Starting phenix.real_space_refine on Fri Mar 6 05:36:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xo5_33337/03_2026/7xo5_33337.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xo5_33337/03_2026/7xo5_33337.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xo5_33337/03_2026/7xo5_33337.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xo5_33337/03_2026/7xo5_33337.map" model { file = "/net/cci-nas-00/data/ceres_data/7xo5_33337/03_2026/7xo5_33337.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xo5_33337/03_2026/7xo5_33337.cif" } resolution = 3.13 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= 0.021 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 133 5.16 5 C 18251 2.51 5 N 4690 2.21 5 O 5428 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 340 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28503 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7763 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 52, 'TRANS': 971} Chain breaks: 7 Unresolved non-hydrogen bonds: 267 Unresolved non-hydrogen angles: 325 Unresolved non-hydrogen dihedrals: 225 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 6, 'ASN:plan1': 2, 'GLU:plan': 6, 'PHE:plan': 2, 'ARG:plan': 4, 'TYR:plan': 4, 'GLN:plan1': 6} Unresolved non-hydrogen planarities: 132 Chain: "B" Number of atoms: 7700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 7700 Classifications: {'peptide': 1022} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 52, 'TRANS': 969} Chain breaks: 7 Unresolved non-hydrogen bonds: 313 Unresolved non-hydrogen angles: 385 Unresolved non-hydrogen dihedrals: 251 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'ASP:plan': 10, 'GLN:plan1': 10, 'ASN:plan1': 9, 'GLU:plan': 9, 'PHE:plan': 2, 'ARG:plan': 7, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 194 Chain: "C" Number of atoms: 7703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 7703 Classifications: {'peptide': 1022} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PTRANS': 52, 'TRANS': 969} Chain breaks: 7 Unresolved non-hydrogen bonds: 310 Unresolved non-hydrogen angles: 381 Unresolved non-hydrogen dihedrals: 249 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'ASP:plan': 10, 'GLN:plan1': 10, 'ASN:plan1': 8, 'GLU:plan': 9, 'PHE:plan': 2, 'ARG:plan': 7, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 191 Chain: "D" Number of atoms: 4818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4818 Classifications: {'peptide': 591} Link IDs: {'PTRANS': 25, 'TRANS': 565} Chain breaks: 1 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' ZN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.37, per 1000 atoms: 0.22 Number of scatterers: 28503 At special positions: 0 Unit cell: (131.84, 136.784, 245.552, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 133 16.00 O 5428 8.00 N 4690 7.00 C 18251 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " 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=2.07 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 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 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 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=2.02 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 133 " - pdb=" SG CYS D 141 " distance=2.04 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " 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=2, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A1074 " " NAG A1302 " - " ASN A 234 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A1098 " " NAG A1305 " - " ASN A 801 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A 616 " " NAG A1309 " - " ASN A 603 " " NAG A1310 " - " ASN A 331 " " NAG A1311 " - " ASN A 165 " " NAG A1312 " - " ASN A 343 " " NAG B1301 " - " ASN B 657 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 603 " " NAG B1305 " - " ASN B1074 " " NAG B1306 " - " ASN B1134 " " NAG B1307 " - " ASN B1098 " " NAG B1308 " - " ASN B 165 " " NAG B1309 " - " ASN B 616 " " NAG B1310 " - " ASN B 709 " " NAG B1311 " - " ASN B 801 " " NAG B1312 " - " ASN B 282 " " NAG C1301 " - " ASN C 657 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C1074 " " NAG C1305 " - " ASN C1134 " " NAG C1306 " - " ASN C1098 " " NAG C1307 " - " ASN C 165 " " NAG C1308 " - " ASN C 616 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C 801 " " NAG C1311 " - " ASN C 282 " " NAG D 902 " - " ASN D 546 " " NAG D 903 " - " ASN D 53 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.16 Conformation dependent library (CDL) restraints added in 1.3 seconds 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6878 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 44 sheets defined 29.0% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.523A pdb=" N LEU A 303 " --> pdb=" O THR A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 341 removed outlier: 3.660A pdb=" N GLU A 340 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 371 removed outlier: 3.839A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU A 371 " --> pdb=" O LEU A 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 366 through 371' Processing helix chain 'A' and resid 385 through 389 removed outlier: 3.792A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 removed outlier: 3.870A pdb=" N TYR A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 754 removed outlier: 3.543A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.789A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.507A pdb=" N ILE A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.600A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 removed outlier: 3.565A pdb=" N GLY A 908 " --> pdb=" O TYR A 904 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.777A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 933 removed outlier: 3.591A pdb=" N ASN A 925 " --> pdb=" O LYS A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.028A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 977 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.869A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 removed outlier: 3.813A pdb=" N LEU A1145 " --> pdb=" O LEU A1141 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.537A pdb=" N THR B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 368 removed outlier: 3.938A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 421 removed outlier: 4.356A pdb=" N TYR B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 738 through 743 Processing helix chain 'B' and resid 748 through 753 Processing helix chain 'B' and resid 754 through 757 removed outlier: 3.718A pdb=" N GLY B 757 " --> pdb=" O LEU B 754 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 754 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.768A pdb=" N LYS B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.754A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.510A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.603A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 4.215A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 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 977 through 984 removed outlier: 3.529A pdb=" N SER B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 1031 Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 3.831A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 removed outlier: 3.543A pdb=" N THR C 299 " --> pdb=" O PRO C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 364 through 368 removed outlier: 3.896A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 390 removed outlier: 3.685A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 386 through 390' Processing helix chain 'C' and resid 404 through 409 removed outlier: 3.674A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 removed outlier: 3.732A pdb=" N ASN C 422 " --> pdb=" O ILE C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.687A pdb=" N HIS C 505 " --> pdb=" O GLY C 502 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 502 through 506' Processing helix chain 'C' and resid 737 through 744 removed outlier: 3.726A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.734A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.521A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.561A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.550A pdb=" N ILE C 882 " --> pdb=" O LEU C 878 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.580A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.525A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.574A pdb=" N LYS C 933 " --> pdb=" O SER C 929 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.547A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 984 removed outlier: 3.570A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 1033 removed outlier: 3.552A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR C 998 " --> pdb=" O ASP C 994 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'D' and resid 21 through 35 removed outlier: 3.802A pdb=" N LEU D 29 " --> pdb=" O ALA D 25 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN D 30 " --> pdb=" O LYS D 26 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU D 35 " --> pdb=" O ASN D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 51 removed outlier: 3.688A pdb=" N ASN D 51 " --> pdb=" O SER D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 79 removed outlier: 3.753A pdb=" N LYS D 61 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS D 68 " --> pdb=" O GLU D 64 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR D 73 " --> pdb=" O TRP D 69 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR D 79 " --> pdb=" O GLU D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 83 removed outlier: 3.667A pdb=" N PHE D 83 " --> pdb=" O ALA D 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 80 through 83' Processing helix chain 'D' and resid 90 through 97 removed outlier: 3.855A pdb=" N ARG D 95 " --> pdb=" O PRO D 91 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN D 96 " --> pdb=" O ILE D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 129 removed outlier: 3.845A pdb=" N ASN D 117 " --> pdb=" O ASN D 113 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N THR D 118 " --> pdb=" O LYS D 114 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N THR D 122 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE D 126 " --> pdb=" O THR D 122 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR D 127 " --> pdb=" O MET D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 149 Processing helix chain 'D' and resid 150 through 155 Processing helix chain 'D' and resid 161 through 171 removed outlier: 3.509A pdb=" N TRP D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU D 171 " --> pdb=" O GLY D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 192 removed outlier: 3.579A pdb=" N TYR D 180 " --> pdb=" O LEU D 176 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLU D 181 " --> pdb=" O ARG D 177 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N TYR D 183 " --> pdb=" O LEU D 179 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL D 184 " --> pdb=" O TYR D 180 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LEU D 186 " --> pdb=" O GLU D 182 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS D 187 " --> pdb=" O TYR D 183 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ARG D 192 " --> pdb=" O ASN D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 195 No H-bonds generated for 'chain 'D' and resid 193 through 195' Processing helix chain 'D' and resid 199 through 205 Processing helix chain 'D' and resid 218 through 220 No H-bonds generated for 'chain 'D' and resid 218 through 220' Processing helix chain 'D' and resid 221 through 226 Processing helix chain 'D' and resid 233 through 242 removed outlier: 3.635A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 251 Processing helix chain 'D' and resid 278 through 282 Processing helix chain 'D' and resid 296 through 301 removed outlier: 3.571A pdb=" N GLN D 300 " --> pdb=" O ALA D 296 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY D 301 " --> pdb=" O MET D 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 296 through 301' Processing helix chain 'D' and resid 306 through 317 Processing helix chain 'D' and resid 325 through 330 Processing helix chain 'D' and resid 365 through 371 Processing helix chain 'D' and resid 374 through 383 removed outlier: 3.944A pdb=" N ILE D 379 " --> pdb=" O GLU D 375 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLN D 380 " --> pdb=" O MET D 376 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR D 381 " --> pdb=" O GLY D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 removed outlier: 3.535A pdb=" N ARG D 393 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 407 removed outlier: 3.732A pdb=" N ALA D 403 " --> pdb=" O GLY D 399 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL D 404 " --> pdb=" O PHE D 400 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 413 removed outlier: 3.808A pdb=" N ALA D 413 " --> pdb=" O LEU D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 removed outlier: 3.655A pdb=" N LEU D 418 " --> pdb=" O THR D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 446 removed outlier: 3.527A pdb=" N ASN D 437 " --> pdb=" O GLU D 433 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N PHE D 438 " --> pdb=" O THR D 434 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU D 439 " --> pdb=" O GLU D 435 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS D 441 " --> pdb=" O ASN D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 464 removed outlier: 4.226A pdb=" N MET D 455 " --> pdb=" O PRO D 451 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU D 456 " --> pdb=" O PHE D 452 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N MET D 462 " --> pdb=" O LYS D 458 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE D 464 " --> pdb=" O ARG D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.741A pdb=" N LYS D 476 " --> pdb=" O GLN D 472 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N TRP D 477 " --> pdb=" O TRP D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 512 through 533 removed outlier: 3.896A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN D 524 " --> pdb=" O ILE D 520 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLU D 527 " --> pdb=" O PHE D 523 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA D 528 " --> pdb=" O GLN D 524 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N CYS D 530 " --> pdb=" O GLN D 526 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN D 531 " --> pdb=" O GLU D 527 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ALA D 533 " --> pdb=" O LEU D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.551A pdb=" N CYS D 542 " --> pdb=" O LEU D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 550 through 558 removed outlier: 3.666A pdb=" N LEU D 554 " --> pdb=" O ALA D 550 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LYS D 556 " --> pdb=" O GLN D 552 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU D 558 " --> pdb=" O LEU D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 570 removed outlier: 3.652A pdb=" N LEU D 570 " --> pdb=" O TRP D 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 588 removed outlier: 4.006A pdb=" N LEU D 585 " --> pdb=" O VAL D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 595 removed outlier: 4.374A pdb=" N ASP D 593 " --> pdb=" O GLN D 589 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TRP D 594 " --> pdb=" O PRO D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 598 No H-bonds generated for 'chain 'D' and resid 596 through 598' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.093A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA A 264 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE A 197 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.808A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.547A pdb=" N TRP A 104 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL A 127 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.217A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 325 removed outlier: 7.274A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU A 585 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.042A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TRP A 436 " --> pdb=" O ARG A 509 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.235A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AA9, first strand: chain 'A' and resid 711 through 713 Processing sheet with id=AB1, first strand: chain 'A' and resid 717 through 728 removed outlier: 3.528A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 734 through 735 Processing sheet with id=AB3, first strand: chain 'A' and resid 788 through 789 removed outlier: 5.860A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AB5, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB6, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.592A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR B 208 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS B 202 " --> pdb=" O LYS B 195 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.574A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.504A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.375A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY B 593 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA B 609 " --> pdb=" O ILE B 598 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR B 612 " --> pdb=" O CYS B 649 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 324 through 325 removed outlier: 7.372A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.755A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU B 585 " --> pdb=" O VAL B 576 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL B 576 " --> pdb=" O LEU B 585 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.060A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 374 through 376 removed outlier: 7.209A pdb=" N ALA B 435 " --> pdb=" O PHE B 375 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TRP B 436 " --> pdb=" O ARG B 509 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ARG B 509 " --> pdb=" O TRP B 436 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL B 510 " --> pdb=" O PHE B 400 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AC5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.106A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR B 695 " --> pdb=" O CYS B 671 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY B 667 " --> pdb=" O ILE B 670 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AC7, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.277A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.277A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.356A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1081 through 1083 Processing sheet with id=AD2, first strand: chain 'C' and resid 28 through 31 removed outlier: 8.885A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA C 264 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU C 189 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.544A pdb=" N HIS C 49 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE C 55 " --> pdb=" O GLN C 271 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN C 271 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL C 289 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.837A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 103 through 106 removed outlier: 4.238A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.218A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.464A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL C 512 " --> pdb=" O ASP C 398 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N THR C 430 " --> pdb=" O PHE C 515 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 361 through 362 removed outlier: 3.984A pdb=" N CYS C 525 " --> pdb=" O CYS C 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 453 through 454 removed outlier: 3.568A pdb=" N TYR C 453 " --> pdb=" O ARG C 493 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 538 through 543 removed outlier: 3.578A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.534A pdb=" N GLY C 667 " --> pdb=" O ILE C 670 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 712 removed outlier: 3.735A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 717 through 728 removed outlier: 3.674A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.344A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE7, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.291A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'D' and resid 347 through 349 removed outlier: 3.833A pdb=" N THR D 347 " --> pdb=" O LYS D 359 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LYS D 359 " --> pdb=" O THR D 347 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N TRP D 349 " --> pdb=" O ARG D 357 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ARG D 357 " --> pdb=" O TRP D 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 921 hydrogen bonds defined for protein. 2580 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: 6.86 Time building geometry restraints manager: 2.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9063 1.34 - 1.47: 7423 1.47 - 1.59: 12521 1.59 - 1.72: 0 1.72 - 1.85: 177 Bond restraints: 29184 Sorted by residual: bond pdb=" C1 NAG A1311 " pdb=" O5 NAG A1311 " ideal model delta sigma weight residual 1.406 1.576 -0.170 2.00e-02 2.50e+03 7.25e+01 bond pdb=" C1 NAG B1307 " pdb=" O5 NAG B1307 " ideal model delta sigma weight residual 1.406 1.526 -0.120 2.00e-02 2.50e+03 3.57e+01 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.522 -0.116 2.00e-02 2.50e+03 3.38e+01 bond pdb=" C CYS C 336 " pdb=" N PRO C 337 " ideal model delta sigma weight residual 1.334 1.395 -0.061 2.34e-02 1.83e+03 6.88e+00 bond pdb=" CA THR A 167 " pdb=" C THR A 167 " ideal model delta sigma weight residual 1.523 1.558 -0.034 1.34e-02 5.57e+03 6.58e+00 ... (remaining 29179 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.35: 39347 3.35 - 6.69: 387 6.69 - 10.04: 54 10.04 - 13.38: 16 13.38 - 16.73: 1 Bond angle restraints: 39805 Sorted by residual: angle pdb=" CA CYS B 131 " pdb=" CB CYS B 131 " pdb=" SG CYS B 131 " ideal model delta sigma weight residual 114.40 131.13 -16.73 2.30e+00 1.89e-01 5.29e+01 angle pdb=" N ASN B 709 " pdb=" CA ASN B 709 " pdb=" CB ASN B 709 " ideal model delta sigma weight residual 110.40 120.49 -10.09 1.63e+00 3.76e-01 3.83e+01 angle pdb=" C ASN B 709 " pdb=" CA ASN B 709 " pdb=" CB ASN B 709 " ideal model delta sigma weight residual 109.99 99.23 10.76 2.09e+00 2.29e-01 2.65e+01 angle pdb=" CA ASN B 709 " pdb=" CB ASN B 709 " pdb=" CG ASN B 709 " ideal model delta sigma weight residual 112.60 117.43 -4.83 1.00e+00 1.00e+00 2.33e+01 angle pdb=" N VAL A1128 " pdb=" CA VAL A1128 " pdb=" C VAL A1128 " ideal model delta sigma weight residual 112.96 108.29 4.67 1.00e+00 1.00e+00 2.18e+01 ... (remaining 39800 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.05: 16369 23.05 - 46.10: 1129 46.10 - 69.15: 127 69.15 - 92.20: 44 92.20 - 115.25: 5 Dihedral angle restraints: 17674 sinusoidal: 7001 harmonic: 10673 Sorted by residual: dihedral pdb=" CB CYS B 743 " pdb=" SG CYS B 743 " pdb=" SG CYS B 749 " pdb=" CB CYS B 749 " ideal model delta sinusoidal sigma weight residual 93.00 -176.70 -90.30 1 1.00e+01 1.00e-02 9.65e+01 dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual -86.00 -168.71 82.71 1 1.00e+01 1.00e-02 8.38e+01 dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual 93.00 174.64 -81.64 1 1.00e+01 1.00e-02 8.20e+01 ... (remaining 17671 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.245: 4617 0.245 - 0.489: 7 0.489 - 0.734: 1 0.734 - 0.978: 1 0.978 - 1.223: 1 Chirality restraints: 4627 Sorted by residual: chirality pdb=" C1 NAG B1305 " pdb=" ND2 ASN B1074 " pdb=" C2 NAG B1305 " pdb=" O5 NAG B1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.18 -1.22 2.00e-01 2.50e+01 3.74e+01 chirality pdb=" C1 NAG A1311 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG A1311 " pdb=" O5 NAG A1311 " both_signs ideal model delta sigma weight residual False -2.40 -1.66 -0.74 2.00e-01 2.50e+01 1.39e+01 chirality pdb=" C1 NAG B1310 " pdb=" ND2 ASN B 709 " pdb=" C2 NAG B1310 " pdb=" O5 NAG B1310 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.82e+00 ... (remaining 4624 not shown) Planarity restraints: 5142 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 709 " -0.066 2.00e-02 2.50e+03 6.42e-02 5.16e+01 pdb=" CG ASN B 709 " 0.096 2.00e-02 2.50e+03 pdb=" OD1 ASN B 709 " -0.025 2.00e-02 2.50e+03 pdb=" ND2 ASN B 709 " 0.054 2.00e-02 2.50e+03 pdb=" C1 NAG B1310 " -0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B1074 " -0.016 2.00e-02 2.50e+03 4.43e-02 2.45e+01 pdb=" CG ASN B1074 " 0.063 2.00e-02 2.50e+03 pdb=" OD1 ASN B1074 " -0.050 2.00e-02 2.50e+03 pdb=" ND2 ASN B1074 " 0.041 2.00e-02 2.50e+03 pdb=" C1 NAG B1305 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 709 " -0.023 2.00e-02 2.50e+03 4.60e-02 2.11e+01 pdb=" CG ASN B 709 " 0.079 2.00e-02 2.50e+03 pdb=" OD1 ASN B 709 " -0.030 2.00e-02 2.50e+03 pdb=" ND2 ASN B 709 " -0.027 2.00e-02 2.50e+03 ... (remaining 5139 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 37 2.42 - 3.04: 14889 3.04 - 3.66: 40826 3.66 - 4.28: 60122 4.28 - 4.90: 99056 Nonbonded interactions: 214930 Sorted by model distance: nonbonded pdb=" O TYR D 127 " pdb=" CD1 LEU D 144 " model vdw 1.796 3.460 nonbonded pdb=" OG SER A 514 " pdb=" OE2 GLU A 516 " model vdw 2.270 3.040 nonbonded pdb=" O GLY A 880 " pdb=" OG SER A 884 " model vdw 2.281 3.040 nonbonded pdb=" O LYS D 441 " pdb=" OG1 THR D 445 " model vdw 2.301 3.040 nonbonded pdb=" O GLY B 880 " pdb=" OG SER B 884 " model vdw 2.301 3.040 ... (remaining 214925 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 27 through 39 or (resid 40 through 41 and (name N or name \ CA or name C or name O or name CB )) or resid 42 through 45 or (resid 46 and (na \ me N or name CA or name C or name O or name CB )) or resid 47 through 51 or (res \ id 52 through 53 and (name N or name CA or name C or name O or name CB )) or res \ id 54 through 68 or (resid 80 and (name N or name CA or name C or name O or name \ CB )) or resid 81 through 86 or (resid 87 and (name N or name CA or name C or n \ ame O or name CB )) or resid 88 through 96 or (resid 97 through 98 and (name N o \ r name CA or name C or name O or name CB )) or resid 99 through 114 or (resid 11 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 116 through \ 133 or (resid 134 and (name N or name CA or name C or name O or name CB )) or re \ sid 135 through 136 or (resid 137 and (name N or name CA or name C or name O or \ name CB )) or resid 138 through 160 or (resid 161 through 164 and (name N or nam \ e CA or name C or name O or name CB )) or resid 165 through 209 or (resid 210 an \ d (name N or name CA or name C or name O or name CB )) or resid 215 through 253 \ or (resid 254 and (name N or name CA or name C or name O or name CB )) or resid \ 255 through 318 or (resid 319 and (name N or name CA or name C or name O or name \ CB )) or resid 320 through 355 or (resid 356 through 357 and (name N or name CA \ or name C or name O or name CB )) or resid 358 through 387 or (resid 388 and (n \ ame N or name CA or name C or name O or name CB )) or resid 389 through 404 or ( \ resid 405 and (name N or name CA or name C or name O or name CB )) or resid 406 \ through 414 or (resid 415 and (name N or name CA or name C or name O or name CB \ )) or resid 416 through 426 or (resid 427 and (name N or name CA or name C or na \ me O or name CB )) or resid 428 through 447 or (resid 448 and (name N or name CA \ or name C or name O or name CB )) or resid 449 through 453 or (resid 454 and (n \ ame N or name CA or name C or name O or name CB )) or resid 455 through 457 or ( \ resid 458 through 459 and (name N or name CA or name C or name O or name CB )) o \ r resid 460 through 464 or (resid 465 and (name N or name CA or name C or name O \ or name CB )) or resid 466 through 473 or (resid 474 through 475 and (name N or \ name CA or name C or name O or name CB )) or resid 476 through 486 or (resid 48 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 488 through \ 499 or (resid 500 and (name N or name CA or name C or name O or name CB )) or re \ sid 501 through 515 or (resid 516 and (name N or name CA or name C or name O or \ name CB )) or resid 517 through 522 or (resid 523 and (name N or name CA or name \ C or name O or name CB )) or resid 524 through 527 or (resid 528 through 529 an \ d (name N or name CA or name C or name O or name CB )) or resid 530 through 553 \ or (resid 554 and (name N or name CA or name C or name O or name CB )) or resid \ 555 or (resid 556 through 558 and (name N or name CA or name C or name O or name \ CB )) or resid 559 through 563 or (resid 564 and (name N or name CA or name C o \ r name O or name CB )) or resid 565 through 570 or (resid 571 through 572 and (n \ ame N or name CA or name C or name O or name CB )) or resid 573 through 620 or r \ esid 641 through 676 or (resid 690 and (name N or name CA or name C or name O or \ name CB )) or resid 691 through 747 or (resid 748 and (name N or name CA or nam \ e C or name O or name CB )) or resid 749 through 827 or (resid 828 and (name N o \ r name CA or name C or name O or name CB )) or resid 855 through 984 or (resid 9 \ 85 and (name N or name CA or name C or name O or name CB )) or resid 986 through \ 987 or (resid 988 through 989 and (name N or name CA or name C or name O or nam \ e CB )) or resid 990 through 1037 or (resid 1038 and (name N or name CA or name \ C or name O or name CB )) or resid 1039 through 1050 or (resid 1051 and (name N \ or name CA or name C or name O or name CB )) or resid 1052 through 1110 or (resi \ d 1111 and (name N or name CA or name C or name O or name CB )) or resid 1112 th \ rough 1143 or (resid 1144 through 1146 and (name N or name CA or name C or name \ O or name CB )) or resid 1301 through 1311)) selection = (chain 'B' and (resid 27 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 67 or (resid 68 through 80 and (na \ me N or name CA or name C or name O or name CB )) or resid 81 through 107 or (re \ sid 108 through 113 and (name N or name CA or name C or name O or name CB )) or \ resid 114 through 175 or (resid 176 through 187 and (name N or name CA or name C \ or name O or name CB )) or resid 188 through 199 or (resid 200 and (name N or n \ ame CA or name C or name O or name CB )) or resid 201 through 217 or (resid 218 \ and (name N or name CA or name C or name O or name CB )) or resid 219 through 22 \ 3 or (resid 224 and (name N or name CA or name C or name O or name CB )) or resi \ d 225 through 248 or (resid 249 through 250 and (name N or name CA or name C or \ name O or name CB )) or resid 251 through 303 or (resid 304 and (name N or name \ CA or name C or name O or name CB )) or resid 305 through 320 or (resid 321 and \ (name N or name CA or name C or name O or name CB )) or resid 322 through 556 or \ (resid 557 through 558 and (name N or name CA or name C or name O or name CB )) \ or resid 559 through 568 or (resid 569 through 572 and (name N or name CA or na \ me C or name O or name CB )) or resid 573 through 662 or (resid 663 and (name N \ or name CA or name C or name O or name CB )) or resid 664 through 701 or (resid \ 702 and (name N or name CA or name C or name O or name CB )) or resid 703 throug \ h 739 or (resid 740 and (name N or name CA or name C or name O or name CB )) or \ resid 741 through 794 or (resid 795 and (name N or name CA or name C or name O o \ r name CB )) or resid 796 through 807 or (resid 808 and (name N or name CA or na \ me C or name O or name CB )) or resid 809 through 818 or (resid 819 and (name N \ or name CA or name C or name O or name CB )) or resid 820 through 824 or (resid \ 825 and (name N or name CA or name C or name O or name CB )) or resid 826 throug \ h 917 or (resid 918 and (name N or name CA or name C or name O or name CB )) or \ resid 919 through 946 or (resid 947 and (name N or name CA or name C or name O o \ r name CB )) or resid 948 through 963 or (resid 964 and (name N or name CA or na \ me C or name O or name CB )) or resid 965 through 1072 or (resid 1073 and (name \ N or name CA or name C or name O or name CB )) or resid 1074 through 1137 or (re \ sid 1138 and (name N or name CA or name C or name O or name CB )) or resid 1139 \ through 1140 or (resid 1141 through 1142 and (name N or name CA or name C or nam \ e O or name CB )) or resid 1143 through 1145 or (resid 1146 and (name N or name \ CA or name C or name O or name CB )) or resid 1301 through 1311)) selection = (chain 'C' and (resid 27 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 67 or (resid 68 through 80 and (na \ me N or name CA or name C or name O or name CB )) or resid 81 through 107 or (re \ sid 108 through 113 and (name N or name CA or name C or name O or name CB )) or \ resid 114 through 175 or (resid 176 through 187 and (name N or name CA or name C \ or name O or name CB )) or resid 188 through 199 or (resid 200 and (name N or n \ ame CA or name C or name O or name CB )) or resid 201 through 217 or (resid 218 \ and (name N or name CA or name C or name O or name CB )) or resid 219 through 22 \ 3 or (resid 224 and (name N or name CA or name C or name O or name CB )) or resi \ d 225 through 248 or (resid 249 through 250 and (name N or name CA or name C or \ name O or name CB )) or resid 251 through 303 or (resid 304 and (name N or name \ CA or name C or name O or name CB )) or resid 305 through 320 or (resid 321 and \ (name N or name CA or name C or name O or name CB )) or resid 322 through 387 or \ (resid 388 and (name N or name CA or name C or name O or name CB )) or resid 38 \ 9 through 556 or (resid 557 through 558 and (name N or name CA or name C or name \ O or name CB )) or resid 559 through 568 or (resid 569 through 572 and (name N \ or name CA or name C or name O or name CB )) or resid 573 through 662 or (resid \ 663 and (name N or name CA or name C or name O or name CB )) or resid 664 throug \ h 701 or (resid 702 and (name N or name CA or name C or name O or name CB )) or \ resid 703 through 739 or (resid 740 and (name N or name CA or name C or name O o \ r name CB )) or resid 741 through 794 or (resid 795 and (name N or name CA or na \ me C or name O or name CB )) or resid 796 through 807 or (resid 808 and (name N \ or name CA or name C or name O or name CB )) or resid 809 through 818 or (resid \ 819 and (name N or name CA or name C or name O or name CB )) or resid 820 throug \ h 824 or (resid 825 and (name N or name CA or name C or name O or name CB )) or \ resid 826 through 917 or (resid 918 and (name N or name CA or name C or name O o \ r name CB )) or resid 919 through 946 or (resid 947 and (name N or name CA or na \ me C or name O or name CB )) or resid 948 through 963 or (resid 964 and (name N \ or name CA or name C or name O or name CB )) or resid 965 through 1072 or (resid \ 1073 and (name N or name CA or name C or name O or name CB )) or resid 1074 thr \ ough 1137 or (resid 1138 and (name N or name CA or name C or name O or name CB ) \ ) or resid 1139 through 1140 or (resid 1141 through 1142 and (name N or name CA \ or name C or name O or name CB )) or resid 1143 through 1145 or (resid 1146 and \ (name N or name CA or name C or name O or name CB )) or resid 1301 through 1311) \ ) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 26.310 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6730 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 : 0.005 0.170 29250 Z= 0.244 Angle : 0.964 26.572 39970 Z= 0.499 Chirality : 0.059 1.223 4627 Planarity : 0.007 0.069 5105 Dihedral : 15.282 115.248 10715 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.07 % Allowed : 4.72 % Favored : 95.21 % Cbeta Deviations : 0.03 % 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: -4.22 (0.10), residues: 3607 helix: -4.66 (0.05), residues: 842 sheet: -1.15 (0.20), residues: 532 loop : -2.57 (0.10), residues: 2233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.002 ARG B 403 TYR 0.044 0.002 TYR A 796 PHE 0.049 0.002 PHE D 438 TRP 0.022 0.002 TRP B 886 HIS 0.011 0.002 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00485 (29184) covalent geometry : angle 0.93542 (39805) SS BOND : bond 0.00891 ( 27) SS BOND : angle 1.75303 ( 54) hydrogen bonds : bond 0.29583 ( 916) hydrogen bonds : angle 10.46885 ( 2580) Misc. bond : bond 0.01060 ( 2) link_NAG-ASN : bond 0.00926 ( 37) link_NAG-ASN : angle 4.36363 ( 111) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 650 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.7179 (p) cc_final: 0.6178 (t) REVERT: A 317 ASN cc_start: 0.7368 (m-40) cc_final: 0.7069 (m-40) REVERT: A 553 THR cc_start: 0.6962 (m) cc_final: 0.6730 (t) REVERT: A 610 VAL cc_start: 0.8158 (m) cc_final: 0.7953 (t) REVERT: A 776 LYS cc_start: 0.8380 (ttmt) cc_final: 0.8151 (tttp) REVERT: A 777 ASN cc_start: 0.6905 (m-40) cc_final: 0.6684 (m-40) REVERT: A 820 ASP cc_start: 0.7370 (t70) cc_final: 0.7161 (t0) REVERT: A 875 SER cc_start: 0.8138 (t) cc_final: 0.7824 (p) REVERT: A 902 MET cc_start: 0.7311 (mmm) cc_final: 0.7096 (mmm) REVERT: A 1031 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7303 (mt-10) REVERT: B 63 THR cc_start: 0.7419 (p) cc_final: 0.6844 (t) REVERT: B 191 GLU cc_start: 0.7069 (mt-10) cc_final: 0.6861 (mt-10) REVERT: B 595 VAL cc_start: 0.7823 (t) cc_final: 0.7486 (p) REVERT: B 723 THR cc_start: 0.7951 (p) cc_final: 0.7738 (p) REVERT: B 737 ASP cc_start: 0.6787 (t0) cc_final: 0.6350 (t0) REVERT: B 804 GLN cc_start: 0.7828 (mt0) cc_final: 0.6843 (mt0) REVERT: B 902 MET cc_start: 0.7689 (tpp) cc_final: 0.7031 (mmm) REVERT: B 922 LEU cc_start: 0.8749 (tt) cc_final: 0.8516 (tp) REVERT: B 935 GLN cc_start: 0.7254 (pt0) cc_final: 0.6930 (pt0) REVERT: B 990 GLU cc_start: 0.6833 (tm-30) cc_final: 0.6227 (tm-30) REVERT: B 1041 ASP cc_start: 0.6601 (t0) cc_final: 0.6360 (t0) REVERT: B 1073 LYS cc_start: 0.6817 (tttt) cc_final: 0.6556 (tttt) REVERT: C 1041 ASP cc_start: 0.6863 (t0) cc_final: 0.6488 (t0) REVERT: C 1128 VAL cc_start: 0.8626 (t) cc_final: 0.8381 (p) REVERT: D 49 ASN cc_start: 0.6840 (t0) cc_final: 0.6385 (t0) REVERT: D 64 GLU cc_start: 0.7580 (tm-30) cc_final: 0.7311 (tm-30) REVERT: D 83 PHE cc_start: 0.6174 (t80) cc_final: 0.5769 (t80) REVERT: D 143 LEU cc_start: 0.3710 (tp) cc_final: 0.3413 (mm) REVERT: D 158 TYR cc_start: 0.0999 (t80) cc_final: -0.0229 (t80) REVERT: D 165 TRP cc_start: 0.1104 (t60) cc_final: -0.0526 (t60) REVERT: D 190 MET cc_start: 0.5126 (mmm) cc_final: 0.4428 (mmm) REVERT: D 306 ARG cc_start: 0.7793 (mmt180) cc_final: 0.7310 (mmm160) REVERT: D 313 LYS cc_start: 0.6358 (ptpt) cc_final: 0.5473 (mttp) REVERT: D 323 MET cc_start: -0.3463 (mmt) cc_final: -0.3889 (mmt) REVERT: D 327 PHE cc_start: 0.6745 (t80) cc_final: 0.5843 (t80) REVERT: D 455 MET cc_start: 0.6181 (ppp) cc_final: 0.5367 (ppp) REVERT: D 462 MET cc_start: 0.3102 (mmt) cc_final: 0.2668 (mmt) REVERT: D 479 GLU cc_start: 0.6952 (tt0) cc_final: 0.6309 (pt0) outliers start: 2 outliers final: 1 residues processed: 651 average time/residue: 0.1564 time to fit residues: 167.2389 Evaluate side-chains 545 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 544 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 709 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 197 optimal weight: 0.1980 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.0670 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 1.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 196 ASN A 370 ASN A 487 ASN A 607 GLN A 613 GLN A 755 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A 914 ASN A 920 GLN A 953 ASN A 960 ASN A 965 GLN A1036 GLN A1064 HIS A1083 HIS A1101 HIS B 81 ASN B 207 HIS B 218 GLN B 280 ASN B 314 GLN B 317 ASN B 437 ASN B 460 ASN B 519 HIS B 563 GLN B 824 ASN B1048 HIS B1054 GLN B1135 ASN C 239 GLN C 481 ASN C 544 ASN C 613 GLN C 755 GLN C 762 GLN C 777 ASN C 907 ASN C 919 ASN C 953 ASN C 960 ASN C1023 ASN C1036 GLN C1054 GLN C1106 GLN D 34 GLN ** D 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 86 GLN D 117 ASN D 216 ASN D 277 ASN D 309 GLN D 472 GLN ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 524 GLN D 536 ASN Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.198222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.148667 restraints weight = 43935.216| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 2.40 r_work: 0.3663 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3518 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 29250 Z= 0.161 Angle : 0.657 21.070 39970 Z= 0.327 Chirality : 0.047 0.441 4627 Planarity : 0.005 0.059 5105 Dihedral : 6.372 108.096 4684 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.73 % Allowed : 13.45 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.82 (0.12), residues: 3607 helix: -2.27 (0.13), residues: 856 sheet: -0.70 (0.19), residues: 617 loop : -2.12 (0.11), residues: 2134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 237 TYR 0.021 0.001 TYR D 454 PHE 0.024 0.002 PHE B 970 TRP 0.017 0.001 TRP D 69 HIS 0.008 0.001 HIS A1101 Details of bonding type rmsd covalent geometry : bond 0.00347 (29184) covalent geometry : angle 0.63158 (39805) SS BOND : bond 0.00444 ( 27) SS BOND : angle 1.50988 ( 54) hydrogen bonds : bond 0.05758 ( 916) hydrogen bonds : angle 5.99654 ( 2580) Misc. bond : bond 0.00265 ( 2) link_NAG-ASN : bond 0.00987 ( 37) link_NAG-ASN : angle 3.37348 ( 111) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 572 time to evaluate : 0.648 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 33 THR cc_start: 0.8018 (OUTLIER) cc_final: 0.7741 (m) REVERT: A 58 PHE cc_start: 0.8392 (m-10) cc_final: 0.8170 (m-80) REVERT: A 189 LEU cc_start: 0.7708 (tp) cc_final: 0.7370 (tp) REVERT: A 273 ARG cc_start: 0.7845 (mtp85) cc_final: 0.7499 (mmt90) REVERT: A 317 ASN cc_start: 0.8019 (m-40) cc_final: 0.7691 (m110) REVERT: A 574 ASP cc_start: 0.8275 (t0) cc_final: 0.8014 (t0) REVERT: A 578 ASP cc_start: 0.7134 (t70) cc_final: 0.6527 (t70) REVERT: A 583 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7294 (pm20) REVERT: A 599 THR cc_start: 0.8720 (t) cc_final: 0.8426 (p) REVERT: A 643 PHE cc_start: 0.8178 (t80) cc_final: 0.7970 (t80) REVERT: A 731 MET cc_start: 0.8636 (ptp) cc_final: 0.8180 (ptt) REVERT: A 735 SER cc_start: 0.8643 (m) cc_final: 0.8230 (p) REVERT: A 737 ASP cc_start: 0.7202 (t0) cc_final: 0.6975 (t0) REVERT: A 774 GLN cc_start: 0.6781 (mt0) cc_final: 0.6527 (mt0) REVERT: A 868 GLU cc_start: 0.7766 (mp0) cc_final: 0.7550 (mp0) REVERT: A 966 LEU cc_start: 0.8942 (mt) cc_final: 0.8731 (mp) REVERT: A 988 GLU cc_start: 0.7899 (tp30) cc_final: 0.7664 (tp30) REVERT: A 1031 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7978 (mt-10) REVERT: B 65 PHE cc_start: 0.7817 (m-10) cc_final: 0.7586 (m-80) REVERT: B 205 SER cc_start: 0.8527 (m) cc_final: 0.8158 (p) REVERT: B 281 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7880 (mp0) REVERT: B 287 ASP cc_start: 0.7901 (m-30) cc_final: 0.7690 (m-30) REVERT: B 535 LYS cc_start: 0.8043 (mmtm) cc_final: 0.7753 (mttm) REVERT: B 574 ASP cc_start: 0.7873 (t0) cc_final: 0.7662 (t0) REVERT: B 587 ILE cc_start: 0.7382 (mt) cc_final: 0.7174 (tt) REVERT: B 643 PHE cc_start: 0.7871 (t80) cc_final: 0.7599 (t80) REVERT: B 737 ASP cc_start: 0.7560 (t0) cc_final: 0.7121 (t0) REVERT: B 804 GLN cc_start: 0.8373 (mt0) cc_final: 0.7866 (mm-40) REVERT: B 902 MET cc_start: 0.8228 (tpp) cc_final: 0.7590 (mmm) REVERT: B 935 GLN cc_start: 0.7527 (pt0) cc_final: 0.7323 (pt0) REVERT: B 964 LYS cc_start: 0.8695 (tmtt) cc_final: 0.8422 (tmtt) REVERT: B 983 ARG cc_start: 0.7630 (mtt180) cc_final: 0.7283 (mtt180) REVERT: B 1041 ASP cc_start: 0.7866 (t0) cc_final: 0.7619 (t0) REVERT: B 1101 HIS cc_start: 0.7955 (m90) cc_final: 0.7382 (m90) REVERT: B 1105 THR cc_start: 0.7681 (t) cc_final: 0.7470 (t) REVERT: C 32 PHE cc_start: 0.7818 (m-80) cc_final: 0.7591 (m-80) REVERT: C 170 TYR cc_start: 0.6839 (t80) cc_final: 0.6580 (t80) REVERT: C 396 TYR cc_start: 0.8336 (m-80) cc_final: 0.8130 (m-10) REVERT: C 442 ASP cc_start: 0.6084 (m-30) cc_final: 0.5822 (t0) REVERT: C 608 VAL cc_start: 0.8604 (p) cc_final: 0.8385 (t) REVERT: C 717 ASN cc_start: 0.8134 (t0) cc_final: 0.7919 (t0) REVERT: C 918 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7501 (mt-10) REVERT: C 964 LYS cc_start: 0.8271 (ptpp) cc_final: 0.8016 (mtpp) REVERT: C 974 SER cc_start: 0.8413 (p) cc_final: 0.8019 (m) REVERT: C 1019 ARG cc_start: 0.8110 (ttm170) cc_final: 0.7880 (ttp-170) REVERT: C 1094 VAL cc_start: 0.8152 (m) cc_final: 0.7638 (m) REVERT: D 49 ASN cc_start: 0.7111 (t0) cc_final: 0.6680 (t0) REVERT: D 64 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7418 (tm-30) REVERT: D 101 GLN cc_start: 0.3574 (mp10) cc_final: 0.3132 (mm-40) REVERT: D 120 LEU cc_start: 0.5070 (OUTLIER) cc_final: 0.4485 (pp) REVERT: D 165 TRP cc_start: 0.1098 (t60) cc_final: -0.1899 (t-100) REVERT: D 190 MET cc_start: 0.5397 (mmm) cc_final: 0.4740 (mmm) REVERT: D 313 LYS cc_start: 0.5957 (ptpt) cc_final: 0.5194 (mmtt) REVERT: D 323 MET cc_start: -0.3207 (mmt) cc_final: -0.3739 (mmt) REVERT: D 327 PHE cc_start: 0.6843 (t80) cc_final: 0.5949 (t80) REVERT: D 455 MET cc_start: 0.6509 (ppp) cc_final: 0.5567 (ppp) REVERT: D 462 MET cc_start: 0.3341 (mmt) cc_final: 0.2907 (mmt) outliers start: 51 outliers final: 28 residues processed: 603 average time/residue: 0.1616 time to fit residues: 158.6718 Evaluate side-chains 560 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 529 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain D residue 34 GLN Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 581 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 47 optimal weight: 0.1980 chunk 265 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 351 optimal weight: 7.9990 chunk 331 optimal weight: 0.5980 chunk 19 optimal weight: 0.0030 chunk 94 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 339 optimal weight: 0.5980 chunk 330 optimal weight: 10.0000 chunk 229 optimal weight: 4.9990 overall best weight: 0.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN A 422 ASN A 957 GLN B 188 ASN B 777 ASN C 544 ASN C 658 ASN C 777 ASN C 955 ASN ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 HIS ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.195774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.145115 restraints weight = 43497.119| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.45 r_work: 0.3615 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29250 Z= 0.127 Angle : 0.591 10.972 39970 Z= 0.293 Chirality : 0.045 0.340 4627 Planarity : 0.004 0.051 5105 Dihedral : 5.968 107.330 4684 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.17 % Allowed : 16.13 % Favored : 81.69 % 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: -1.86 (0.13), residues: 3607 helix: -0.65 (0.17), residues: 868 sheet: -0.20 (0.19), residues: 640 loop : -1.89 (0.12), residues: 2099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1091 TYR 0.019 0.001 TYR D 454 PHE 0.019 0.001 PHE A 194 TRP 0.027 0.001 TRP D 275 HIS 0.003 0.001 HIS D 505 Details of bonding type rmsd covalent geometry : bond 0.00284 (29184) covalent geometry : angle 0.57686 (39805) SS BOND : bond 0.00396 ( 27) SS BOND : angle 1.49719 ( 54) hydrogen bonds : bond 0.04286 ( 916) hydrogen bonds : angle 5.30285 ( 2580) Misc. bond : bond 0.00212 ( 2) link_NAG-ASN : bond 0.00831 ( 37) link_NAG-ASN : angle 2.33699 ( 111) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 532 time to evaluate : 0.984 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 33 THR cc_start: 0.8077 (OUTLIER) cc_final: 0.7798 (m) REVERT: A 47 VAL cc_start: 0.8221 (p) cc_final: 0.7980 (p) REVERT: A 317 ASN cc_start: 0.8114 (m110) cc_final: 0.7837 (m-40) REVERT: A 574 ASP cc_start: 0.8237 (t0) cc_final: 0.7895 (t0) REVERT: A 578 ASP cc_start: 0.7065 (t0) cc_final: 0.6734 (t0) REVERT: A 583 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7254 (pm20) REVERT: A 592 PHE cc_start: 0.8418 (p90) cc_final: 0.8202 (p90) REVERT: A 599 THR cc_start: 0.8801 (t) cc_final: 0.8531 (p) REVERT: A 723 THR cc_start: 0.8395 (OUTLIER) cc_final: 0.8163 (p) REVERT: A 735 SER cc_start: 0.8659 (m) cc_final: 0.8289 (p) REVERT: A 737 ASP cc_start: 0.7408 (t0) cc_final: 0.7095 (t0) REVERT: A 988 GLU cc_start: 0.7962 (tp30) cc_final: 0.7577 (tp30) REVERT: A 1031 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7982 (mt-10) REVERT: A 1051 SER cc_start: 0.8192 (p) cc_final: 0.7939 (m) REVERT: B 65 PHE cc_start: 0.7991 (m-10) cc_final: 0.7646 (m-80) REVERT: B 281 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7973 (mp0) REVERT: B 317 ASN cc_start: 0.8135 (m-40) cc_final: 0.7804 (m110) REVERT: B 535 LYS cc_start: 0.8033 (mmtm) cc_final: 0.7775 (mttm) REVERT: B 574 ASP cc_start: 0.7984 (t0) cc_final: 0.7734 (t0) REVERT: B 643 PHE cc_start: 0.8150 (t80) cc_final: 0.7940 (t80) REVERT: B 737 ASP cc_start: 0.7519 (t0) cc_final: 0.7228 (t0) REVERT: B 804 GLN cc_start: 0.8443 (mt0) cc_final: 0.7970 (mm-40) REVERT: B 902 MET cc_start: 0.8247 (tpp) cc_final: 0.7727 (mmm) REVERT: B 929 SER cc_start: 0.8412 (p) cc_final: 0.8209 (m) REVERT: B 935 GLN cc_start: 0.7524 (pt0) cc_final: 0.7245 (pt0) REVERT: B 964 LYS cc_start: 0.8743 (tmtt) cc_final: 0.8452 (tmtt) REVERT: B 983 ARG cc_start: 0.7656 (mtt180) cc_final: 0.7338 (mtt180) REVERT: B 1041 ASP cc_start: 0.7998 (t0) cc_final: 0.7753 (t0) REVERT: B 1101 HIS cc_start: 0.8152 (m90) cc_final: 0.7821 (m-70) REVERT: B 1105 THR cc_start: 0.7862 (t) cc_final: 0.7638 (t) REVERT: C 170 TYR cc_start: 0.6915 (t80) cc_final: 0.6611 (t80) REVERT: C 326 ILE cc_start: 0.8203 (OUTLIER) cc_final: 0.7921 (pt) REVERT: C 329 PHE cc_start: 0.7843 (m-80) cc_final: 0.7400 (m-80) REVERT: C 396 TYR cc_start: 0.8404 (m-80) cc_final: 0.8010 (m-10) REVERT: C 608 VAL cc_start: 0.8723 (p) cc_final: 0.8502 (t) REVERT: C 918 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7687 (mt-10) REVERT: C 964 LYS cc_start: 0.8305 (ptpp) cc_final: 0.8105 (mtpp) REVERT: C 974 SER cc_start: 0.8595 (p) cc_final: 0.8276 (m) REVERT: C 976 VAL cc_start: 0.8712 (OUTLIER) cc_final: 0.8477 (m) REVERT: C 984 LEU cc_start: 0.8287 (mm) cc_final: 0.8061 (mp) REVERT: C 1019 ARG cc_start: 0.8140 (ttm170) cc_final: 0.7910 (ttp-170) REVERT: D 49 ASN cc_start: 0.7176 (t0) cc_final: 0.6765 (t0) REVERT: D 64 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7549 (tm-30) REVERT: D 101 GLN cc_start: 0.3241 (mp10) cc_final: 0.2947 (mm-40) REVERT: D 120 LEU cc_start: 0.5368 (OUTLIER) cc_final: 0.4861 (pp) REVERT: D 190 MET cc_start: 0.5465 (mmm) cc_final: 0.4908 (mmm) REVERT: D 327 PHE cc_start: 0.6843 (t80) cc_final: 0.5969 (t80) REVERT: D 390 PHE cc_start: 0.7996 (t80) cc_final: 0.7577 (t80) REVERT: D 408 MET cc_start: 0.3358 (mmp) cc_final: 0.2883 (mmm) REVERT: D 455 MET cc_start: 0.6403 (ppp) cc_final: 0.5395 (ppp) REVERT: D 462 MET cc_start: 0.3332 (mmt) cc_final: 0.2932 (mmt) REVERT: D 524 GLN cc_start: 0.5602 (mp10) cc_final: 0.5304 (mp10) outliers start: 64 outliers final: 42 residues processed: 573 average time/residue: 0.1577 time to fit residues: 147.9508 Evaluate side-chains 546 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 498 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain D residue 34 GLN Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 308 PHE Chi-restraints excluded: chain D residue 310 GLU Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 581 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 236 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 322 optimal weight: 20.0000 chunk 194 optimal weight: 0.7980 chunk 148 optimal weight: 8.9990 chunk 309 optimal weight: 5.9990 chunk 262 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 132 optimal weight: 8.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 544 ASN A 762 GLN A 907 ASN A 913 GLN A 955 ASN A1106 GLN B 30 ASN B 188 ASN B 658 ASN B 703 ASN B 895 GLN B 907 ASN B1010 GLN C 644 GLN C 777 ASN C 784 GLN C 935 GLN C 955 ASN ** D 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 ASN D 472 GLN D 607 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.190461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.138633 restraints weight = 42883.773| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.41 r_work: 0.3522 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 29250 Z= 0.212 Angle : 0.641 15.871 39970 Z= 0.319 Chirality : 0.048 0.766 4627 Planarity : 0.004 0.050 5105 Dihedral : 6.046 103.370 4684 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.63 % Allowed : 16.75 % Favored : 79.62 % 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: -1.59 (0.13), residues: 3607 helix: -0.33 (0.17), residues: 894 sheet: -0.16 (0.19), residues: 688 loop : -1.76 (0.12), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1091 TYR 0.017 0.002 TYR A 265 PHE 0.018 0.002 PHE A 58 TRP 0.032 0.001 TRP D 275 HIS 0.005 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00503 (29184) covalent geometry : angle 0.61406 (39805) SS BOND : bond 0.00498 ( 27) SS BOND : angle 2.34066 ( 54) hydrogen bonds : bond 0.04607 ( 916) hydrogen bonds : angle 5.17966 ( 2580) Misc. bond : bond 0.00227 ( 2) link_NAG-ASN : bond 0.01255 ( 37) link_NAG-ASN : angle 3.20471 ( 111) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 527 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 ASN cc_start: 0.8083 (m110) cc_final: 0.7840 (m110) REVERT: A 574 ASP cc_start: 0.8255 (t0) cc_final: 0.7927 (t0) REVERT: A 578 ASP cc_start: 0.7052 (t0) cc_final: 0.6688 (t0) REVERT: A 599 THR cc_start: 0.8844 (t) cc_final: 0.8598 (p) REVERT: A 723 THR cc_start: 0.8452 (OUTLIER) cc_final: 0.8229 (p) REVERT: A 735 SER cc_start: 0.8658 (m) cc_final: 0.8265 (p) REVERT: A 756 TYR cc_start: 0.7980 (m-80) cc_final: 0.7767 (m-80) REVERT: A 776 LYS cc_start: 0.8810 (ttpp) cc_final: 0.8514 (ttmm) REVERT: A 988 GLU cc_start: 0.8014 (tp30) cc_final: 0.7460 (tp30) REVERT: A 992 GLN cc_start: 0.7828 (mm-40) cc_final: 0.7622 (mm-40) REVERT: A 1051 SER cc_start: 0.8293 (p) cc_final: 0.8062 (m) REVERT: B 58 PHE cc_start: 0.8847 (m-10) cc_final: 0.8431 (m-10) REVERT: B 65 PHE cc_start: 0.8195 (m-10) cc_final: 0.7755 (m-10) REVERT: B 100 ILE cc_start: 0.8420 (pt) cc_final: 0.8205 (mt) REVERT: B 205 SER cc_start: 0.8654 (m) cc_final: 0.8256 (p) REVERT: B 307 THR cc_start: 0.8641 (p) cc_final: 0.8366 (p) REVERT: B 737 ASP cc_start: 0.7714 (t0) cc_final: 0.7481 (t0) REVERT: B 776 LYS cc_start: 0.8734 (ttpt) cc_final: 0.8387 (ttmm) REVERT: B 804 GLN cc_start: 0.8566 (mt0) cc_final: 0.8215 (mm-40) REVERT: B 964 LYS cc_start: 0.8858 (tmtt) cc_final: 0.8450 (tmtt) REVERT: B 983 ARG cc_start: 0.7766 (mtt180) cc_final: 0.7415 (mtt180) REVERT: B 1041 ASP cc_start: 0.8116 (t0) cc_final: 0.7886 (t0) REVERT: B 1101 HIS cc_start: 0.8369 (m90) cc_final: 0.7972 (m-70) REVERT: C 58 PHE cc_start: 0.8571 (m-10) cc_final: 0.8029 (m-80) REVERT: C 396 TYR cc_start: 0.8442 (m-80) cc_final: 0.8103 (m-10) REVERT: C 698 SER cc_start: 0.8728 (t) cc_final: 0.8484 (p) REVERT: C 756 TYR cc_start: 0.7372 (m-80) cc_final: 0.6994 (m-80) REVERT: C 821 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.8033 (tp) REVERT: C 929 SER cc_start: 0.8337 (OUTLIER) cc_final: 0.8100 (m) REVERT: C 964 LYS cc_start: 0.8407 (ptpp) cc_final: 0.8202 (mtpp) REVERT: C 976 VAL cc_start: 0.8916 (OUTLIER) cc_final: 0.8680 (m) REVERT: C 1019 ARG cc_start: 0.8184 (ttm170) cc_final: 0.7932 (ttp-110) REVERT: C 1096 VAL cc_start: 0.8542 (OUTLIER) cc_final: 0.8336 (m) REVERT: D 28 PHE cc_start: 0.6725 (m-10) cc_final: 0.6520 (m-10) REVERT: D 35 GLU cc_start: 0.6759 (pt0) cc_final: 0.6084 (mp0) REVERT: D 49 ASN cc_start: 0.7189 (t0) cc_final: 0.6826 (t0) REVERT: D 101 GLN cc_start: 0.3604 (mp10) cc_final: 0.3172 (mm110) REVERT: D 120 LEU cc_start: 0.5353 (OUTLIER) cc_final: 0.4732 (pp) REVERT: D 124 SER cc_start: 0.7082 (m) cc_final: 0.6842 (p) REVERT: D 158 TYR cc_start: 0.0989 (t80) cc_final: -0.0668 (t80) REVERT: D 190 MET cc_start: 0.5467 (mmm) cc_final: 0.4884 (mmm) REVERT: D 275 TRP cc_start: 0.5572 (m-90) cc_final: 0.5095 (m-90) REVERT: D 323 MET cc_start: -0.3066 (mmt) cc_final: -0.3347 (mmt) REVERT: D 327 PHE cc_start: 0.6810 (t80) cc_final: 0.6190 (t80) REVERT: D 330 ASN cc_start: 0.0733 (m-40) cc_final: 0.0491 (m110) REVERT: D 379 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.8110 (mp) REVERT: D 388 GLN cc_start: 0.4633 (tt0) cc_final: 0.4377 (pp30) REVERT: D 390 PHE cc_start: 0.7993 (t80) cc_final: 0.7761 (t80) REVERT: D 408 MET cc_start: 0.3398 (mmp) cc_final: 0.2897 (mmm) REVERT: D 455 MET cc_start: 0.6591 (ppp) cc_final: 0.5815 (ppp) REVERT: D 462 MET cc_start: 0.3313 (mmt) cc_final: 0.2960 (mmt) outliers start: 107 outliers final: 65 residues processed: 602 average time/residue: 0.1558 time to fit residues: 155.5953 Evaluate side-chains 573 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 501 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1135 ASN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 442 ASP Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 309 GLN Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 587 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 319 optimal weight: 1.9990 chunk 167 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 293 optimal weight: 0.5980 chunk 90 optimal weight: 0.9980 chunk 345 optimal weight: 10.0000 chunk 174 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 244 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 332 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A 774 GLN A 907 ASN B 30 ASN B 703 ASN B 907 ASN B 935 GLN B 955 ASN C 207 HIS C 317 ASN C 540 ASN C 784 GLN C 935 GLN D 34 GLN ** D 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 ASN ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.190268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.138425 restraints weight = 42668.552| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.39 r_work: 0.3519 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 29250 Z= 0.165 Angle : 0.611 17.066 39970 Z= 0.301 Chirality : 0.047 0.479 4627 Planarity : 0.004 0.048 5105 Dihedral : 5.919 103.012 4684 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.80 % Allowed : 18.51 % Favored : 77.68 % 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: -1.32 (0.13), residues: 3607 helix: 0.03 (0.18), residues: 900 sheet: -0.01 (0.19), residues: 661 loop : -1.64 (0.12), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 328 TYR 0.020 0.001 TYR D 381 PHE 0.021 0.001 PHE A 194 TRP 0.012 0.001 TRP D 275 HIS 0.003 0.001 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00390 (29184) covalent geometry : angle 0.58141 (39805) SS BOND : bond 0.00510 ( 27) SS BOND : angle 2.06291 ( 54) hydrogen bonds : bond 0.04208 ( 916) hydrogen bonds : angle 5.03996 ( 2580) Misc. bond : bond 0.00196 ( 2) link_NAG-ASN : bond 0.00730 ( 37) link_NAG-ASN : angle 3.33919 ( 111) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 515 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 ASN cc_start: 0.8140 (m110) cc_final: 0.7863 (m110) REVERT: A 574 ASP cc_start: 0.8302 (t0) cc_final: 0.7957 (t0) REVERT: A 583 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7307 (pm20) REVERT: A 592 PHE cc_start: 0.8485 (p90) cc_final: 0.8231 (p90) REVERT: A 599 THR cc_start: 0.8822 (t) cc_final: 0.8584 (p) REVERT: A 723 THR cc_start: 0.8479 (p) cc_final: 0.8270 (p) REVERT: A 735 SER cc_start: 0.8660 (m) cc_final: 0.8258 (p) REVERT: A 776 LYS cc_start: 0.8774 (ttpp) cc_final: 0.8448 (ttmm) REVERT: A 988 GLU cc_start: 0.7978 (tp30) cc_final: 0.7371 (tp30) REVERT: A 1051 SER cc_start: 0.8312 (p) cc_final: 0.8071 (m) REVERT: B 58 PHE cc_start: 0.8855 (m-10) cc_final: 0.8445 (m-10) REVERT: B 65 PHE cc_start: 0.8128 (m-10) cc_final: 0.7854 (m-10) REVERT: B 205 SER cc_start: 0.8670 (m) cc_final: 0.8227 (p) REVERT: B 281 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.8003 (mp0) REVERT: B 304 LYS cc_start: 0.8442 (mttp) cc_final: 0.8197 (mptt) REVERT: B 307 THR cc_start: 0.8586 (p) cc_final: 0.8379 (p) REVERT: B 567 ARG cc_start: 0.7089 (mtm-85) cc_final: 0.6824 (mtt180) REVERT: B 737 ASP cc_start: 0.7698 (t0) cc_final: 0.7458 (t0) REVERT: B 776 LYS cc_start: 0.8671 (ttpt) cc_final: 0.8325 (ttmm) REVERT: B 804 GLN cc_start: 0.8510 (mt0) cc_final: 0.7776 (mt0) REVERT: B 825 LYS cc_start: 0.8520 (ttmm) cc_final: 0.8292 (ttmm) REVERT: B 935 GLN cc_start: 0.7757 (pt0) cc_final: 0.7199 (pt0) REVERT: B 964 LYS cc_start: 0.8837 (tmtt) cc_final: 0.8406 (tmtt) REVERT: B 983 ARG cc_start: 0.7723 (mtt180) cc_final: 0.7390 (mtt180) REVERT: B 995 ARG cc_start: 0.8030 (tpp80) cc_final: 0.7710 (ttp80) REVERT: B 998 THR cc_start: 0.8449 (t) cc_final: 0.8076 (p) REVERT: B 1041 ASP cc_start: 0.8081 (t0) cc_final: 0.7846 (t0) REVERT: B 1100 THR cc_start: 0.8439 (p) cc_final: 0.8030 (p) REVERT: B 1101 HIS cc_start: 0.8400 (m90) cc_final: 0.7842 (m-70) REVERT: B 1139 ASP cc_start: 0.7958 (t0) cc_final: 0.7757 (t0) REVERT: C 396 TYR cc_start: 0.8439 (m-80) cc_final: 0.8069 (m-10) REVERT: C 698 SER cc_start: 0.8709 (t) cc_final: 0.8472 (p) REVERT: C 929 SER cc_start: 0.8295 (OUTLIER) cc_final: 0.8078 (m) REVERT: C 976 VAL cc_start: 0.8882 (OUTLIER) cc_final: 0.8654 (m) REVERT: C 984 LEU cc_start: 0.8384 (mm) cc_final: 0.8130 (mp) REVERT: C 1019 ARG cc_start: 0.8149 (ttm170) cc_final: 0.7889 (ttp-110) REVERT: D 35 GLU cc_start: 0.6782 (pt0) cc_final: 0.6097 (mp0) REVERT: D 49 ASN cc_start: 0.7183 (t0) cc_final: 0.6850 (t0) REVERT: D 64 GLU cc_start: 0.7939 (tm-30) cc_final: 0.7726 (tm-30) REVERT: D 94 LYS cc_start: 0.8562 (ptmt) cc_final: 0.7967 (tptp) REVERT: D 101 GLN cc_start: 0.3539 (mp10) cc_final: 0.3134 (mm110) REVERT: D 120 LEU cc_start: 0.5461 (OUTLIER) cc_final: 0.4654 (pp) REVERT: D 124 SER cc_start: 0.7041 (m) cc_final: 0.6802 (p) REVERT: D 158 TYR cc_start: 0.0883 (t80) cc_final: -0.0736 (t80) REVERT: D 190 MET cc_start: 0.5560 (mmm) cc_final: 0.4975 (mmm) REVERT: D 327 PHE cc_start: 0.6871 (t80) cc_final: 0.6301 (t80) REVERT: D 330 ASN cc_start: 0.0497 (m-40) cc_final: 0.0273 (m110) REVERT: D 408 MET cc_start: 0.3496 (mmp) cc_final: 0.2833 (mmm) REVERT: D 452 PHE cc_start: 0.6462 (t80) cc_final: 0.5749 (t80) REVERT: D 455 MET cc_start: 0.6543 (ppp) cc_final: 0.5546 (ppp) REVERT: D 462 MET cc_start: 0.3333 (mmt) cc_final: 0.3004 (mmt) REVERT: D 497 TYR cc_start: 0.0673 (m-80) cc_final: -0.1114 (m-80) REVERT: D 579 MET cc_start: -0.1363 (mmm) cc_final: -0.2694 (mmm) outliers start: 112 outliers final: 69 residues processed: 591 average time/residue: 0.1553 time to fit residues: 151.4653 Evaluate side-chains 573 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 499 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 442 ASP Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 34 GLN Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 309 GLN Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 587 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 277 optimal weight: 0.6980 chunk 317 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 53 optimal weight: 0.3980 chunk 134 optimal weight: 0.0270 chunk 344 optimal weight: 7.9990 chunk 64 optimal weight: 0.9980 chunk 261 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 313 optimal weight: 5.9990 chunk 1 optimal weight: 0.0980 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN B 30 ASN B 188 ASN B 703 ASN B 895 GLN B 907 ASN C 317 ASN D 300 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.191199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.139703 restraints weight = 42620.960| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.32 r_work: 0.3539 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 29250 Z= 0.130 Angle : 0.592 18.925 39970 Z= 0.289 Chirality : 0.047 0.729 4627 Planarity : 0.004 0.047 5105 Dihedral : 5.721 101.612 4684 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.26 % Allowed : 19.77 % Favored : 76.97 % 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: -1.06 (0.13), residues: 3607 helix: 0.35 (0.18), residues: 880 sheet: 0.12 (0.19), residues: 671 loop : -1.51 (0.13), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 328 TYR 0.020 0.001 TYR D 385 PHE 0.024 0.001 PHE A 201 TRP 0.029 0.001 TRP D 275 HIS 0.002 0.001 HIS D 265 Details of bonding type rmsd covalent geometry : bond 0.00306 (29184) covalent geometry : angle 0.55843 (39805) SS BOND : bond 0.00460 ( 27) SS BOND : angle 1.88522 ( 54) hydrogen bonds : bond 0.03930 ( 916) hydrogen bonds : angle 4.90614 ( 2580) Misc. bond : bond 0.00202 ( 2) link_NAG-ASN : bond 0.00740 ( 37) link_NAG-ASN : angle 3.53663 ( 111) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 519 time to evaluate : 0.845 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 319 ARG cc_start: 0.8154 (ttm110) cc_final: 0.7889 (ttm110) REVERT: A 574 ASP cc_start: 0.8240 (t0) cc_final: 0.7904 (t0) REVERT: A 578 ASP cc_start: 0.7044 (t0) cc_final: 0.6746 (t70) REVERT: A 583 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7307 (pm20) REVERT: A 592 PHE cc_start: 0.8453 (p90) cc_final: 0.8240 (p90) REVERT: A 599 THR cc_start: 0.8790 (t) cc_final: 0.8569 (p) REVERT: A 723 THR cc_start: 0.8484 (p) cc_final: 0.8277 (p) REVERT: A 735 SER cc_start: 0.8664 (m) cc_final: 0.8294 (p) REVERT: A 776 LYS cc_start: 0.8785 (ttpp) cc_final: 0.8467 (ttmm) REVERT: A 988 GLU cc_start: 0.7974 (tp30) cc_final: 0.7354 (tp30) REVERT: A 1051 SER cc_start: 0.8289 (p) cc_final: 0.8035 (m) REVERT: B 58 PHE cc_start: 0.8824 (m-10) cc_final: 0.8226 (m-80) REVERT: B 99 ASN cc_start: 0.8551 (t0) cc_final: 0.8289 (t0) REVERT: B 125 ASN cc_start: 0.7401 (p0) cc_final: 0.7117 (p0) REVERT: B 205 SER cc_start: 0.8657 (m) cc_final: 0.8243 (p) REVERT: B 281 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7980 (mp0) REVERT: B 304 LYS cc_start: 0.8417 (mttp) cc_final: 0.8181 (mptt) REVERT: B 307 THR cc_start: 0.8573 (p) cc_final: 0.8364 (p) REVERT: B 567 ARG cc_start: 0.7057 (mtm-85) cc_final: 0.6800 (mtt180) REVERT: B 776 LYS cc_start: 0.8691 (ttpt) cc_final: 0.8361 (ttmm) REVERT: B 964 LYS cc_start: 0.8843 (tmtt) cc_final: 0.8413 (tmtt) REVERT: B 970 PHE cc_start: 0.7307 (m-10) cc_final: 0.7059 (m-10) REVERT: B 983 ARG cc_start: 0.7688 (mtt180) cc_final: 0.7368 (mtt180) REVERT: B 1100 THR cc_start: 0.8456 (p) cc_final: 0.8055 (p) REVERT: B 1101 HIS cc_start: 0.8393 (m90) cc_final: 0.7907 (m-70) REVERT: C 396 TYR cc_start: 0.8397 (m-80) cc_final: 0.7994 (m-10) REVERT: C 698 SER cc_start: 0.8677 (t) cc_final: 0.8463 (p) REVERT: C 976 VAL cc_start: 0.8846 (OUTLIER) cc_final: 0.8643 (m) REVERT: C 984 LEU cc_start: 0.8362 (mm) cc_final: 0.8108 (mp) REVERT: C 1094 VAL cc_start: 0.8188 (m) cc_final: 0.7958 (p) REVERT: D 49 ASN cc_start: 0.7181 (t0) cc_final: 0.6839 (t0) REVERT: D 60 GLN cc_start: 0.7361 (mm-40) cc_final: 0.7139 (mm-40) REVERT: D 94 LYS cc_start: 0.8554 (ptmt) cc_final: 0.7944 (tptp) REVERT: D 101 GLN cc_start: 0.3490 (mp10) cc_final: 0.3111 (mm-40) REVERT: D 120 LEU cc_start: 0.6109 (OUTLIER) cc_final: 0.5506 (pp) REVERT: D 124 SER cc_start: 0.6997 (m) cc_final: 0.6747 (p) REVERT: D 190 MET cc_start: 0.5555 (mmm) cc_final: 0.5049 (mmm) REVERT: D 275 TRP cc_start: 0.5286 (m-90) cc_final: 0.4894 (m-90) REVERT: D 327 PHE cc_start: 0.6838 (t80) cc_final: 0.6270 (t80) REVERT: D 330 ASN cc_start: 0.0592 (m-40) cc_final: 0.0362 (m110) REVERT: D 379 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.8152 (mp) REVERT: D 408 MET cc_start: 0.3393 (mmp) cc_final: 0.2899 (mmm) REVERT: D 452 PHE cc_start: 0.6491 (t80) cc_final: 0.6266 (t80) REVERT: D 455 MET cc_start: 0.6519 (ppp) cc_final: 0.6163 (ppp) REVERT: D 462 MET cc_start: 0.3257 (mmt) cc_final: 0.2970 (mmt) REVERT: D 497 TYR cc_start: 0.0635 (m-80) cc_final: -0.1104 (m-80) outliers start: 96 outliers final: 69 residues processed: 583 average time/residue: 0.1558 time to fit residues: 148.7562 Evaluate side-chains 588 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 514 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 547 LYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 442 ASP Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 34 GLN Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 309 GLN Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 581 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 69 optimal weight: 1.9990 chunk 268 optimal weight: 0.3980 chunk 9 optimal weight: 3.9990 chunk 147 optimal weight: 9.9990 chunk 357 optimal weight: 20.0000 chunk 14 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 90 optimal weight: 0.5980 chunk 167 optimal weight: 2.9990 chunk 337 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 474 GLN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN B 703 ASN B 907 ASN B 935 GLN C 540 ASN C 901 GLN D 34 GLN D 378 HIS ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.189171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.137260 restraints weight = 42544.083| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.41 r_work: 0.3482 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 29250 Z= 0.213 Angle : 0.647 17.837 39970 Z= 0.318 Chirality : 0.048 0.542 4627 Planarity : 0.004 0.049 5105 Dihedral : 5.772 98.357 4684 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.40 % Allowed : 20.65 % Favored : 75.95 % 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: -1.04 (0.13), residues: 3607 helix: 0.29 (0.18), residues: 909 sheet: 0.03 (0.19), residues: 672 loop : -1.44 (0.13), residues: 2026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 190 TYR 0.021 0.002 TYR D 385 PHE 0.027 0.002 PHE D 28 TRP 0.016 0.001 TRP D 275 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00509 (29184) covalent geometry : angle 0.61529 (39805) SS BOND : bond 0.00628 ( 27) SS BOND : angle 2.48009 ( 54) hydrogen bonds : bond 0.04569 ( 916) hydrogen bonds : angle 5.03503 ( 2580) Misc. bond : bond 0.00185 ( 2) link_NAG-ASN : bond 0.00688 ( 37) link_NAG-ASN : angle 3.46438 ( 111) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 533 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7532 (mtm110) cc_final: 0.7022 (ttp-110) REVERT: A 319 ARG cc_start: 0.8215 (ttm110) cc_final: 0.7968 (ttm110) REVERT: A 574 ASP cc_start: 0.8305 (t0) cc_final: 0.8013 (t0) REVERT: A 578 ASP cc_start: 0.7107 (t0) cc_final: 0.6786 (t0) REVERT: A 583 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7368 (pm20) REVERT: A 591 SER cc_start: 0.8463 (OUTLIER) cc_final: 0.8204 (t) REVERT: A 599 THR cc_start: 0.8816 (t) cc_final: 0.8591 (p) REVERT: A 723 THR cc_start: 0.8524 (OUTLIER) cc_final: 0.8310 (p) REVERT: A 735 SER cc_start: 0.8724 (m) cc_final: 0.8270 (p) REVERT: A 737 ASP cc_start: 0.8054 (t0) cc_final: 0.7719 (t0) REVERT: A 976 VAL cc_start: 0.8570 (t) cc_final: 0.8368 (m) REVERT: A 988 GLU cc_start: 0.7975 (tp30) cc_final: 0.7304 (tp30) REVERT: A 1031 GLU cc_start: 0.8293 (mt-10) cc_final: 0.8046 (mt-10) REVERT: A 1094 VAL cc_start: 0.8390 (m) cc_final: 0.8187 (p) REVERT: B 58 PHE cc_start: 0.8817 (m-10) cc_final: 0.8216 (m-80) REVERT: B 65 PHE cc_start: 0.7909 (m-10) cc_final: 0.7664 (m-10) REVERT: B 99 ASN cc_start: 0.8523 (t0) cc_final: 0.8299 (t0) REVERT: B 125 ASN cc_start: 0.7597 (p0) cc_final: 0.7326 (p0) REVERT: B 205 SER cc_start: 0.8718 (m) cc_final: 0.8363 (p) REVERT: B 281 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.8018 (mp0) REVERT: B 567 ARG cc_start: 0.7144 (mtm-85) cc_final: 0.6916 (mtt180) REVERT: B 607 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.8417 (mt0) REVERT: B 776 LYS cc_start: 0.8721 (ttpt) cc_final: 0.8451 (ttmm) REVERT: B 778 THR cc_start: 0.8809 (t) cc_final: 0.8520 (m) REVERT: B 804 GLN cc_start: 0.8666 (mm-40) cc_final: 0.7830 (mt0) REVERT: B 935 GLN cc_start: 0.7902 (pt0) cc_final: 0.7216 (pt0) REVERT: B 964 LYS cc_start: 0.8878 (tmtt) cc_final: 0.8417 (tmtt) REVERT: B 983 ARG cc_start: 0.7748 (mtt180) cc_final: 0.7426 (mtt180) REVERT: B 1041 ASP cc_start: 0.8168 (t0) cc_final: 0.7954 (t0) REVERT: B 1100 THR cc_start: 0.8540 (p) cc_final: 0.8259 (p) REVERT: B 1101 HIS cc_start: 0.8390 (m90) cc_final: 0.8034 (m-70) REVERT: C 396 TYR cc_start: 0.8476 (m-80) cc_final: 0.8177 (m-10) REVERT: C 698 SER cc_start: 0.8701 (t) cc_final: 0.8488 (p) REVERT: C 984 LEU cc_start: 0.8411 (mm) cc_final: 0.8143 (mp) REVERT: C 1002 GLN cc_start: 0.8165 (tm-30) cc_final: 0.7914 (tm-30) REVERT: C 1072 GLU cc_start: 0.8104 (mp0) cc_final: 0.7849 (mp0) REVERT: C 1094 VAL cc_start: 0.8455 (m) cc_final: 0.8242 (p) REVERT: D 35 GLU cc_start: 0.6766 (pt0) cc_final: 0.5940 (mp0) REVERT: D 49 ASN cc_start: 0.7173 (t0) cc_final: 0.6824 (t0) REVERT: D 101 GLN cc_start: 0.3644 (mp10) cc_final: 0.3332 (mm110) REVERT: D 120 LEU cc_start: 0.5928 (OUTLIER) cc_final: 0.5621 (pp) REVERT: D 124 SER cc_start: 0.6996 (m) cc_final: 0.6732 (p) REVERT: D 152 MET cc_start: 0.0060 (tmm) cc_final: -0.0207 (ppp) REVERT: D 162 LEU cc_start: 0.6690 (tt) cc_final: 0.6452 (mt) REVERT: D 190 MET cc_start: 0.5613 (mmm) cc_final: 0.5115 (mmm) REVERT: D 275 TRP cc_start: 0.5318 (m-90) cc_final: 0.4942 (m-90) REVERT: D 306 ARG cc_start: 0.8028 (mmt180) cc_final: 0.7615 (mmm-85) REVERT: D 323 MET cc_start: -0.3055 (mmt) cc_final: -0.3448 (mmt) REVERT: D 327 PHE cc_start: 0.6919 (t80) cc_final: 0.6347 (t80) REVERT: D 330 ASN cc_start: 0.0559 (m-40) cc_final: 0.0298 (m110) REVERT: D 369 PHE cc_start: 0.3155 (m-10) cc_final: 0.2795 (m-10) REVERT: D 379 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.8196 (mp) REVERT: D 402 GLU cc_start: 0.5020 (tp30) cc_final: 0.4564 (tp30) REVERT: D 408 MET cc_start: 0.3467 (mmp) cc_final: 0.3174 (mmm) REVERT: D 455 MET cc_start: 0.6501 (ppp) cc_final: 0.6227 (ppp) REVERT: D 460 ARG cc_start: 0.6934 (ptp90) cc_final: 0.6661 (ptp-170) REVERT: D 462 MET cc_start: 0.3261 (mmt) cc_final: 0.3009 (mmp) REVERT: D 497 TYR cc_start: 0.0724 (m-80) cc_final: -0.1024 (m-80) outliers start: 100 outliers final: 72 residues processed: 602 average time/residue: 0.1597 time to fit residues: 156.9048 Evaluate side-chains 604 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 525 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 607 GLN Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1135 ASN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 442 ASP Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 34 GLN Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 309 GLN Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 587 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 148 optimal weight: 0.0770 chunk 238 optimal weight: 0.1980 chunk 155 optimal weight: 0.4980 chunk 33 optimal weight: 0.9990 chunk 194 optimal weight: 0.9980 chunk 265 optimal weight: 0.8980 chunk 262 optimal weight: 0.9990 chunk 198 optimal weight: 0.5980 chunk 171 optimal weight: 0.6980 chunk 293 optimal weight: 0.5980 chunk 233 optimal weight: 2.9990 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN B 30 ASN B 703 ASN B 907 ASN B 955 ASN C 901 GLN C 907 ASN ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.191389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.139676 restraints weight = 42586.693| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.29 r_work: 0.3529 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 29250 Z= 0.125 Angle : 0.599 17.782 39970 Z= 0.293 Chirality : 0.046 0.494 4627 Planarity : 0.004 0.048 5105 Dihedral : 5.624 97.252 4684 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.09 % Allowed : 21.30 % Favored : 75.61 % 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: -0.86 (0.14), residues: 3607 helix: 0.49 (0.18), residues: 901 sheet: 0.20 (0.19), residues: 662 loop : -1.36 (0.13), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 161 TYR 0.020 0.001 TYR D 385 PHE 0.030 0.001 PHE D 28 TRP 0.017 0.001 TRP A 436 HIS 0.003 0.000 HIS D 265 Details of bonding type rmsd covalent geometry : bond 0.00293 (29184) covalent geometry : angle 0.56681 (39805) SS BOND : bond 0.00600 ( 27) SS BOND : angle 2.47813 ( 54) hydrogen bonds : bond 0.03879 ( 916) hydrogen bonds : angle 4.90717 ( 2580) Misc. bond : bond 0.00200 ( 2) link_NAG-ASN : bond 0.00673 ( 37) link_NAG-ASN : angle 3.29187 ( 111) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 525 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7447 (mtm110) cc_final: 0.7061 (ttp-110) REVERT: A 303 LEU cc_start: 0.8598 (mt) cc_final: 0.8347 (mp) REVERT: A 574 ASP cc_start: 0.8247 (t0) cc_final: 0.7933 (t0) REVERT: A 578 ASP cc_start: 0.7107 (t0) cc_final: 0.6863 (t0) REVERT: A 591 SER cc_start: 0.8467 (OUTLIER) cc_final: 0.8231 (t) REVERT: A 599 THR cc_start: 0.8774 (t) cc_final: 0.8567 (p) REVERT: A 695 TYR cc_start: 0.8369 (p90) cc_final: 0.7815 (p90) REVERT: A 723 THR cc_start: 0.8520 (p) cc_final: 0.8308 (p) REVERT: A 735 SER cc_start: 0.8680 (m) cc_final: 0.8239 (p) REVERT: A 976 VAL cc_start: 0.8540 (t) cc_final: 0.8313 (m) REVERT: A 988 GLU cc_start: 0.7963 (tp30) cc_final: 0.7274 (tp30) REVERT: A 1031 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7940 (mt-10) REVERT: A 1051 SER cc_start: 0.8286 (p) cc_final: 0.8033 (m) REVERT: B 58 PHE cc_start: 0.8744 (m-10) cc_final: 0.8146 (m-80) REVERT: B 65 PHE cc_start: 0.7864 (m-10) cc_final: 0.7656 (m-10) REVERT: B 125 ASN cc_start: 0.7526 (p0) cc_final: 0.7248 (p0) REVERT: B 205 SER cc_start: 0.8628 (m) cc_final: 0.8202 (p) REVERT: B 281 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7977 (mp0) REVERT: B 567 ARG cc_start: 0.7131 (mtm-85) cc_final: 0.6756 (mtt180) REVERT: B 776 LYS cc_start: 0.8731 (ttpt) cc_final: 0.8464 (ttmm) REVERT: B 804 GLN cc_start: 0.8631 (mm-40) cc_final: 0.7885 (mt0) REVERT: B 935 GLN cc_start: 0.7816 (pt0) cc_final: 0.7127 (pt0) REVERT: B 964 LYS cc_start: 0.8861 (tmtt) cc_final: 0.8407 (tmtt) REVERT: B 983 ARG cc_start: 0.7696 (mtt180) cc_final: 0.7400 (mtt180) REVERT: B 994 ASP cc_start: 0.7704 (m-30) cc_final: 0.7454 (t0) REVERT: B 995 ARG cc_start: 0.8028 (ttm-80) cc_final: 0.7822 (ttm-80) REVERT: B 1101 HIS cc_start: 0.8394 (m90) cc_final: 0.8039 (m-70) REVERT: C 58 PHE cc_start: 0.8567 (m-10) cc_final: 0.8277 (m-10) REVERT: C 220 PHE cc_start: 0.8477 (t80) cc_final: 0.8276 (t80) REVERT: C 396 TYR cc_start: 0.8430 (m-80) cc_final: 0.8050 (m-10) REVERT: C 588 THR cc_start: 0.8544 (OUTLIER) cc_final: 0.8128 (p) REVERT: C 698 SER cc_start: 0.8688 (t) cc_final: 0.8481 (p) REVERT: C 859 THR cc_start: 0.8602 (m) cc_final: 0.8331 (p) REVERT: C 984 LEU cc_start: 0.8399 (mm) cc_final: 0.8133 (mp) REVERT: C 1072 GLU cc_start: 0.8030 (mp0) cc_final: 0.7815 (mp0) REVERT: D 35 GLU cc_start: 0.6395 (OUTLIER) cc_final: 0.5903 (mp0) REVERT: D 49 ASN cc_start: 0.7142 (t0) cc_final: 0.6774 (t0) REVERT: D 120 LEU cc_start: 0.6288 (OUTLIER) cc_final: 0.5917 (pp) REVERT: D 124 SER cc_start: 0.7021 (m) cc_final: 0.6766 (p) REVERT: D 152 MET cc_start: -0.0076 (tmm) cc_final: -0.0446 (ppp) REVERT: D 158 TYR cc_start: 0.1464 (t80) cc_final: -0.0199 (t80) REVERT: D 190 MET cc_start: 0.5638 (mmm) cc_final: 0.5118 (mmm) REVERT: D 275 TRP cc_start: 0.5207 (m-90) cc_final: 0.4933 (m-90) REVERT: D 323 MET cc_start: -0.3134 (mmt) cc_final: -0.3540 (mmt) REVERT: D 327 PHE cc_start: 0.6857 (t80) cc_final: 0.6282 (t80) REVERT: D 369 PHE cc_start: 0.2893 (m-10) cc_final: 0.2558 (m-10) REVERT: D 370 LEU cc_start: 0.7086 (mm) cc_final: 0.6394 (tp) REVERT: D 379 ILE cc_start: 0.8401 (OUTLIER) cc_final: 0.8175 (mp) REVERT: D 402 GLU cc_start: 0.5040 (tp30) cc_final: 0.4562 (tp30) REVERT: D 408 MET cc_start: 0.3528 (mmp) cc_final: 0.3294 (mmm) REVERT: D 452 PHE cc_start: 0.6536 (t80) cc_final: 0.6083 (t80) REVERT: D 455 MET cc_start: 0.6470 (ppp) cc_final: 0.6182 (ppp) REVERT: D 460 ARG cc_start: 0.6815 (ptp90) cc_final: 0.6613 (ptp-170) REVERT: D 462 MET cc_start: 0.3224 (mmt) cc_final: 0.3001 (mmp) REVERT: D 497 TYR cc_start: 0.0691 (m-80) cc_final: -0.1035 (m-80) outliers start: 91 outliers final: 66 residues processed: 581 average time/residue: 0.1622 time to fit residues: 153.5637 Evaluate side-chains 579 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 507 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 LYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 442 ASP Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 309 GLN Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 587 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 261 optimal weight: 1.9990 chunk 155 optimal weight: 0.0980 chunk 309 optimal weight: 7.9990 chunk 125 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 266 optimal weight: 0.6980 chunk 181 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 281 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN B 30 ASN B 703 ASN B 895 GLN B 907 ASN C 804 GLN D 34 GLN D 265 HIS D 330 ASN ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.190043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.138385 restraints weight = 42534.504| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.26 r_work: 0.3521 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.4584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 29250 Z= 0.151 Angle : 0.615 17.526 39970 Z= 0.301 Chirality : 0.046 0.475 4627 Planarity : 0.004 0.048 5105 Dihedral : 5.552 95.106 4684 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.19 % Allowed : 21.50 % Favored : 75.31 % 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: -0.85 (0.14), residues: 3607 helix: 0.50 (0.18), residues: 904 sheet: 0.13 (0.19), residues: 675 loop : -1.33 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 102 TYR 0.019 0.001 TYR D 385 PHE 0.035 0.002 PHE D 28 TRP 0.043 0.001 TRP D 69 HIS 0.003 0.000 HIS D 265 Details of bonding type rmsd covalent geometry : bond 0.00358 (29184) covalent geometry : angle 0.58548 (39805) SS BOND : bond 0.00579 ( 27) SS BOND : angle 2.45470 ( 54) hydrogen bonds : bond 0.04025 ( 916) hydrogen bonds : angle 4.89408 ( 2580) Misc. bond : bond 0.00190 ( 2) link_NAG-ASN : bond 0.00820 ( 37) link_NAG-ASN : angle 3.22771 ( 111) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 518 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7467 (mtm110) cc_final: 0.7126 (ttp-110) REVERT: A 269 TYR cc_start: 0.8138 (m-10) cc_final: 0.7898 (m-80) REVERT: A 303 LEU cc_start: 0.8609 (mt) cc_final: 0.8338 (mp) REVERT: A 574 ASP cc_start: 0.8246 (t0) cc_final: 0.7915 (t0) REVERT: A 578 ASP cc_start: 0.7107 (t0) cc_final: 0.6902 (t0) REVERT: A 591 SER cc_start: 0.8489 (OUTLIER) cc_final: 0.8261 (t) REVERT: A 599 THR cc_start: 0.8779 (t) cc_final: 0.8570 (p) REVERT: A 695 TYR cc_start: 0.8345 (p90) cc_final: 0.7892 (p90) REVERT: A 723 THR cc_start: 0.8522 (OUTLIER) cc_final: 0.8314 (p) REVERT: A 735 SER cc_start: 0.8686 (m) cc_final: 0.8257 (p) REVERT: A 976 VAL cc_start: 0.8593 (t) cc_final: 0.8366 (m) REVERT: A 988 GLU cc_start: 0.7957 (tp30) cc_final: 0.7276 (tp30) REVERT: A 1031 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7967 (mt-10) REVERT: A 1051 SER cc_start: 0.8281 (p) cc_final: 0.8037 (m) REVERT: B 58 PHE cc_start: 0.8733 (m-10) cc_final: 0.8100 (m-80) REVERT: B 125 ASN cc_start: 0.7561 (p0) cc_final: 0.7280 (p0) REVERT: B 205 SER cc_start: 0.8651 (m) cc_final: 0.8275 (p) REVERT: B 281 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7961 (mp0) REVERT: B 328 ARG cc_start: 0.7658 (mmm-85) cc_final: 0.7069 (mmm-85) REVERT: B 567 ARG cc_start: 0.7144 (mtm-85) cc_final: 0.6786 (mtt180) REVERT: B 776 LYS cc_start: 0.8732 (ttpt) cc_final: 0.8451 (ttmm) REVERT: B 804 GLN cc_start: 0.8604 (mm-40) cc_final: 0.7912 (mt0) REVERT: B 935 GLN cc_start: 0.7838 (pt0) cc_final: 0.7112 (pt0) REVERT: B 964 LYS cc_start: 0.8853 (tmtt) cc_final: 0.8394 (tmtt) REVERT: B 983 ARG cc_start: 0.7716 (mtt180) cc_final: 0.7421 (mtt180) REVERT: B 994 ASP cc_start: 0.7703 (m-30) cc_final: 0.7438 (t0) REVERT: B 1101 HIS cc_start: 0.8331 (m90) cc_final: 0.7806 (m90) REVERT: C 396 TYR cc_start: 0.8394 (m-80) cc_final: 0.8021 (m-10) REVERT: C 588 THR cc_start: 0.8549 (OUTLIER) cc_final: 0.8127 (p) REVERT: C 698 SER cc_start: 0.8693 (t) cc_final: 0.8489 (p) REVERT: C 859 THR cc_start: 0.8624 (m) cc_final: 0.8346 (p) REVERT: C 927 PHE cc_start: 0.8412 (t80) cc_final: 0.8205 (t80) REVERT: C 984 LEU cc_start: 0.8419 (mm) cc_final: 0.8156 (mp) REVERT: C 1019 ARG cc_start: 0.8136 (ttp-170) cc_final: 0.7933 (ttp-110) REVERT: C 1072 GLU cc_start: 0.8060 (mp0) cc_final: 0.7859 (mp0) REVERT: D 49 ASN cc_start: 0.7165 (t0) cc_final: 0.6792 (t0) REVERT: D 120 LEU cc_start: 0.6266 (OUTLIER) cc_final: 0.5906 (pp) REVERT: D 124 SER cc_start: 0.6977 (m) cc_final: 0.6714 (p) REVERT: D 190 MET cc_start: 0.5684 (mmm) cc_final: 0.5171 (mmm) REVERT: D 275 TRP cc_start: 0.5272 (m-90) cc_final: 0.4956 (m-90) REVERT: D 323 MET cc_start: -0.3093 (mmt) cc_final: -0.3501 (mmt) REVERT: D 327 PHE cc_start: 0.6888 (t80) cc_final: 0.6310 (t80) REVERT: D 366 MET cc_start: 0.2747 (tpp) cc_final: 0.2221 (tpp) REVERT: D 370 LEU cc_start: 0.7154 (OUTLIER) cc_final: 0.6557 (tp) REVERT: D 379 ILE cc_start: 0.8417 (OUTLIER) cc_final: 0.8191 (mp) REVERT: D 402 GLU cc_start: 0.5127 (tp30) cc_final: 0.4642 (tp30) REVERT: D 408 MET cc_start: 0.3542 (mmp) cc_final: 0.3321 (mmm) REVERT: D 452 PHE cc_start: 0.6530 (t80) cc_final: 0.6143 (t80) REVERT: D 455 MET cc_start: 0.6496 (ppp) cc_final: 0.6295 (ppp) outliers start: 94 outliers final: 73 residues processed: 576 average time/residue: 0.1641 time to fit residues: 153.9425 Evaluate side-chains 595 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 515 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 LYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 442 ASP Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 34 GLN Chi-restraints excluded: chain D residue 73 TYR Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 309 GLN Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 581 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 294 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 chunk 280 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 205 optimal weight: 0.9990 chunk 214 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 213 optimal weight: 5.9990 chunk 113 optimal weight: 0.6980 chunk 269 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 907 ASN B 30 ASN B 703 ASN B 907 ASN C 613 GLN ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.188994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.137177 restraints weight = 42335.008| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.31 r_work: 0.3503 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.4683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 29250 Z= 0.185 Angle : 0.640 17.323 39970 Z= 0.311 Chirality : 0.048 0.471 4627 Planarity : 0.004 0.048 5105 Dihedral : 5.610 95.235 4684 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.09 % Allowed : 21.84 % Favored : 75.07 % 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: -0.89 (0.13), residues: 3607 helix: 0.42 (0.18), residues: 911 sheet: 0.17 (0.19), residues: 672 loop : -1.36 (0.13), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 273 TYR 0.019 0.001 TYR C 660 PHE 0.041 0.002 PHE A 643 TRP 0.038 0.001 TRP D 69 HIS 0.003 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00443 (29184) covalent geometry : angle 0.60427 (39805) SS BOND : bond 0.00598 ( 27) SS BOND : angle 2.56414 ( 54) hydrogen bonds : bond 0.04180 ( 916) hydrogen bonds : angle 4.95625 ( 2580) Misc. bond : bond 0.00182 ( 2) link_NAG-ASN : bond 0.00694 ( 37) link_NAG-ASN : angle 3.63774 ( 111) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 518 time to evaluate : 0.910 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 237 ARG cc_start: 0.7524 (mtm110) cc_final: 0.7234 (ttp-110) REVERT: A 269 TYR cc_start: 0.8158 (m-10) cc_final: 0.7914 (m-80) REVERT: A 303 LEU cc_start: 0.8618 (mt) cc_final: 0.8339 (mp) REVERT: A 574 ASP cc_start: 0.8264 (t0) cc_final: 0.7935 (t0) REVERT: A 578 ASP cc_start: 0.7136 (t0) cc_final: 0.6919 (t0) REVERT: A 591 SER cc_start: 0.8504 (OUTLIER) cc_final: 0.8266 (t) REVERT: A 599 THR cc_start: 0.8789 (t) cc_final: 0.8578 (p) REVERT: A 695 TYR cc_start: 0.8352 (p90) cc_final: 0.7918 (p90) REVERT: A 723 THR cc_start: 0.8539 (p) cc_final: 0.8317 (p) REVERT: A 735 SER cc_start: 0.8686 (m) cc_final: 0.8242 (p) REVERT: A 754 LEU cc_start: 0.8844 (mt) cc_final: 0.8640 (mt) REVERT: A 804 GLN cc_start: 0.8315 (mm-40) cc_final: 0.7718 (mt0) REVERT: A 976 VAL cc_start: 0.8618 (t) cc_final: 0.8395 (m) REVERT: A 988 GLU cc_start: 0.7955 (tp30) cc_final: 0.7277 (tp30) REVERT: B 58 PHE cc_start: 0.8717 (m-10) cc_final: 0.8083 (m-80) REVERT: B 125 ASN cc_start: 0.7587 (p0) cc_final: 0.7294 (p0) REVERT: B 205 SER cc_start: 0.8667 (m) cc_final: 0.8296 (p) REVERT: B 237 ARG cc_start: 0.7829 (ttm-80) cc_final: 0.7464 (ttm-80) REVERT: B 328 ARG cc_start: 0.7696 (mmm-85) cc_final: 0.7097 (mmm-85) REVERT: B 567 ARG cc_start: 0.7165 (mtm-85) cc_final: 0.6810 (mtt180) REVERT: B 574 ASP cc_start: 0.8046 (t0) cc_final: 0.7769 (t0) REVERT: B 710 ASN cc_start: 0.8341 (p0) cc_final: 0.8101 (p0) REVERT: B 776 LYS cc_start: 0.8740 (ttpt) cc_final: 0.8449 (ttmm) REVERT: B 778 THR cc_start: 0.8828 (t) cc_final: 0.8536 (m) REVERT: B 804 GLN cc_start: 0.8650 (mm-40) cc_final: 0.7895 (mt0) REVERT: B 907 ASN cc_start: 0.8304 (OUTLIER) cc_final: 0.8102 (m110) REVERT: B 935 GLN cc_start: 0.7847 (pt0) cc_final: 0.7118 (pt0) REVERT: B 983 ARG cc_start: 0.7741 (mtt180) cc_final: 0.7455 (mtt180) REVERT: B 994 ASP cc_start: 0.7736 (m-30) cc_final: 0.7469 (t0) REVERT: B 1101 HIS cc_start: 0.8372 (m90) cc_final: 0.7859 (m90) REVERT: C 396 TYR cc_start: 0.8412 (m-80) cc_final: 0.8099 (m-10) REVERT: C 588 THR cc_start: 0.8555 (OUTLIER) cc_final: 0.8138 (p) REVERT: C 859 THR cc_start: 0.8631 (m) cc_final: 0.8350 (p) REVERT: C 927 PHE cc_start: 0.8411 (t80) cc_final: 0.8208 (t80) REVERT: C 984 LEU cc_start: 0.8435 (mm) cc_final: 0.8170 (mp) REVERT: C 1072 GLU cc_start: 0.8115 (mp0) cc_final: 0.7907 (mp0) REVERT: D 49 ASN cc_start: 0.7169 (t0) cc_final: 0.6789 (t0) REVERT: D 120 LEU cc_start: 0.6338 (OUTLIER) cc_final: 0.5981 (pp) REVERT: D 124 SER cc_start: 0.6979 (m) cc_final: 0.6735 (p) REVERT: D 152 MET cc_start: -0.0118 (tmm) cc_final: -0.0572 (ppp) REVERT: D 190 MET cc_start: 0.5685 (mmm) cc_final: 0.5111 (mmm) REVERT: D 275 TRP cc_start: 0.5295 (m-90) cc_final: 0.5007 (m-90) REVERT: D 323 MET cc_start: -0.3118 (mmt) cc_final: -0.3515 (mmt) REVERT: D 327 PHE cc_start: 0.6923 (t80) cc_final: 0.6339 (t80) REVERT: D 366 MET cc_start: 0.2780 (tpp) cc_final: 0.2254 (tpp) REVERT: D 370 LEU cc_start: 0.7178 (OUTLIER) cc_final: 0.6636 (tp) REVERT: D 379 ILE cc_start: 0.8422 (OUTLIER) cc_final: 0.8193 (mp) REVERT: D 402 GLU cc_start: 0.5178 (tp30) cc_final: 0.4670 (tp30) REVERT: D 408 MET cc_start: 0.3423 (mmp) cc_final: 0.3197 (mmm) REVERT: D 455 MET cc_start: 0.6438 (ppp) cc_final: 0.6144 (ppp) outliers start: 91 outliers final: 78 residues processed: 574 average time/residue: 0.1643 time to fit residues: 153.9247 Evaluate side-chains 601 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 517 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 547 LYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 442 ASP Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 34 GLN Chi-restraints excluded: chain D residue 73 TYR Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 309 GLN Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 581 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 115 optimal weight: 0.5980 chunk 114 optimal weight: 0.9980 chunk 137 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 278 optimal weight: 0.4980 chunk 292 optimal weight: 0.1980 chunk 214 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 chunk 184 optimal weight: 0.7980 chunk 215 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN A1134 ASN B 703 ASN B 907 ASN D 34 GLN ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 ASN ** 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 = 0.4310 r_free = 0.4310 target = 0.189573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.137899 restraints weight = 42198.979| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.27 r_work: 0.3512 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 29250 Z= 0.152 Angle : 0.627 17.028 39970 Z= 0.304 Chirality : 0.047 0.462 4627 Planarity : 0.004 0.048 5105 Dihedral : 5.688 94.803 4684 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.89 % Allowed : 22.01 % Favored : 75.10 % 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: -0.82 (0.14), residues: 3607 helix: 0.46 (0.18), residues: 909 sheet: 0.19 (0.19), residues: 673 loop : -1.30 (0.13), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 328 TYR 0.018 0.001 TYR D 385 PHE 0.039 0.002 PHE D 28 TRP 0.034 0.001 TRP D 69 HIS 0.002 0.000 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00363 (29184) covalent geometry : angle 0.59187 (39805) SS BOND : bond 0.00557 ( 27) SS BOND : angle 2.36718 ( 54) hydrogen bonds : bond 0.03975 ( 916) hydrogen bonds : angle 4.94111 ( 2580) Misc. bond : bond 0.00195 ( 2) link_NAG-ASN : bond 0.00656 ( 37) link_NAG-ASN : angle 3.60846 ( 111) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9553.87 seconds wall clock time: 163 minutes 13.09 seconds (9793.09 seconds total)