optimal weight: 0.4980 chunk 215 optimal weight: 0.9990 chunk 310 optimal weight: 1.9990 chunk 351 optimal weight: 20.0000 chunk 140 optimal weight: 5.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN A1113 GLN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.196274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.143739 restraints weight = 54481.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.146305 restraints weight = 26840.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.149006 restraints weight = 14088.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.149199 restraints weight = 9998.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.149031 restraints weight = 8629.025| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.4418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 30432 Z= 0.180 Angle : 0.680 22.111 41486 Z= 0.335 Chirality : 0.047 0.502 4711 Planarity : 0.005 0.060 5333 Dihedral : 5.720 79.779 4186 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 3.95 % Allowed : 19.08 % Favored : 76.97 % Cbeta Deviations : 0.03 % 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: -2.47 (0.13), residues: 3739 helix: 0.91 (0.21), residues: 660 sheet: -1.44 (0.19), residues: 676 loop : -2.62 (0.12), residues: 2403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 102 TYR 0.031 0.001 TYR A 655 PHE 0.043 0.002 PHE C 190 TRP 0.053 0.002 TRP C 104 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 (30365) covalent geometry : angle 0.66605 / 0.33 (41329) SS BOND : bond 0.00577 / 0.46 ( 44) SS BOND : angle 2.45619 / 1.58 ( 88) hydrogen bonds : bond 0.03612 / 2.39 ( 800) hydrogen bonds : angle 5.01171 / 3.46 ( 2136) link_NAG-ASN : bond 0.00329 / 0.21 ( 23) link_NAG-ASN : angle 2.19325 / 1.32 ( 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 581 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 453 time to evaluate : 1.037 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: A 38 TYR cc_start: 0.8159 (m-10) cc_final: 0.7938 (m-10) REVERT: A 106 PHE cc_start: 0.7542 (m-80) cc_final: 0.7134 (m-80) REVERT: A 177 MET cc_start: 0.4526 (tpp) cc_final: 0.4269 (tpp) REVERT: A 190 PHE cc_start: 0.7645 (m-80) cc_final: 0.7068 (m-80) REVERT: A 223 LEU cc_start: 0.7379 (mp) cc_final: 0.6916 (mp) REVERT: A 298 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7320 (tp30) REVERT: A 300 LYS cc_start: 0.8402 (mttp) cc_final: 0.8174 (mttm) REVERT: A 396 TYR cc_start: 0.6317 (m-80) cc_final: 0.6002 (m-80) REVERT: A 429 PHE cc_start: 0.7044 (t80) cc_final: 0.5971 (t80) REVERT: A 528 LYS cc_start: 0.8161 (pttp) cc_final: 0.7934 (pttp) REVERT: A 562 PHE cc_start: 0.7589 (p90) cc_final: 0.7310 (p90) REVERT: A 596 SER cc_start: 0.9004 (m) cc_final: 0.8525 (p) REVERT: A 602 THR cc_start: 0.8321 (m) cc_final: 0.7850 (p) REVERT: A 743 CYS cc_start: 0.6714 (OUTLIER) cc_final: 0.5698 (t) REVERT: A 790 LYS cc_start: 0.8575 (ptpp) cc_final: 0.8166 (ptpp) REVERT: A 820 ASP cc_start: 0.7944 (m-30) cc_final: 0.7619 (t0) REVERT: A 825 LYS cc_start: 0.8856 (mtpp) cc_final: 0.8594 (tttt) REVERT: A 868 GLU cc_start: 0.7284 (mm-30) cc_final: 0.6904 (mm-30) REVERT: A 921 LYS cc_start: 0.8514 (mmmt) cc_final: 0.7902 (mmmt) REVERT: A 950 ASP cc_start: 0.7430 (t70) cc_final: 0.6668 (t0) REVERT: A 954 HIS cc_start: 0.7049 (m-70) cc_final: 0.6622 (m170) REVERT: A 955 ASN cc_start: 0.8383 (t0) cc_final: 0.8049 (t0) REVERT: A 969 LYS cc_start: 0.7750 (mppt) cc_final: 0.7444 (mmtm) REVERT: A 984 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8159 (mt) REVERT: A 988 GLU cc_start: 0.7513 (tp30) cc_final: 0.7126 (tp30) REVERT: A 1005 GLN cc_start: 0.7938 (mm-40) cc_final: 0.7732 (tp40) REVERT: A 1057 PRO cc_start: 0.8914 (Cg_exo) cc_final: 0.8600 (Cg_endo) REVERT: B 105 ILE cc_start: 0.8624 (mm) cc_final: 0.8309 (pt) REVERT: B 188 ARG cc_start: 0.7755 (mtt-85) cc_final: 0.7018 (mtm-85) REVERT: B 193 LYS cc_start: 0.8098 (ttpt) cc_final: 0.7772 (ttmt) REVERT: B 200 LYS cc_start: 0.8674 (mttt) cc_final: 0.8329 (mptp) REVERT: B 201 ILE cc_start: 0.9172 (mp) cc_final: 0.8830 (pt) REVERT: B 224 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6584 (mp0) REVERT: B 271 GLN cc_start: 0.8162 (tm-30) cc_final: 0.7553 (tm-30) REVERT: B 307 THR cc_start: 0.8288 (m) cc_final: 0.7896 (p) REVERT: B 403 ARG cc_start: 0.6855 (mtm-85) cc_final: 0.6193 (ttm170) REVERT: B 410 ILE cc_start: 0.7975 (mm) cc_final: 0.7707 (mp) REVERT: B 602 THR cc_start: 0.8599 (OUTLIER) cc_final: 0.8278 (p) REVERT: B 773 GLU cc_start: 0.7491 (tp30) cc_final: 0.6941 (tp30) REVERT: B 803 SER cc_start: 0.8700 (m) cc_final: 0.8375 (p) REVERT: B 851 CYS cc_start: 0.8356 (t) cc_final: 0.7765 (p) REVERT: B 933 LYS cc_start: 0.8109 (mtmt) cc_final: 0.7840 (mtmt) REVERT: B 957 GLN cc_start: 0.7110 (tm-30) cc_final: 0.6616 (tm-30) REVERT: B 960 ASN cc_start: 0.8273 (m-40) cc_final: 0.7956 (t0) REVERT: B 965 GLN cc_start: 0.7747 (mm110) cc_final: 0.7463 (mm-40) REVERT: B 1019 ARG cc_start: 0.8075 (ttm110) cc_final: 0.7764 (ttp80) REVERT: C 34 ARG cc_start: 0.6791 (mtp85) cc_final: 0.6209 (mtt-85) REVERT: C 41 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7981 (mtmt) REVERT: C 190 PHE cc_start: 0.7789 (m-10) cc_final: 0.7549 (m-10) REVERT: C 229 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7522 (pp) REVERT: C 274 THR cc_start: 0.8417 (p) cc_final: 0.8139 (m) REVERT: C 303 LEU cc_start: 0.8144 (tp) cc_final: 0.7785 (tp) REVERT: C 355 ARG cc_start: 0.7005 (OUTLIER) cc_final: 0.6459 (tmt90) REVERT: C 489 TYR cc_start: 0.2585 (OUTLIER) cc_final: -0.0094 (m-80) REVERT: C 552 LEU cc_start: 0.8318 (mt) cc_final: 0.8099 (mp) REVERT: C 558 LYS cc_start: 0.8593 (mttt) cc_final: 0.8326 (mttt) REVERT: C 564 GLN cc_start: 0.8101 (mt0) cc_final: 0.7773 (mt0) REVERT: C 707 TYR cc_start: 0.8102 (t80) cc_final: 0.7535 (t80) REVERT: C 773 GLU cc_start: 0.7208 (tm-30) cc_final: 0.6427 (tm-30) REVERT: C 1136 THR cc_start: 0.8845 (OUTLIER) cc_final: 0.8505 (p) REVERT: D 111 LEU cc_start: 0.5167 (OUTLIER) cc_final: 0.4782 (tm) REVERT: D 208 MET cc_start: 0.2619 (tmm) cc_final: 0.2337 (tmm) REVERT: D 234 MET cc_start: -0.3998 (pmt) cc_final: -0.4247 (pmt) REVERT: F 160 MET cc_start: -0.1247 (ptp) cc_final: -0.1960 (mmm) outliers start: 128 outliers final: 105 residues processed: 548 average time/residue: 0.1727 time to fit residues: 151.5148 Evaluate side-chains 553 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 438 time to evaluate : 0.736 ------------------------------------------------------------------------------- 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 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 549 THR Chi-restraints excluded: chain A residue 616 ASN 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 1001 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 90 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 318 PHE 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 564 GLN 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 730 SER Chi-restraints excluded: chain B residue 746 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 1104 VAL 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 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 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 489 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 572 THR 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 791 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 907 ASN 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 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 E residue 247 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 155 VAL 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: 0.9980 chunk 255 optimal weight: 0.7980 chunk 342 optimal weight: 0.0870 chunk 17 optimal weight: 9.9990 chunk 180 optimal weight: 0.9980 chunk 281 optimal weight: 0.6980 chunk 42 optimal weight: 9.9990 chunk 189 optimal weight: 0.9980 chunk 266 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN A1101 HIS B 205 HIS ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN B 955 ASN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4433 r_free = 0.4433 target = 0.197450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.146992 restraints weight = 54158.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.147508 restraints weight = 27918.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.149567 restraints weight = 16439.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.149889 restraints weight = 11925.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.150145 restraints weight = 10752.846| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.4461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30432 Z= 0.133 Angle : 0.663 18.451 41486 Z= 0.326 Chirality : 0.046 0.430 4711 Planarity : 0.005 0.058 5333 Dihedral : 5.627 79.694 4181 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 3.89 % Allowed : 19.23 % Favored : 76.88 % 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: -2.36 (0.13), residues: 3739 helix: 1.03 (0.21), residues: 655 sheet: -1.37 (0.20), residues: 654 loop : -2.54 (0.12), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG B1107 TYR 0.023 0.001 TYR A 655 PHE 0.043 0.001 PHE C 190 TRP 0.066 0.002 TRP C 104 HIS 0.005 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (30365) covalent geometry : angle 0.65101 / 0.32 (41329) SS BOND : bond 0.00454 / 0.36 ( 44) SS BOND : angle 2.15834 / 1.39 ( 88) hydrogen bonds : bond 0.03350 / 2.22 ( 800) hydrogen bonds : angle 4.95842 / 3.43 ( 2136) link_NAG-ASN : bond 0.00351 / 0.23 ( 23) link_NAG-ASN : angle 2.07261 / 1.23 ( 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 570 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 444 time to evaluate : 0.813 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: A 106 PHE cc_start: 0.7438 (m-80) cc_final: 0.7073 (m-80) REVERT: A 190 PHE cc_start: 0.7685 (m-80) cc_final: 0.7132 (m-80) REVERT: A 223 LEU cc_start: 0.7336 (mp) cc_final: 0.6913 (mp) REVERT: A 300 LYS cc_start: 0.8401 (mttp) cc_final: 0.8199 (mttm) REVERT: A 429 PHE cc_start: 0.7053 (t80) cc_final: 0.6108 (t80) REVERT: A 562 PHE cc_start: 0.7583 (p90) cc_final: 0.7316 (p90) REVERT: A 596 SER cc_start: 0.9042 (m) cc_final: 0.8538 (p) REVERT: A 602 THR cc_start: 0.8315 (m) cc_final: 0.7850 (p) REVERT: A 743 CYS cc_start: 0.6655 (OUTLIER) cc_final: 0.5442 (t) REVERT: A 790 LYS cc_start: 0.8563 (ptpp) cc_final: 0.8156 (ptpp) REVERT: A 819 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7352 (mt-10) REVERT: A 820 ASP cc_start: 0.7948 (m-30) cc_final: 0.7654 (t0) REVERT: A 825 LYS cc_start: 0.8861 (mtpp) cc_final: 0.8593 (tttt) REVERT: A 868 GLU cc_start: 0.7329 (mm-30) cc_final: 0.6909 (mm-30) REVERT: A 921 LYS cc_start: 0.8510 (mmmt) cc_final: 0.7893 (mmmt) REVERT: A 950 ASP cc_start: 0.7411 (t70) cc_final: 0.6637 (t0) REVERT: A 954 HIS cc_start: 0.7023 (m-70) cc_final: 0.6585 (m170) REVERT: A 955 ASN cc_start: 0.8389 (t0) cc_final: 0.8059 (t0) REVERT: A 969 LYS cc_start: 0.7625 (mppt) cc_final: 0.7319 (mmtm) REVERT: A 981 PHE cc_start: 0.7607 (m-10) cc_final: 0.7277 (m-10) REVERT: A 983 ARG cc_start: 0.8072 (ttp80) cc_final: 0.7527 (ttp80) REVERT: A 984 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.7985 (mt) REVERT: A 988 GLU cc_start: 0.7437 (tp30) cc_final: 0.7087 (tp30) REVERT: A 1005 GLN cc_start: 0.7906 (mm-40) cc_final: 0.7698 (tp40) REVERT: A 1057 PRO cc_start: 0.8891 (Cg_exo) cc_final: 0.8591 (Cg_endo) REVERT: B 193 LYS cc_start: 0.8068 (ttpt) cc_final: 0.7747 (ttmt) REVERT: B 200 LYS cc_start: 0.8781 (mttt) cc_final: 0.8275 (mttp) REVERT: B 224 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.6799 (mp0) REVERT: B 271 GLN cc_start: 0.8149 (tm-30) cc_final: 0.7562 (tm-30) REVERT: B 307 THR cc_start: 0.8234 (m) cc_final: 0.7836 (p) REVERT: B 403 ARG cc_start: 0.6722 (mtm-85) cc_final: 0.6116 (ttm170) REVERT: B 410 ILE cc_start: 0.7995 (mm) cc_final: 0.7722 (mp) REVERT: B 602 THR cc_start: 0.8520 (OUTLIER) cc_final: 0.8181 (p) REVERT: B 726 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8223 (mt) REVERT: B 773 GLU cc_start: 0.7411 (tp30) cc_final: 0.6889 (tp30) REVERT: B 803 SER cc_start: 0.8677 (m) cc_final: 0.8414 (p) REVERT: B 851 CYS cc_start: 0.8377 (t) cc_final: 0.7767 (p) REVERT: B 933 LYS cc_start: 0.8127 (mtmt) cc_final: 0.7553 (ttmm) REVERT: B 957 GLN cc_start: 0.7066 (tm-30) cc_final: 0.6560 (tm-30) REVERT: B 960 ASN cc_start: 0.8228 (m-40) cc_final: 0.7936 (t0) REVERT: B 1019 ARG cc_start: 0.8046 (ttm110) cc_final: 0.7648 (ttp80) REVERT: C 34 ARG cc_start: 0.6421 (mtp85) cc_final: 0.6113 (mtt-85) REVERT: C 41 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7996 (mtmt) REVERT: C 129 LYS cc_start: 0.8384 (ttmt) cc_final: 0.7605 (tppt) REVERT: C 229 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7476 (pp) REVERT: C 275 PHE cc_start: 0.7853 (m-80) cc_final: 0.7652 (m-80) REVERT: C 303 LEU cc_start: 0.8137 (tp) cc_final: 0.7806 (tp) REVERT: C 355 ARG cc_start: 0.7001 (OUTLIER) cc_final: 0.6449 (tmt90) REVERT: C 489 TYR cc_start: 0.2562 (OUTLIER) cc_final: -0.0058 (m-80) REVERT: C 552 LEU cc_start: 0.8302 (mt) cc_final: 0.8073 (mp) REVERT: C 558 LYS cc_start: 0.8605 (mttt) cc_final: 0.8312 (mttt) REVERT: C 564 GLN cc_start: 0.8034 (mt0) cc_final: 0.7701 (mt0) REVERT: C 707 TYR cc_start: 0.8094 (t80) cc_final: 0.7547 (t80) REVERT: C 773 GLU cc_start: 0.7177 (tm-30) cc_final: 0.6274 (tm-30) REVERT: C 1136 THR cc_start: 0.8849 (OUTLIER) cc_final: 0.8499 (p) REVERT: D 111 LEU cc_start: 0.5239 (OUTLIER) cc_final: 0.4834 (tm) REVERT: D 208 MET cc_start: 0.2542 (tmm) cc_final: 0.2258 (tmm) REVERT: D 234 MET cc_start: -0.3996 (pmt) cc_final: -0.4254 (pmt) outliers start: 126 outliers final: 104 residues processed: 536 average time/residue: 0.1753 time to fit residues: 151.3304 Evaluate side-chains 556 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 441 time to evaluate : 0.790 ------------------------------------------------------------------------------- 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 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 616 ASN 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 984 LEU Chi-restraints excluded: chain A residue 1001 LEU 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 90 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 318 PHE 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 564 GLN 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 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 1086 LYS Chi-restraints excluded: chain B residue 1104 VAL 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 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 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 489 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 572 THR 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 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 1050 MET Chi-restraints excluded: chain C residue 1072 GLU 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 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 E residue 247 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 155 VAL 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: 1.9990 chunk 120 optimal weight: 3.9990 chunk 233 optimal weight: 0.0070 chunk 55 optimal weight: 0.5980 chunk 199 optimal weight: 2.9990 chunk 184 optimal weight: 0.6980 chunk 232 optimal weight: 0.9990 chunk 181 optimal weight: 0.4980 chunk 173 optimal weight: 0.9990 chunk 163 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN A1101 HIS ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN B 965 GLN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.198223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.147853 restraints weight = 54623.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.148785 restraints weight = 27492.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.149951 restraints weight = 16130.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.150857 restraints weight = 12909.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.150899 restraints weight = 11443.863| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.4509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30432 Z= 0.122 Angle : 0.661 15.605 41486 Z= 0.325 Chirality : 0.046 0.409 4711 Planarity : 0.005 0.057 5333 Dihedral : 5.521 79.577 4179 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 3.52 % Allowed : 19.64 % Favored : 76.84 % 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: -2.29 (0.13), residues: 3739 helix: 1.05 (0.21), residues: 657 sheet: -1.36 (0.19), residues: 698 loop : -2.49 (0.12), residues: 2384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1014 TYR 0.020 0.001 TYR A 655 PHE 0.064 0.001 PHE C 190 TRP 0.058 0.001 TRP C 104 HIS 0.005 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (30365) covalent geometry : angle 0.64937 / 0.32 (41329) SS BOND : bond 0.00399 / 0.32 ( 44) SS BOND : angle 2.14549 / 1.48 ( 88) hydrogen bonds : bond 0.03184 / 2.09 ( 800) hydrogen bonds : angle 4.92160 / 3.40 ( 2136) link_NAG-ASN : bond 0.00375 / 0.25 ( 23) link_NAG-ASN : angle 1.99192 / 1.17 ( 69) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5302.03 seconds wall clock time: 92 minutes 17.05 seconds (5537.05 seconds total)