Starting phenix.real_space_refine on Sun Jul 5 14:42:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xo5_33337/07_2026/7xo5_33337.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xo5_33337/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/7xo5_33337/07_2026/7xo5_33337.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xo5_33337/07_2026/7xo5_33337.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7xo5_33337/07_2026/7xo5_33337.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xo5_33337/07_2026/7xo5_33337.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xo5_33337/07_2026/7xo5_33337.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xo5_33337/07_2026/7xo5_33337.map" } 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-6108/lib/python3.11/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 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 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 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 chiralities: 2 Time building chain proxies: 6.29, 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: 2.39 Conformation dependent library (CDL) restraints added in 1.4 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: 1.25 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: 3.22 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 - 18.06: 14998 18.06 - 36.12: 1513 36.12 - 54.18: 308 54.18 - 72.24: 48 72.24 - 90.30: 30 Dihedral angle restraints: 16897 sinusoidal: 6224 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 16894 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: 7.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 28.040 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 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 : 15.285 89.247 9938 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/Z covalent geometry : bond 0.00485 / 0.24 (29184) covalent geometry : angle 0.93542 / 0.49 (39805) SS BOND : bond 0.00891 / 0.40 ( 27) SS BOND : angle 1.75303 / 1.18 ( 54) hydrogen bonds : bond 0.29583 / 19.79 ( 916) hydrogen bonds : angle 10.46885 / 7.10 ( 2580) Misc. bond : bond 0.01060 / 0.56 ( 2) link_NAG-ASN : bond 0.00926 / 0.70 ( 37) link_NAG-ASN : angle 4.36363 / 3.06 ( 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 : 1.121 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: 0.1737 time to fit residues: 185.2340 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 : 1.064 ------------------------------------------------------------------------------- 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... 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 641 ASN 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 C1106 GLN D 34 GLN ** D 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 86 GLN D 117 ASN D 216 ASN ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 524 GLN D 536 ASN D 607 ASN Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.198019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.148011 restraints weight = 43877.825| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 2.46 r_work: 0.3650 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3508 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29250 Z= 0.155 Angle : 0.655 20.364 39970 Z= 0.326 Chirality : 0.047 0.398 4627 Planarity : 0.005 0.057 5105 Dihedral : 4.524 37.085 3907 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.80 % Allowed : 13.76 % Favored : 84.44 % 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: -2.70 (0.12), residues: 3607 helix: -2.09 (0.13), residues: 852 sheet: -0.65 (0.20), residues: 596 loop : -2.07 (0.11), residues: 2159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 190 TYR 0.022 0.001 TYR D 454 PHE 0.025 0.002 PHE A 541 TRP 0.020 0.001 TRP D 69 HIS 0.008 0.001 HIS A1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (29184) covalent geometry : angle 0.63045 / 0.32 (39805) SS BOND : bond 0.00444 / 0.22 ( 27) SS BOND : angle 1.58165 / 1.08 ( 54) hydrogen bonds : bond 0.04847 / 3.32 ( 916) hydrogen bonds : angle 5.81942 / 3.97 ( 2580) Misc. bond : bond 0.00273 / 0.14 ( 2) link_NAG-ASN : bond 0.00709 / 0.53 ( 37) link_NAG-ASN : angle 3.27855 / 2.18 ( 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 626 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 573 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8029 (OUTLIER) cc_final: 0.7748 (m) REVERT: A 58 PHE cc_start: 0.8448 (m-10) cc_final: 0.8241 (m-80) REVERT: A 189 LEU cc_start: 0.7722 (tp) cc_final: 0.7376 (tp) REVERT: A 317 ASN cc_start: 0.8037 (m-40) cc_final: 0.7723 (m-40) REVERT: A 574 ASP cc_start: 0.8267 (t0) cc_final: 0.7993 (t0) REVERT: A 578 ASP cc_start: 0.7195 (t70) cc_final: 0.6623 (t70) REVERT: A 599 THR cc_start: 0.8753 (t) cc_final: 0.8474 (p) REVERT: A 735 SER cc_start: 0.8650 (m) cc_final: 0.8233 (p) REVERT: A 737 ASP cc_start: 0.7282 (t0) cc_final: 0.7013 (t0) REVERT: A 868 GLU cc_start: 0.7792 (mp0) cc_final: 0.7571 (mp0) REVERT: A 904 TYR cc_start: 0.7253 (m-80) cc_final: 0.7032 (m-10) REVERT: A 988 GLU cc_start: 0.7903 (tp30) cc_final: 0.7614 (tp30) REVERT: A 1031 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7984 (mt-10) REVERT: A 1051 SER cc_start: 0.8177 (p) cc_final: 0.7872 (m) REVERT: B 205 SER cc_start: 0.8559 (m) cc_final: 0.8209 (p) REVERT: B 273 ARG cc_start: 0.7927 (mmm160) cc_final: 0.7602 (mmm160) REVERT: B 281 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7936 (mp0) REVERT: B 535 LYS cc_start: 0.8043 (mmtm) cc_final: 0.7762 (mttp) REVERT: B 587 ILE cc_start: 0.7373 (mt) cc_final: 0.7166 (tt) REVERT: B 643 PHE cc_start: 0.7883 (t80) cc_final: 0.7589 (t80) REVERT: B 737 ASP cc_start: 0.7561 (t0) cc_final: 0.7191 (t0) REVERT: B 804 GLN cc_start: 0.8404 (mt0) cc_final: 0.7608 (mt0) REVERT: B 902 MET cc_start: 0.8253 (tpp) cc_final: 0.7632 (mmm) REVERT: B 929 SER cc_start: 0.8422 (p) cc_final: 0.8150 (m) REVERT: B 935 GLN cc_start: 0.7493 (pt0) cc_final: 0.7060 (pt0) REVERT: B 964 LYS cc_start: 0.8712 (tmtt) cc_final: 0.8437 (tmtt) REVERT: B 983 ARG cc_start: 0.7637 (mtt180) cc_final: 0.7296 (mtt180) REVERT: B 1041 ASP cc_start: 0.7893 (t0) cc_final: 0.7661 (t0) REVERT: B 1101 HIS cc_start: 0.8013 (m90) cc_final: 0.7675 (m-70) REVERT: B 1105 THR cc_start: 0.7733 (t) cc_final: 0.7482 (t) REVERT: C 32 PHE cc_start: 0.7868 (m-80) cc_final: 0.7657 (m-80) REVERT: C 170 TYR cc_start: 0.6903 (t80) cc_final: 0.6608 (t80) REVERT: C 326 ILE cc_start: 0.8075 (tt) cc_final: 0.7791 (pt) REVERT: C 396 TYR cc_start: 0.8388 (m-80) cc_final: 0.8119 (m-10) REVERT: C 442 ASP cc_start: 0.6144 (m-30) cc_final: 0.5878 (t0) REVERT: C 608 VAL cc_start: 0.8680 (p) cc_final: 0.8437 (t) REVERT: C 725 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.8047 (tt0) REVERT: C 918 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7531 (mt-10) REVERT: C 964 LYS cc_start: 0.8301 (ptpp) cc_final: 0.8091 (mtpp) REVERT: C 974 SER cc_start: 0.8470 (p) cc_final: 0.8080 (m) REVERT: C 976 VAL cc_start: 0.8524 (p) cc_final: 0.8319 (m) REVERT: C 1019 ARG cc_start: 0.8130 (ttm170) cc_final: 0.7892 (ttp-170) REVERT: C 1094 VAL cc_start: 0.8231 (m) cc_final: 0.7709 (m) REVERT: C 1128 VAL cc_start: 0.8790 (t) cc_final: 0.8525 (m) REVERT: D 49 ASN cc_start: 0.7147 (t0) cc_final: 0.6710 (t0) REVERT: D 64 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7487 (tm-30) REVERT: D 120 LEU cc_start: 0.5054 (OUTLIER) cc_final: 0.4506 (pp) REVERT: D 175 GLN cc_start: 0.6395 (tp-100) cc_final: 0.6138 (tp-100) REVERT: D 190 MET cc_start: 0.5402 (mmm) cc_final: 0.4753 (mmm) REVERT: D 313 LYS cc_start: 0.5881 (ptpt) cc_final: 0.5096 (mmtt) REVERT: D 323 MET cc_start: -0.3124 (mmt) cc_final: -0.3654 (mmt) REVERT: D 327 PHE cc_start: 0.6890 (t80) cc_final: 0.5981 (t80) REVERT: D 455 MET cc_start: 0.6443 (ppp) cc_final: 0.5491 (ppp) REVERT: D 462 MET cc_start: 0.3492 (mmt) cc_final: 0.3039 (mmt) outliers start: 53 outliers final: 28 residues processed: 607 average time/residue: 0.1748 time to fit residues: 172.2895 Evaluate side-chains 550 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 519 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 54 LEU 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 407 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 C residue 514 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 725 GLU 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: 0.6980 chunk 265 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 351 optimal weight: 3.9990 chunk 331 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 94 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 339 optimal weight: 8.9990 chunk 330 optimal weight: 10.0000 chunk 229 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN A 317 ASN A 422 ASN A 544 ASN A 955 ASN A 957 GLN A1106 GLN B 188 ASN B 658 ASN B 895 GLN B 919 ASN C 540 ASN C 544 ASN C 644 GLN C 658 ASN C 777 ASN C 784 GLN C 955 ASN C1054 GLN D 34 GLN ** D 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.189888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.138396 restraints weight = 42920.450| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.31 r_work: 0.3526 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 29250 Z= 0.230 Angle : 0.688 10.684 39970 Z= 0.345 Chirality : 0.049 0.386 4627 Planarity : 0.005 0.056 5105 Dihedral : 4.776 51.670 3907 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.50 % Allowed : 16.47 % Favored : 80.03 % 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: -1.94 (0.13), residues: 3607 helix: -0.83 (0.16), residues: 888 sheet: -0.29 (0.19), residues: 676 loop : -1.90 (0.12), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 34 TYR 0.021 0.002 TYR C 38 PHE 0.021 0.002 PHE C 559 TRP 0.029 0.002 TRP D 275 HIS 0.005 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.23 (29184) covalent geometry : angle 0.66867 / 0.34 (39805) SS BOND : bond 0.00573 / 0.30 ( 27) SS BOND : angle 2.44815 / 1.66 ( 54) hydrogen bonds : bond 0.05417 / 3.70 ( 916) hydrogen bonds : angle 5.45553 / 3.72 ( 2580) Misc. bond : bond 0.00234 / 0.12 ( 2) link_NAG-ASN : bond 0.00576 / 0.37 ( 37) link_NAG-ASN : angle 2.70471 / 1.86 ( 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 656 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 553 time to evaluate : 1.069 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 574 ASP cc_start: 0.8202 (t0) cc_final: 0.7871 (t0) REVERT: A 578 ASP cc_start: 0.7152 (t0) cc_final: 0.6872 (t0) REVERT: A 591 SER cc_start: 0.8397 (m) cc_final: 0.8151 (t) REVERT: A 599 THR cc_start: 0.8836 (t) cc_final: 0.8573 (p) REVERT: A 723 THR cc_start: 0.8437 (p) cc_final: 0.8212 (p) REVERT: A 735 SER cc_start: 0.8680 (m) cc_final: 0.8281 (p) REVERT: A 904 TYR cc_start: 0.7290 (m-80) cc_final: 0.7055 (m-10) REVERT: A 981 PHE cc_start: 0.8463 (m-80) cc_final: 0.8257 (m-80) REVERT: A 988 GLU cc_start: 0.7970 (tp30) cc_final: 0.7465 (tp30) REVERT: A 992 GLN cc_start: 0.7806 (mm-40) cc_final: 0.7466 (mt0) REVERT: B 188 ASN cc_start: 0.8201 (OUTLIER) cc_final: 0.7968 (p0) REVERT: B 281 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7994 (mp0) REVERT: B 307 THR cc_start: 0.8652 (p) cc_final: 0.8383 (p) REVERT: B 776 LYS cc_start: 0.8718 (ttpt) cc_final: 0.8426 (ttmm) REVERT: B 804 GLN cc_start: 0.8558 (mt0) cc_final: 0.8221 (mm-40) REVERT: B 929 SER cc_start: 0.8568 (p) cc_final: 0.8365 (m) REVERT: B 935 GLN cc_start: 0.7910 (pt0) cc_final: 0.7692 (pt0) REVERT: B 964 LYS cc_start: 0.8851 (tmtt) cc_final: 0.8432 (tmtt) REVERT: B 983 ARG cc_start: 0.7735 (mtt180) cc_final: 0.7385 (mtt180) REVERT: B 995 ARG cc_start: 0.7997 (tpp80) cc_final: 0.7779 (ttp80) REVERT: B 1041 ASP cc_start: 0.8120 (t0) cc_final: 0.7904 (t0) REVERT: C 307 THR cc_start: 0.8389 (p) cc_final: 0.8154 (p) REVERT: C 317 ASN cc_start: 0.8035 (m110) cc_final: 0.7761 (m-40) REVERT: C 391 CYS cc_start: 0.6802 (m) cc_final: 0.6572 (m) REVERT: C 396 TYR cc_start: 0.8472 (m-80) cc_final: 0.8147 (m-10) REVERT: C 645 THR cc_start: 0.8621 (OUTLIER) cc_final: 0.8402 (p) REVERT: C 654 GLU cc_start: 0.7425 (tm-30) cc_final: 0.7158 (tm-30) REVERT: C 698 SER cc_start: 0.8696 (t) cc_final: 0.8423 (p) REVERT: C 821 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.8030 (tp) REVERT: C 964 LYS cc_start: 0.8393 (ptpp) cc_final: 0.8145 (mtpp) REVERT: C 976 VAL cc_start: 0.8901 (p) cc_final: 0.8692 (m) REVERT: C 1002 GLN cc_start: 0.8132 (tm-30) cc_final: 0.7863 (tm-30) REVERT: C 1096 VAL cc_start: 0.8555 (OUTLIER) cc_final: 0.8318 (m) REVERT: D 49 ASN cc_start: 0.7170 (t0) cc_final: 0.6799 (t0) REVERT: D 120 LEU cc_start: 0.5256 (OUTLIER) cc_final: 0.4670 (pp) REVERT: D 158 TYR cc_start: 0.1016 (t80) cc_final: -0.0608 (t80) REVERT: D 190 MET cc_start: 0.5523 (mmm) cc_final: 0.4972 (mmm) REVERT: D 297 MET cc_start: 0.5383 (mmm) cc_final: 0.5059 (mtt) REVERT: D 323 MET cc_start: -0.3215 (mmt) cc_final: -0.3724 (mmt) REVERT: D 327 PHE cc_start: 0.6906 (t80) cc_final: 0.6087 (t80) REVERT: D 408 MET cc_start: 0.3383 (mmp) cc_final: 0.2925 (mmm) REVERT: D 455 MET cc_start: 0.6396 (ppp) cc_final: 0.5408 (ppp) REVERT: D 462 MET cc_start: 0.3443 (mmt) cc_final: 0.3069 (mmt) REVERT: D 497 TYR cc_start: 0.0863 (m-80) cc_final: -0.1118 (m-80) outliers start: 103 outliers final: 53 residues processed: 621 average time/residue: 0.1629 time to fit residues: 167.8677 Evaluate side-chains 563 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 505 time to evaluate : 0.959 ------------------------------------------------------------------------------- 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 826 VAL Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 608 VAL 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 825 LYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1135 ASN Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 359 SER 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 604 THR Chi-restraints excluded: chain C residue 645 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 821 LEU Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 34 GLN Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 120 LEU 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: 0.5980 chunk 58 optimal weight: 0.1980 chunk 87 optimal weight: 0.2980 chunk 322 optimal weight: 20.0000 chunk 194 optimal weight: 0.8980 chunk 148 optimal weight: 7.9990 chunk 309 optimal weight: 4.9990 chunk 262 optimal weight: 0.8980 chunk 36 optimal weight: 7.9990 chunk 132 optimal weight: 10.0000 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN A 87 ASN A 474 GLN A 762 GLN B 30 ASN B 188 ASN B 644 GLN B 703 ASN B 895 GLN B 907 ASN B1101 HIS C 784 GLN ** D 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 ASN D 368 ASN D 374 HIS ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.190390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.138852 restraints weight = 42779.438| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.28 r_work: 0.3537 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 29250 Z= 0.151 Angle : 0.602 15.049 39970 Z= 0.297 Chirality : 0.047 0.545 4627 Planarity : 0.004 0.048 5105 Dihedral : 4.520 56.699 3907 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.33 % Allowed : 19.33 % Favored : 77.34 % 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: -1.49 (0.13), residues: 3607 helix: -0.17 (0.17), residues: 882 sheet: -0.04 (0.19), residues: 680 loop : -1.75 (0.12), residues: 2045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 190 TYR 0.018 0.001 TYR D 385 PHE 0.021 0.001 PHE A 194 TRP 0.031 0.001 TRP D 275 HIS 0.003 0.001 HIS D 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (29184) covalent geometry : angle 0.57218 / 0.29 (39805) SS BOND : bond 0.00473 / 0.25 ( 27) SS BOND : angle 1.88140 / 1.26 ( 54) hydrogen bonds : bond 0.04224 / 2.88 ( 916) hydrogen bonds : angle 5.10989 / 3.49 ( 2580) Misc. bond : bond 0.00186 / 0.10 ( 2) link_NAG-ASN : bond 0.00981 / 0.53 ( 37) link_NAG-ASN : angle 3.39011 / 2.28 ( 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 620 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 522 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 574 ASP cc_start: 0.8243 (t0) cc_final: 0.7905 (t0) REVERT: A 591 SER cc_start: 0.8443 (m) cc_final: 0.8195 (t) REVERT: A 592 PHE cc_start: 0.8491 (p90) cc_final: 0.8199 (p90) REVERT: A 599 THR cc_start: 0.8820 (t) cc_final: 0.8574 (p) REVERT: A 735 SER cc_start: 0.8613 (m) cc_final: 0.8218 (p) REVERT: A 904 TYR cc_start: 0.7300 (m-80) cc_final: 0.7039 (m-10) REVERT: A 988 GLU cc_start: 0.7962 (tp30) cc_final: 0.7392 (tp30) REVERT: B 58 PHE cc_start: 0.8812 (m-10) cc_final: 0.8366 (m-10) REVERT: B 205 SER cc_start: 0.8633 (m) cc_final: 0.8188 (p) REVERT: B 281 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7978 (mp0) REVERT: B 307 THR cc_start: 0.8575 (p) cc_final: 0.8361 (p) REVERT: B 776 LYS cc_start: 0.8704 (ttpt) cc_final: 0.8428 (ttmm) REVERT: B 804 GLN cc_start: 0.8564 (mt0) cc_final: 0.7737 (mt0) REVERT: B 935 GLN cc_start: 0.7871 (pt0) cc_final: 0.7344 (pt0) REVERT: B 964 LYS cc_start: 0.8843 (tmtt) cc_final: 0.8432 (tmtt) REVERT: B 983 ARG cc_start: 0.7707 (mtt180) cc_final: 0.7392 (mtt180) REVERT: B 995 ARG cc_start: 0.7987 (tpp80) cc_final: 0.7734 (ttp80) REVERT: B 1041 ASP cc_start: 0.8087 (t0) cc_final: 0.7876 (t0) REVERT: C 58 PHE cc_start: 0.8566 (m-10) cc_final: 0.8013 (m-80) REVERT: C 307 THR cc_start: 0.8389 (p) cc_final: 0.8171 (p) REVERT: C 317 ASN cc_start: 0.7968 (m110) cc_final: 0.7711 (m-40) REVERT: C 391 CYS cc_start: 0.6792 (m) cc_final: 0.6571 (m) REVERT: C 396 TYR cc_start: 0.8431 (m-80) cc_final: 0.8086 (m-10) REVERT: C 604 THR cc_start: 0.8236 (OUTLIER) cc_final: 0.7976 (m) REVERT: C 654 GLU cc_start: 0.7367 (tm-30) cc_final: 0.7037 (tm-30) REVERT: C 698 SER cc_start: 0.8692 (t) cc_final: 0.8460 (p) REVERT: C 859 THR cc_start: 0.8551 (m) cc_final: 0.8242 (p) REVERT: C 918 GLU cc_start: 0.8268 (mt-10) cc_final: 0.8032 (mt-10) REVERT: C 929 SER cc_start: 0.8294 (OUTLIER) cc_final: 0.8075 (m) REVERT: C 976 VAL cc_start: 0.8888 (OUTLIER) cc_final: 0.8676 (m) REVERT: C 1019 ARG cc_start: 0.8154 (ttm170) cc_final: 0.7893 (ttp-110) REVERT: D 49 ASN cc_start: 0.7162 (t0) cc_final: 0.6796 (t0) REVERT: D 60 GLN cc_start: 0.7341 (mm-40) cc_final: 0.7097 (mm-40) REVERT: D 120 LEU cc_start: 0.5440 (OUTLIER) cc_final: 0.4874 (pp) REVERT: D 124 SER cc_start: 0.7031 (m) cc_final: 0.6780 (p) REVERT: D 158 TYR cc_start: 0.0842 (t80) cc_final: -0.0781 (t80) REVERT: D 190 MET cc_start: 0.5470 (mmm) cc_final: 0.4960 (mmm) REVERT: D 275 TRP cc_start: 0.5439 (m-90) cc_final: 0.5105 (m-90) REVERT: D 323 MET cc_start: -0.3193 (mmt) cc_final: -0.3732 (mmt) REVERT: D 327 PHE cc_start: 0.6870 (t80) cc_final: 0.5976 (t80) REVERT: D 330 ASN cc_start: 0.0741 (m-40) cc_final: 0.0493 (m110) REVERT: D 379 ILE cc_start: 0.8506 (OUTLIER) cc_final: 0.8229 (mp) REVERT: D 408 MET cc_start: 0.3508 (mmp) cc_final: 0.3001 (mmm) REVERT: D 455 MET cc_start: 0.6514 (ppp) cc_final: 0.5581 (ppp) REVERT: D 462 MET cc_start: 0.3382 (mmt) cc_final: 0.3012 (mmt) outliers start: 98 outliers final: 63 residues processed: 592 average time/residue: 0.1604 time to fit residues: 157.2354 Evaluate side-chains 579 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 511 time to evaluate : 0.866 ------------------------------------------------------------------------------- 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 433 VAL 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 887 THR Chi-restraints excluded: chain A residue 895 GLN 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 126 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 483 VAL 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 775 ASP 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 1068 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 287 ASP Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 389 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 585 LEU Chi-restraints excluded: chain C residue 604 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 764 LYS Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 929 SER 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 1141 LEU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 368 ASN 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: 0.0980 chunk 167 optimal weight: 0.0020 chunk 15 optimal weight: 5.9990 chunk 293 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 345 optimal weight: 30.0000 chunk 174 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 244 optimal weight: 0.0670 chunk 67 optimal weight: 0.5980 chunk 332 optimal weight: 0.5980 overall best weight: 0.2726 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN A 762 GLN B 30 ASN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B 895 GLN B 907 ASN B 955 ASN B 957 GLN C 540 ASN ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.191766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.139953 restraints weight = 42645.735| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.36 r_work: 0.3550 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 29250 Z= 0.113 Angle : 0.577 17.790 39970 Z= 0.283 Chirality : 0.045 0.422 4627 Planarity : 0.004 0.047 5105 Dihedral : 4.333 58.171 3907 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.43 % Allowed : 20.04 % Favored : 76.53 % 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: -1.21 (0.13), residues: 3607 helix: 0.18 (0.18), residues: 889 sheet: 0.13 (0.19), residues: 674 loop : -1.63 (0.13), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 190 TYR 0.019 0.001 TYR D 385 PHE 0.016 0.001 PHE D 28 TRP 0.014 0.001 TRP D 275 HIS 0.003 0.000 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (29184) covalent geometry : angle 0.55176 / 0.28 (39805) SS BOND : bond 0.00441 / 0.24 ( 27) SS BOND : angle 1.56466 / 1.06 ( 54) hydrogen bonds : bond 0.03889 / 2.66 ( 916) hydrogen bonds : angle 4.93267 / 3.38 ( 2580) Misc. bond : bond 0.00191 / 0.10 ( 2) link_NAG-ASN : bond 0.00695 / 0.40 ( 37) link_NAG-ASN : angle 3.10133 / 2.06 ( 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 624 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 523 time to evaluate : 1.064 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 319 ARG cc_start: 0.8172 (ttm110) cc_final: 0.7936 (ttm110) REVERT: A 574 ASP cc_start: 0.8260 (t0) cc_final: 0.7912 (t0) REVERT: A 591 SER cc_start: 0.8467 (m) cc_final: 0.8198 (t) REVERT: A 592 PHE cc_start: 0.8485 (p90) cc_final: 0.8274 (p90) REVERT: A 599 THR cc_start: 0.8810 (t) cc_final: 0.8584 (p) REVERT: A 735 SER cc_start: 0.8660 (m) cc_final: 0.8257 (p) REVERT: A 904 TYR cc_start: 0.7293 (m-80) cc_final: 0.6972 (m-10) REVERT: A 988 GLU cc_start: 0.7983 (tp30) cc_final: 0.7377 (tp30) REVERT: A 1029 MET cc_start: 0.8654 (tpp) cc_final: 0.8443 (ttm) REVERT: B 58 PHE cc_start: 0.8825 (m-10) cc_final: 0.8407 (m-10) REVERT: B 99 ASN cc_start: 0.8552 (t0) cc_final: 0.8305 (t0) REVERT: B 205 SER cc_start: 0.8647 (m) cc_final: 0.8179 (p) REVERT: B 281 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7971 (mp0) REVERT: B 307 THR cc_start: 0.8557 (p) cc_final: 0.8351 (p) REVERT: B 328 ARG cc_start: 0.7683 (mmm-85) cc_final: 0.7230 (mmm-85) REVERT: B 776 LYS cc_start: 0.8673 (ttpt) cc_final: 0.8429 (ttmm) REVERT: B 804 GLN cc_start: 0.8571 (mt0) cc_final: 0.8341 (mm-40) REVERT: B 964 LYS cc_start: 0.8832 (tmtt) cc_final: 0.8406 (tmtt) REVERT: B 983 ARG cc_start: 0.7702 (mtt180) cc_final: 0.7373 (mtt180) REVERT: B 994 ASP cc_start: 0.7834 (m-30) cc_final: 0.7540 (t0) REVERT: C 287 ASP cc_start: 0.8032 (OUTLIER) cc_final: 0.7782 (m-30) REVERT: C 307 THR cc_start: 0.8401 (p) cc_final: 0.8177 (p) REVERT: C 317 ASN cc_start: 0.7970 (m110) cc_final: 0.7724 (m-40) REVERT: C 338 PHE cc_start: 0.8357 (m-80) cc_final: 0.7961 (m-80) REVERT: C 391 CYS cc_start: 0.6861 (m) cc_final: 0.6632 (m) REVERT: C 396 TYR cc_start: 0.8388 (m-80) cc_final: 0.8019 (m-10) REVERT: C 588 THR cc_start: 0.8529 (OUTLIER) cc_final: 0.8086 (p) REVERT: C 645 THR cc_start: 0.8647 (OUTLIER) cc_final: 0.8443 (p) REVERT: C 654 GLU cc_start: 0.7400 (tm-30) cc_final: 0.7044 (tm-30) REVERT: C 698 SER cc_start: 0.8695 (t) cc_final: 0.8474 (p) REVERT: C 859 THR cc_start: 0.8568 (m) cc_final: 0.8269 (p) REVERT: C 918 GLU cc_start: 0.8283 (mt-10) cc_final: 0.8071 (mt-10) REVERT: D 49 ASN cc_start: 0.7190 (t0) cc_final: 0.6839 (t0) REVERT: D 60 GLN cc_start: 0.7350 (mm-40) cc_final: 0.7094 (mm-40) REVERT: D 64 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7717 (tm-30) REVERT: D 120 LEU cc_start: 0.5499 (OUTLIER) cc_final: 0.4510 (pp) REVERT: D 124 SER cc_start: 0.7026 (m) cc_final: 0.6775 (p) REVERT: D 158 TYR cc_start: 0.0792 (t80) cc_final: 0.0218 (t80) REVERT: D 190 MET cc_start: 0.5516 (mmm) cc_final: 0.5045 (mmm) REVERT: D 306 ARG cc_start: 0.7978 (mmt180) cc_final: 0.7443 (mmm-85) REVERT: D 323 MET cc_start: -0.3161 (mmt) cc_final: -0.3404 (mmt) REVERT: D 327 PHE cc_start: 0.6936 (t80) cc_final: 0.6134 (t80) REVERT: D 379 ILE cc_start: 0.8378 (OUTLIER) cc_final: 0.8163 (mp) REVERT: D 402 GLU cc_start: 0.4786 (tp30) cc_final: 0.4393 (tp30) REVERT: D 408 MET cc_start: 0.3445 (mmp) cc_final: 0.2758 (mmm) REVERT: D 452 PHE cc_start: 0.6365 (t80) cc_final: 0.5810 (t80) REVERT: D 455 MET cc_start: 0.6551 (ppp) cc_final: 0.5752 (ppp) REVERT: D 462 MET cc_start: 0.3347 (mmt) cc_final: 0.3003 (mmt) REVERT: D 497 TYR cc_start: 0.0641 (m-80) cc_final: -0.1186 (m-80) outliers start: 101 outliers final: 62 residues processed: 591 average time/residue: 0.1651 time to fit residues: 159.4404 Evaluate side-chains 573 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 506 time to evaluate : 0.946 ------------------------------------------------------------------------------- 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 433 VAL Chi-restraints excluded: chain A residue 547 LYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 887 THR 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 1136 THR Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 382 VAL 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 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 775 ASP Chi-restraints excluded: chain B residue 805 ILE 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 1072 GLU Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 287 ASP 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 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 645 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 764 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 1068 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 249 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 277 optimal weight: 0.8980 chunk 317 optimal weight: 0.2980 chunk 116 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 344 optimal weight: 9.9990 chunk 64 optimal weight: 0.4980 chunk 261 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 313 optimal weight: 10.0000 chunk 1 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN A 907 ASN A 913 GLN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B 907 ASN B 935 GLN B 957 GLN C 644 GLN C 804 GLN D 330 ASN D 378 HIS ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 472 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.190585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.138513 restraints weight = 42482.200| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.52 r_work: 0.3504 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 29250 Z= 0.162 Angle : 0.603 19.428 39970 Z= 0.294 Chirality : 0.047 0.540 4627 Planarity : 0.004 0.046 5105 Dihedral : 4.373 58.938 3907 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.33 % Allowed : 20.72 % 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: -1.08 (0.13), residues: 3607 helix: 0.29 (0.18), residues: 903 sheet: 0.13 (0.19), residues: 703 loop : -1.55 (0.13), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 190 TYR 0.019 0.001 TYR D 385 PHE 0.023 0.001 PHE A 201 TRP 0.030 0.001 TRP D 275 HIS 0.003 0.001 HIS D 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 (29184) covalent geometry : angle 0.57270 / 0.29 (39805) SS BOND : bond 0.00522 / 0.26 ( 27) SS BOND : angle 1.88776 / 1.28 ( 54) hydrogen bonds : bond 0.04149 / 2.83 ( 916) hydrogen bonds : angle 4.91013 / 3.35 ( 2580) Misc. bond : bond 0.00181 / 0.10 ( 2) link_NAG-ASN : bond 0.00741 / 0.40 ( 37) link_NAG-ASN : angle 3.37718 / 2.23 ( 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 630 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 532 time to evaluate : 1.055 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 319 ARG cc_start: 0.8201 (ttm110) cc_final: 0.7985 (ttm110) REVERT: A 574 ASP cc_start: 0.8261 (t0) cc_final: 0.7921 (t0) REVERT: A 591 SER cc_start: 0.8483 (m) cc_final: 0.8229 (t) REVERT: A 592 PHE cc_start: 0.8494 (p90) cc_final: 0.8273 (p90) REVERT: A 599 THR cc_start: 0.8798 (t) cc_final: 0.8574 (p) REVERT: A 735 SER cc_start: 0.8700 (m) cc_final: 0.8273 (p) REVERT: A 904 TYR cc_start: 0.7306 (m-80) cc_final: 0.6991 (m-10) REVERT: A 988 GLU cc_start: 0.7968 (tp30) cc_final: 0.7337 (tp30) REVERT: B 58 PHE cc_start: 0.8817 (m-10) cc_final: 0.8410 (m-10) REVERT: B 99 ASN cc_start: 0.8527 (t0) cc_final: 0.8272 (t0) REVERT: B 205 SER cc_start: 0.8697 (m) cc_final: 0.8291 (p) REVERT: B 281 GLU cc_start: 0.8245 (mt-10) cc_final: 0.8036 (mp0) REVERT: B 307 THR cc_start: 0.8587 (p) cc_final: 0.8376 (p) REVERT: B 328 ARG cc_start: 0.7818 (mmm-85) cc_final: 0.7045 (mmm-85) REVERT: B 567 ARG cc_start: 0.7065 (mtm-85) cc_final: 0.6812 (mtt180) REVERT: B 776 LYS cc_start: 0.8702 (ttpt) cc_final: 0.8429 (ttmm) REVERT: B 867 ASP cc_start: 0.7664 (m-30) cc_final: 0.7452 (m-30) REVERT: B 964 LYS cc_start: 0.8853 (tmtt) cc_final: 0.8403 (tmtt) REVERT: B 983 ARG cc_start: 0.7690 (mtt180) cc_final: 0.7378 (mtt180) REVERT: C 58 PHE cc_start: 0.8591 (m-10) cc_final: 0.8096 (m-10) REVERT: C 287 ASP cc_start: 0.8052 (OUTLIER) cc_final: 0.7783 (m-30) REVERT: C 317 ASN cc_start: 0.8010 (m110) cc_final: 0.7772 (m-40) REVERT: C 391 CYS cc_start: 0.6871 (m) cc_final: 0.6619 (m) REVERT: C 396 TYR cc_start: 0.8408 (m-80) cc_final: 0.8049 (m-10) REVERT: C 588 THR cc_start: 0.8564 (OUTLIER) cc_final: 0.8139 (p) REVERT: C 654 GLU cc_start: 0.7482 (tm-30) cc_final: 0.7137 (tm-30) REVERT: C 698 SER cc_start: 0.8713 (t) cc_final: 0.8480 (p) REVERT: C 717 ASN cc_start: 0.8123 (t0) cc_final: 0.7883 (t0) REVERT: C 821 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.8002 (tp) REVERT: C 859 THR cc_start: 0.8621 (m) cc_final: 0.8332 (p) REVERT: C 887 THR cc_start: 0.8325 (p) cc_final: 0.8094 (p) REVERT: C 918 GLU cc_start: 0.8373 (mt-10) cc_final: 0.8110 (mt-10) REVERT: C 977 LEU cc_start: 0.8372 (mp) cc_final: 0.8168 (mp) REVERT: D 49 ASN cc_start: 0.7205 (t0) cc_final: 0.6866 (t0) REVERT: D 60 GLN cc_start: 0.7333 (mm-40) cc_final: 0.7090 (mm-40) REVERT: D 120 LEU cc_start: 0.5834 (OUTLIER) cc_final: 0.5227 (pp) REVERT: D 124 SER cc_start: 0.7026 (m) cc_final: 0.6779 (p) REVERT: D 190 MET cc_start: 0.5545 (mmm) cc_final: 0.5075 (mmm) REVERT: D 275 TRP cc_start: 0.5335 (m-90) cc_final: 0.4944 (m-90) REVERT: D 306 ARG cc_start: 0.7995 (mmt180) cc_final: 0.7646 (mmm-85) REVERT: D 323 MET cc_start: -0.3367 (mmt) cc_final: -0.4025 (mmt) REVERT: D 327 PHE cc_start: 0.7020 (t80) cc_final: 0.6242 (t80) REVERT: D 379 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.8179 (mp) REVERT: D 402 GLU cc_start: 0.5255 (tp30) cc_final: 0.4892 (tp30) REVERT: D 408 MET cc_start: 0.3446 (mmp) cc_final: 0.2983 (mmm) REVERT: D 452 PHE cc_start: 0.6399 (t80) cc_final: 0.6174 (t80) REVERT: D 455 MET cc_start: 0.6540 (ppp) cc_final: 0.6145 (ppp) REVERT: D 462 MET cc_start: 0.3306 (mmt) cc_final: 0.3018 (mmt) outliers start: 98 outliers final: 70 residues processed: 597 average time/residue: 0.1679 time to fit residues: 163.3996 Evaluate side-chains 596 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 521 time to evaluate : 1.058 ------------------------------------------------------------------------------- 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 335 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 887 THR 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 33 THR Chi-restraints excluded: chain B residue 159 VAL 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 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 1068 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 287 ASP 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 399 SER Chi-restraints excluded: chain C residue 489 TYR 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 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 1068 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 249 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 69 optimal weight: 0.3980 chunk 268 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 357 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 90 optimal weight: 0.5980 chunk 167 optimal weight: 1.9990 chunk 337 optimal weight: 20.0000 chunk 207 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN A 762 GLN A 907 ASN B 30 ASN B 188 ASN B 703 ASN B 895 GLN B 935 GLN D 265 HIS ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.190052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.138228 restraints weight = 42492.290| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.47 r_work: 0.3500 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 29250 Z= 0.156 Angle : 0.597 17.917 39970 Z= 0.294 Chirality : 0.047 0.503 4627 Planarity : 0.004 0.046 5105 Dihedral : 4.405 59.325 3907 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.53 % Allowed : 21.20 % Favored : 75.27 % 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: -0.99 (0.14), residues: 3607 helix: 0.32 (0.18), residues: 906 sheet: 0.18 (0.19), residues: 706 loop : -1.48 (0.13), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 190 TYR 0.019 0.001 TYR D 385 PHE 0.028 0.001 PHE B 168 TRP 0.015 0.001 TRP D 275 HIS 0.003 0.001 HIS D 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (29184) covalent geometry : angle 0.56955 / 0.29 (39805) SS BOND : bond 0.00474 / 0.25 ( 27) SS BOND : angle 1.94625 / 1.31 ( 54) hydrogen bonds : bond 0.04105 / 2.81 ( 916) hydrogen bonds : angle 4.90933 / 3.36 ( 2580) Misc. bond : bond 0.00179 / 0.09 ( 2) link_NAG-ASN : bond 0.00639 / 0.36 ( 37) link_NAG-ASN : angle 3.18802 / 2.11 ( 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 641 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 537 time to evaluate : 1.045 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: 0.7497 (mtm110) cc_final: 0.7113 (ttm110) REVERT: A 303 LEU cc_start: 0.8517 (mt) cc_final: 0.8313 (mp) REVERT: A 574 ASP cc_start: 0.8272 (t0) cc_final: 0.7957 (t0) REVERT: A 591 SER cc_start: 0.8487 (m) cc_final: 0.8252 (t) REVERT: A 599 THR cc_start: 0.8798 (t) cc_final: 0.8577 (p) REVERT: A 735 SER cc_start: 0.8692 (m) cc_final: 0.8254 (p) REVERT: A 737 ASP cc_start: 0.7990 (t0) cc_final: 0.7532 (t0) REVERT: A 904 TYR cc_start: 0.7328 (m-80) cc_final: 0.7007 (m-10) REVERT: A 988 GLU cc_start: 0.7961 (tp30) cc_final: 0.7321 (tp30) REVERT: B 58 PHE cc_start: 0.8799 (m-10) cc_final: 0.8396 (m-10) REVERT: B 99 ASN cc_start: 0.8504 (t0) cc_final: 0.8277 (t0) REVERT: B 125 ASN cc_start: 0.7366 (p0) cc_final: 0.7087 (p0) REVERT: B 205 SER cc_start: 0.8707 (m) cc_final: 0.8312 (p) REVERT: B 226 LEU cc_start: 0.7733 (mt) cc_final: 0.7495 (mp) REVERT: B 307 THR cc_start: 0.8590 (p) cc_final: 0.8376 (p) REVERT: B 328 ARG cc_start: 0.7861 (mmm-85) cc_final: 0.7045 (mmm-85) REVERT: B 567 ARG cc_start: 0.7103 (mtm-85) cc_final: 0.6845 (mtt180) REVERT: B 574 ASP cc_start: 0.8032 (t0) cc_final: 0.7734 (t0) REVERT: B 776 LYS cc_start: 0.8733 (ttpt) cc_final: 0.8478 (ttmm) REVERT: B 804 GLN cc_start: 0.8514 (mm-40) cc_final: 0.8168 (mt0) REVERT: B 935 GLN cc_start: 0.7440 (pt0) cc_final: 0.7135 (pt0) REVERT: B 964 LYS cc_start: 0.8863 (tmtt) cc_final: 0.8406 (tmtt) REVERT: B 983 ARG cc_start: 0.7694 (mtt180) cc_final: 0.7396 (mtt180) REVERT: B 994 ASP cc_start: 0.7839 (m-30) cc_final: 0.7567 (t0) REVERT: B 1041 ASP cc_start: 0.8130 (t0) cc_final: 0.7804 (t0) REVERT: C 391 CYS cc_start: 0.6891 (m) cc_final: 0.6632 (m) REVERT: C 588 THR cc_start: 0.8571 (OUTLIER) cc_final: 0.8157 (p) REVERT: C 654 GLU cc_start: 0.7510 (tm-30) cc_final: 0.7133 (tm-30) REVERT: C 698 SER cc_start: 0.8701 (t) cc_final: 0.8482 (p) REVERT: C 717 ASN cc_start: 0.8099 (t0) cc_final: 0.7836 (t0) REVERT: C 859 THR cc_start: 0.8611 (m) cc_final: 0.8350 (p) REVERT: C 887 THR cc_start: 0.8303 (p) cc_final: 0.8066 (p) REVERT: C 918 GLU cc_start: 0.8380 (mt-10) cc_final: 0.8160 (mt-10) REVERT: C 977 LEU cc_start: 0.8376 (mp) cc_final: 0.8136 (mt) REVERT: D 49 ASN cc_start: 0.7192 (t0) cc_final: 0.6854 (t0) REVERT: D 120 LEU cc_start: 0.6138 (OUTLIER) cc_final: 0.5749 (pp) REVERT: D 124 SER cc_start: 0.7019 (m) cc_final: 0.6773 (p) REVERT: D 190 MET cc_start: 0.5508 (mmm) cc_final: 0.5061 (mmm) REVERT: D 275 TRP cc_start: 0.5341 (m-90) cc_final: 0.5004 (m-90) REVERT: D 306 ARG cc_start: 0.7984 (mmt180) cc_final: 0.7710 (mmm-85) REVERT: D 323 MET cc_start: -0.3492 (mmt) cc_final: -0.4174 (mmt) REVERT: D 327 PHE cc_start: 0.7044 (t80) cc_final: 0.6280 (t80) REVERT: D 379 ILE cc_start: 0.8420 (OUTLIER) cc_final: 0.8193 (mp) REVERT: D 408 MET cc_start: 0.3496 (mmp) cc_final: 0.2957 (mmm) REVERT: D 452 PHE cc_start: 0.6437 (t80) cc_final: 0.6211 (t80) REVERT: D 455 MET cc_start: 0.6521 (ppp) cc_final: 0.6148 (ppp) REVERT: D 462 MET cc_start: 0.3143 (mmt) cc_final: 0.2915 (mmt) outliers start: 104 outliers final: 87 residues processed: 611 average time/residue: 0.1699 time to fit residues: 169.2908 Evaluate side-chains 612 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 522 time to evaluate : 0.932 ------------------------------------------------------------------------------- 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 165 ASN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 895 GLN 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 30 ASN Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 238 PHE 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 546 LEU 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 720 ILE 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 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 C residue 42 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 287 ASP 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 489 TYR 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 720 ILE Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 752 LEU 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 1068 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 519 THR 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: 0.8980 chunk 238 optimal weight: 1.9990 chunk 155 optimal weight: 0.0980 chunk 33 optimal weight: 0.4980 chunk 194 optimal weight: 1.9990 chunk 265 optimal weight: 0.9980 chunk 262 optimal weight: 0.2980 chunk 198 optimal weight: 0.7980 chunk 171 optimal weight: 0.0060 chunk 293 optimal weight: 1.9990 chunk 233 optimal weight: 1.9990 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN A 907 ASN B 30 ASN B 703 ASN ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.191048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.139472 restraints weight = 42611.752| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.29 r_work: 0.3540 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.4388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 29250 Z= 0.116 Angle : 0.574 17.826 39970 Z= 0.281 Chirality : 0.045 0.467 4627 Planarity : 0.004 0.045 5105 Dihedral : 4.285 59.107 3907 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.33 % Allowed : 21.60 % 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: -0.80 (0.14), residues: 3607 helix: 0.53 (0.18), residues: 903 sheet: 0.28 (0.19), residues: 706 loop : -1.38 (0.13), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 190 TYR 0.016 0.001 TYR D 385 PHE 0.023 0.001 PHE A 201 TRP 0.021 0.001 TRP A 436 HIS 0.002 0.000 HIS D 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (29184) covalent geometry : angle 0.54778 / 0.27 (39805) SS BOND : bond 0.00487 / 0.29 ( 27) SS BOND : angle 1.61565 / 1.09 ( 54) hydrogen bonds : bond 0.03773 / 2.56 ( 916) hydrogen bonds : angle 4.79152 / 3.27 ( 2580) Misc. bond : bond 0.00184 / 0.10 ( 2) link_NAG-ASN : bond 0.00668 / 0.38 ( 37) link_NAG-ASN : angle 3.09762 / 2.06 ( 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 628 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 530 time to evaluate : 0.840 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: 0.7463 (mtm110) cc_final: 0.7114 (ttp-110) REVERT: A 319 ARG cc_start: 0.8163 (ttm110) cc_final: 0.7926 (ttm110) REVERT: A 574 ASP cc_start: 0.8237 (t0) cc_final: 0.7927 (t0) REVERT: A 591 SER cc_start: 0.8477 (m) cc_final: 0.8266 (t) REVERT: A 599 THR cc_start: 0.8779 (t) cc_final: 0.8564 (p) REVERT: A 644 GLN cc_start: 0.8446 (tp-100) cc_final: 0.8148 (tp40) REVERT: A 735 SER cc_start: 0.8656 (m) cc_final: 0.8234 (p) REVERT: A 904 TYR cc_start: 0.7268 (m-80) cc_final: 0.6984 (m-10) REVERT: A 976 VAL cc_start: 0.8540 (t) cc_final: 0.8311 (m) REVERT: A 988 GLU cc_start: 0.7947 (tp30) cc_final: 0.7320 (tp30) REVERT: A 994 ASP cc_start: 0.7489 (m-30) cc_final: 0.7155 (t0) REVERT: A 1029 MET cc_start: 0.8644 (tpp) cc_final: 0.8431 (ttm) REVERT: B 58 PHE cc_start: 0.8784 (m-10) cc_final: 0.8405 (m-10) REVERT: B 125 ASN cc_start: 0.7278 (p0) cc_final: 0.7002 (p0) REVERT: B 205 SER cc_start: 0.8574 (m) cc_final: 0.8174 (p) REVERT: B 226 LEU cc_start: 0.7658 (mt) cc_final: 0.7428 (mp) REVERT: B 307 THR cc_start: 0.8569 (p) cc_final: 0.8354 (p) REVERT: B 567 ARG cc_start: 0.7102 (mtm-85) cc_final: 0.6696 (mtt180) REVERT: B 574 ASP cc_start: 0.8027 (t0) cc_final: 0.7720 (t0) REVERT: B 776 LYS cc_start: 0.8707 (ttpt) cc_final: 0.8366 (ttmm) REVERT: B 804 GLN cc_start: 0.8447 (mm-40) cc_final: 0.7990 (mt0) REVERT: B 935 GLN cc_start: 0.7333 (pt0) cc_final: 0.6831 (pt0) REVERT: B 964 LYS cc_start: 0.8869 (tmtt) cc_final: 0.8422 (tmtt) REVERT: B 983 ARG cc_start: 0.7685 (mtt180) cc_final: 0.7398 (mtt180) REVERT: B 994 ASP cc_start: 0.7728 (m-30) cc_final: 0.7440 (t0) REVERT: B 1050 MET cc_start: 0.7925 (ttm) cc_final: 0.7701 (ttp) REVERT: C 58 PHE cc_start: 0.8561 (m-10) cc_final: 0.8328 (m-10) REVERT: C 391 CYS cc_start: 0.6729 (m) cc_final: 0.6417 (m) REVERT: C 588 THR cc_start: 0.8522 (OUTLIER) cc_final: 0.8112 (p) REVERT: C 654 GLU cc_start: 0.7460 (tm-30) cc_final: 0.7068 (tm-30) REVERT: C 717 ASN cc_start: 0.8077 (t0) cc_final: 0.7829 (t0) REVERT: C 859 THR cc_start: 0.8594 (m) cc_final: 0.8356 (p) REVERT: C 887 THR cc_start: 0.8302 (p) cc_final: 0.8056 (p) REVERT: C 918 GLU cc_start: 0.8303 (mt-10) cc_final: 0.8026 (mt-10) REVERT: C 977 LEU cc_start: 0.8352 (mp) cc_final: 0.8096 (mt) REVERT: D 49 ASN cc_start: 0.7163 (t0) cc_final: 0.6795 (t0) REVERT: D 120 LEU cc_start: 0.6010 (OUTLIER) cc_final: 0.5730 (pp) REVERT: D 124 SER cc_start: 0.6986 (m) cc_final: 0.6739 (p) REVERT: D 158 TYR cc_start: 0.1394 (t80) cc_final: 0.0148 (t80) REVERT: D 190 MET cc_start: 0.5509 (mmm) cc_final: 0.5041 (mmm) REVERT: D 275 TRP cc_start: 0.5044 (m-90) cc_final: 0.4824 (m-90) REVERT: D 306 ARG cc_start: 0.7978 (mmt180) cc_final: 0.7718 (mtt90) REVERT: D 323 MET cc_start: -0.3603 (mmt) cc_final: -0.4223 (mmt) REVERT: D 327 PHE cc_start: 0.6994 (t80) cc_final: 0.6240 (t80) REVERT: D 379 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.8166 (mp) REVERT: D 408 MET cc_start: 0.3692 (mmp) cc_final: 0.3470 (mmm) REVERT: D 455 MET cc_start: 0.6429 (ppp) cc_final: 0.6036 (ppp) REVERT: D 462 MET cc_start: 0.3080 (mmt) cc_final: 0.2771 (mmt) outliers start: 98 outliers final: 73 residues processed: 599 average time/residue: 0.1617 time to fit residues: 158.1991 Evaluate side-chains 599 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 523 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 36 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 650 LEU Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 963 VAL 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 108 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 238 PHE 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 546 LEU 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 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 996 LEU 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 361 CYS Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 489 TYR 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 738 CYS Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 752 LEU 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 1068 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 581 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 261 optimal weight: 0.8980 chunk 155 optimal weight: 0.5980 chunk 309 optimal weight: 4.9990 chunk 125 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 138 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 266 optimal weight: 0.5980 chunk 181 optimal weight: 0.0970 chunk 21 optimal weight: 0.6980 chunk 281 optimal weight: 0.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN A 751 ASN A 907 ASN B 30 ASN B 703 ASN B 895 GLN C 317 ASN D 34 GLN ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.190552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.138901 restraints weight = 42501.944| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.45 r_work: 0.3516 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29250 Z= 0.142 Angle : 0.604 17.498 39970 Z= 0.294 Chirality : 0.046 0.455 4627 Planarity : 0.004 0.046 5105 Dihedral : 4.346 59.328 3907 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.02 % Allowed : 22.25 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.14), residues: 3607 helix: 0.53 (0.18), residues: 907 sheet: 0.28 (0.19), residues: 705 loop : -1.33 (0.13), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 102 TYR 0.016 0.001 TYR A 655 PHE 0.028 0.001 PHE B 168 TRP 0.013 0.001 TRP A 436 HIS 0.002 0.000 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (29184) covalent geometry : angle 0.57691 / 0.29 (39805) SS BOND : bond 0.00441 / 0.23 ( 27) SS BOND : angle 1.80946 / 1.22 ( 54) hydrogen bonds : bond 0.03921 / 2.68 ( 916) hydrogen bonds : angle 4.78483 / 3.27 ( 2580) Misc. bond : bond 0.00175 / 0.09 ( 2) link_NAG-ASN : bond 0.00757 / 0.41 ( 37) link_NAG-ASN : angle 3.24370 / 2.07 ( 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 614 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 525 time to evaluate : 1.042 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: 0.7532 (mtm110) cc_final: 0.7230 (ttp-110) REVERT: A 574 ASP cc_start: 0.8272 (t0) cc_final: 0.7957 (t0) REVERT: A 591 SER cc_start: 0.8534 (m) cc_final: 0.8301 (t) REVERT: A 599 THR cc_start: 0.8800 (t) cc_final: 0.8588 (p) REVERT: A 644 GLN cc_start: 0.8472 (tp-100) cc_final: 0.8262 (tp40) REVERT: A 695 TYR cc_start: 0.8456 (p90) cc_final: 0.7629 (p90) REVERT: A 735 SER cc_start: 0.8682 (m) cc_final: 0.8268 (p) REVERT: A 904 TYR cc_start: 0.7288 (m-80) cc_final: 0.6973 (m-10) REVERT: A 976 VAL cc_start: 0.8589 (t) cc_final: 0.8352 (m) REVERT: A 988 GLU cc_start: 0.7969 (tp30) cc_final: 0.7288 (tp30) REVERT: A 994 ASP cc_start: 0.7601 (m-30) cc_final: 0.7255 (t0) REVERT: B 58 PHE cc_start: 0.8787 (m-10) cc_final: 0.8417 (m-10) REVERT: B 125 ASN cc_start: 0.7369 (p0) cc_final: 0.7084 (p0) REVERT: B 205 SER cc_start: 0.8683 (m) cc_final: 0.8306 (p) REVERT: B 226 LEU cc_start: 0.7754 (mt) cc_final: 0.7526 (mp) REVERT: B 307 THR cc_start: 0.8582 (p) cc_final: 0.8366 (p) REVERT: B 328 ARG cc_start: 0.7711 (mmm-85) cc_final: 0.7017 (mmm-85) REVERT: B 567 ARG cc_start: 0.7135 (mtm-85) cc_final: 0.6741 (mtt180) REVERT: B 574 ASP cc_start: 0.8050 (t0) cc_final: 0.7731 (t0) REVERT: B 710 ASN cc_start: 0.8365 (p0) cc_final: 0.8132 (p0) REVERT: B 776 LYS cc_start: 0.8715 (ttpt) cc_final: 0.8432 (ttmm) REVERT: B 804 GLN cc_start: 0.8444 (mm-40) cc_final: 0.8039 (mt0) REVERT: B 825 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.8025 (mmmm) REVERT: B 935 GLN cc_start: 0.7441 (pt0) cc_final: 0.6892 (pt0) REVERT: B 964 LYS cc_start: 0.8862 (tmtt) cc_final: 0.8399 (tmtt) REVERT: B 983 ARG cc_start: 0.7690 (mtt180) cc_final: 0.7400 (mtt180) REVERT: B 994 ASP cc_start: 0.7745 (m-30) cc_final: 0.7430 (t0) REVERT: C 391 CYS cc_start: 0.6833 (m) cc_final: 0.6519 (m) REVERT: C 588 THR cc_start: 0.8541 (OUTLIER) cc_final: 0.8124 (p) REVERT: C 654 GLU cc_start: 0.7524 (tm-30) cc_final: 0.7124 (tm-30) REVERT: C 717 ASN cc_start: 0.8078 (t0) cc_final: 0.7820 (t0) REVERT: C 859 THR cc_start: 0.8606 (m) cc_final: 0.8361 (p) REVERT: C 887 THR cc_start: 0.8313 (p) cc_final: 0.8074 (p) REVERT: C 918 GLU cc_start: 0.8347 (mt-10) cc_final: 0.8058 (mt-10) REVERT: C 977 LEU cc_start: 0.8354 (mp) cc_final: 0.8090 (mt) REVERT: D 49 ASN cc_start: 0.7224 (t0) cc_final: 0.6864 (t0) REVERT: D 120 LEU cc_start: 0.6140 (OUTLIER) cc_final: 0.5799 (pp) REVERT: D 124 SER cc_start: 0.7044 (m) cc_final: 0.6807 (p) REVERT: D 177 ARG cc_start: 0.5592 (mmm160) cc_final: 0.5023 (mmm160) REVERT: D 190 MET cc_start: 0.5519 (mmm) cc_final: 0.5071 (mmm) REVERT: D 275 TRP cc_start: 0.5305 (m-90) cc_final: 0.5060 (m-90) REVERT: D 306 ARG cc_start: 0.8049 (mmt180) cc_final: 0.7746 (mtt90) REVERT: D 323 MET cc_start: -0.3607 (mmt) cc_final: -0.4230 (mmt) REVERT: D 327 PHE cc_start: 0.7102 (t80) cc_final: 0.6346 (t80) REVERT: D 379 ILE cc_start: 0.8429 (OUTLIER) cc_final: 0.8209 (mp) REVERT: D 408 MET cc_start: 0.3515 (mmp) cc_final: 0.3298 (mmm) REVERT: D 452 PHE cc_start: 0.5835 (t80) cc_final: 0.5630 (t80) REVERT: D 455 MET cc_start: 0.6501 (ppp) cc_final: 0.6102 (ppp) REVERT: D 462 MET cc_start: 0.3201 (mmt) cc_final: 0.2915 (mmt) outliers start: 89 outliers final: 80 residues processed: 589 average time/residue: 0.1784 time to fit residues: 171.9556 Evaluate side-chains 603 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 519 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 555 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 884 SER Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 963 VAL 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 30 ASN Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 159 VAL 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 546 LEU 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 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 996 LEU Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 489 TYR 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 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 727 LEU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 752 LEU 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 913 GLN 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 1128 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 34 GLN Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 519 THR 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: 1.9990 chunk 119 optimal weight: 4.9990 chunk 280 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 205 optimal weight: 0.9990 chunk 214 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 213 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 269 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN B 703 ASN B 895 GLN C 901 GLN ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 GLN ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 472 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 = 0.4296 r_free = 0.4296 target = 0.188226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.136272 restraints weight = 42274.241| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.51 r_work: 0.3482 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.4741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 29250 Z= 0.201 Angle : 0.643 17.069 39970 Z= 0.316 Chirality : 0.048 0.457 4627 Planarity : 0.004 0.047 5105 Dihedral : 4.507 59.077 3907 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.19 % Allowed : 22.08 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.14), residues: 3607 helix: 0.41 (0.18), residues: 906 sheet: 0.19 (0.19), residues: 715 loop : -1.34 (0.13), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 102 TYR 0.017 0.001 TYR A 266 PHE 0.025 0.002 PHE B 168 TRP 0.013 0.001 TRP A 436 HIS 0.004 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.20 (29184) covalent geometry : angle 0.61259 / 0.31 (39805) SS BOND : bond 0.00511 / 0.27 ( 27) SS BOND : angle 2.18378 / 1.48 ( 54) hydrogen bonds : bond 0.04380 / 2.98 ( 916) hydrogen bonds : angle 4.94256 / 3.38 ( 2580) Misc. bond : bond 0.00168 / 0.09 ( 2) link_NAG-ASN : bond 0.00702 / 0.39 ( 37) link_NAG-ASN : angle 3.43615 / 2.29 ( 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 639 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 545 time to evaluate : 1.012 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 203 ILE cc_start: 0.8344 (mp) cc_final: 0.8100 (mm) REVERT: A 237 ARG cc_start: 0.7598 (mtm110) cc_final: 0.7324 (ttp-110) REVERT: A 574 ASP cc_start: 0.8283 (t0) cc_final: 0.7964 (t0) REVERT: A 591 SER cc_start: 0.8522 (m) cc_final: 0.8284 (t) REVERT: A 599 THR cc_start: 0.8814 (t) cc_final: 0.8602 (p) REVERT: A 695 TYR cc_start: 0.8483 (p90) cc_final: 0.7866 (p90) REVERT: A 735 SER cc_start: 0.8703 (m) cc_final: 0.8252 (p) REVERT: A 904 TYR cc_start: 0.7367 (m-80) cc_final: 0.7039 (m-10) REVERT: A 976 VAL cc_start: 0.8622 (t) cc_final: 0.8391 (m) REVERT: A 988 GLU cc_start: 0.7966 (tp30) cc_final: 0.7282 (tp30) REVERT: A 1031 GLU cc_start: 0.8295 (mt-10) cc_final: 0.8075 (mt-10) REVERT: A 1094 VAL cc_start: 0.8458 (m) cc_final: 0.8236 (p) REVERT: B 58 PHE cc_start: 0.8764 (m-10) cc_final: 0.8407 (m-10) REVERT: B 125 ASN cc_start: 0.7395 (p0) cc_final: 0.7117 (p0) REVERT: B 205 SER cc_start: 0.8699 (m) cc_final: 0.8341 (p) REVERT: B 307 THR cc_start: 0.8670 (p) cc_final: 0.8466 (p) REVERT: B 328 ARG cc_start: 0.7792 (mmm-85) cc_final: 0.7104 (mmm-85) REVERT: B 567 ARG cc_start: 0.7189 (mtm-85) cc_final: 0.6841 (mtt180) REVERT: B 574 ASP cc_start: 0.8081 (t0) cc_final: 0.7754 (t0) REVERT: B 710 ASN cc_start: 0.8350 (p0) cc_final: 0.8106 (p0) REVERT: B 776 LYS cc_start: 0.8762 (ttpt) cc_final: 0.8487 (ttmm) REVERT: B 778 THR cc_start: 0.8826 (t) cc_final: 0.8546 (m) REVERT: B 804 GLN cc_start: 0.8544 (mm-40) cc_final: 0.8048 (mt0) REVERT: B 935 GLN cc_start: 0.7586 (pt0) cc_final: 0.6994 (pt0) REVERT: B 983 ARG cc_start: 0.7740 (mtt180) cc_final: 0.7454 (mtt180) REVERT: B 994 ASP cc_start: 0.7793 (m-30) cc_final: 0.7513 (t0) REVERT: C 391 CYS cc_start: 0.6862 (m) cc_final: 0.6580 (m) REVERT: C 396 TYR cc_start: 0.8436 (m-10) cc_final: 0.8019 (m-10) REVERT: C 588 THR cc_start: 0.8574 (OUTLIER) cc_final: 0.8175 (p) REVERT: C 654 GLU cc_start: 0.7576 (tm-30) cc_final: 0.7174 (tm-30) REVERT: C 717 ASN cc_start: 0.8099 (t0) cc_final: 0.7844 (t0) REVERT: C 751 ASN cc_start: 0.7787 (m-40) cc_final: 0.7484 (m-40) REVERT: C 821 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.8009 (tp) REVERT: C 859 THR cc_start: 0.8621 (m) cc_final: 0.8354 (p) REVERT: C 887 THR cc_start: 0.8336 (p) cc_final: 0.8098 (p) REVERT: C 977 LEU cc_start: 0.8388 (mp) cc_final: 0.8137 (mt) REVERT: D 49 ASN cc_start: 0.7238 (t0) cc_final: 0.6875 (t0) REVERT: D 120 LEU cc_start: 0.6081 (OUTLIER) cc_final: 0.5670 (pp) REVERT: D 124 SER cc_start: 0.7076 (m) cc_final: 0.6841 (p) REVERT: D 158 TYR cc_start: 0.1685 (t80) cc_final: 0.0330 (t80) REVERT: D 177 ARG cc_start: 0.5580 (mmm160) cc_final: 0.5236 (mmm160) REVERT: D 190 MET cc_start: 0.5507 (mmm) cc_final: 0.5030 (mmm) REVERT: D 306 ARG cc_start: 0.8087 (mmt180) cc_final: 0.7802 (mtt90) REVERT: D 323 MET cc_start: -0.3693 (mmt) cc_final: -0.4245 (mmt) REVERT: D 327 PHE cc_start: 0.7124 (t80) cc_final: 0.6379 (t80) REVERT: D 363 LYS cc_start: 0.4759 (tptt) cc_final: 0.4115 (mmpt) REVERT: D 379 ILE cc_start: 0.8432 (OUTLIER) cc_final: 0.8194 (mp) REVERT: D 408 MET cc_start: 0.3430 (mmp) cc_final: 0.3213 (mmm) REVERT: D 452 PHE cc_start: 0.5930 (t80) cc_final: 0.4951 (t80) REVERT: D 455 MET cc_start: 0.6522 (ppp) cc_final: 0.6148 (ppp) REVERT: D 462 MET cc_start: 0.3120 (mmt) cc_final: 0.2860 (mmt) outliers start: 94 outliers final: 81 residues processed: 614 average time/residue: 0.1731 time to fit residues: 172.7516 Evaluate side-chains 620 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 535 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 36 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 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 875 SER Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 963 VAL 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 30 ASN Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 159 VAL 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 546 LEU 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 708 SER Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 720 ILE 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 996 LEU Chi-restraints excluded: chain B residue 1068 VAL 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 489 TYR 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 727 LEU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 752 LEU 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 913 GLN 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 1128 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 34 GLN Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 519 THR 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: 0.6980 chunk 114 optimal weight: 0.8980 chunk 137 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 278 optimal weight: 0.8980 chunk 292 optimal weight: 0.5980 chunk 214 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 chunk 184 optimal weight: 0.5980 chunk 215 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN A 762 GLN A 907 ASN B 30 ASN B 703 ASN C 317 ASN C 901 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.188871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.136896 restraints weight = 42338.210| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.48 r_work: 0.3491 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.4765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 29250 Z= 0.173 Angle : 0.745 57.740 39970 Z= 0.385 Chirality : 0.049 0.837 4627 Planarity : 0.004 0.111 5105 Dihedral : 4.504 59.189 3907 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.06 % Allowed : 22.15 % Favored : 74.80 % 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: -0.81 (0.14), residues: 3607 helix: 0.47 (0.18), residues: 900 sheet: 0.20 (0.19), residues: 715 loop : -1.33 (0.13), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 102 TYR 0.024 0.001 TYR D 587 PHE 0.028 0.002 PHE D 369 TRP 0.047 0.001 TRP D 69 HIS 0.003 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 (29184) covalent geometry : angle 0.71389 / 0.38 (39805) SS BOND : bond 0.00502 / 0.27 ( 27) SS BOND : angle 2.10609 / 1.43 ( 54) hydrogen bonds : bond 0.04286 / 2.93 ( 916) hydrogen bonds : angle 4.93649 / 3.37 ( 2580) Misc. bond : bond 0.00172 / 0.09 ( 2) link_NAG-ASN : bond 0.00859 / 0.45 ( 37) link_NAG-ASN : angle 3.88289 / 2.47 ( 111) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9648.27 seconds wall clock time: 164 minutes 56.66 seconds (9896.66 seconds total)