Starting phenix.real_space_refine on Fri Feb 6 21:46:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uea_64079/02_2026/9uea_64079_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uea_64079/02_2026/9uea_64079.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9uea_64079/02_2026/9uea_64079_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uea_64079/02_2026/9uea_64079_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9uea_64079/02_2026/9uea_64079.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uea_64079/02_2026/9uea_64079.map" } resolution = 2.94 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= 0.003 sd= 0.120 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 144 5.16 5 C 17545 2.51 5 N 4501 2.21 5 O 5472 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27662 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 9008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1170, 9008 Classifications: {'peptide': 1170} Link IDs: {'PTRANS': 57, 'TRANS': 1112} Chain breaks: 4 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 9005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1170, 9005 Classifications: {'peptide': 1170} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 57, 'TRANS': 1112} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 9009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1170, 9009 Classifications: {'peptide': 1170} Link IDs: {'PTRANS': 57, 'TRANS': 1112} Chain breaks: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 6.75, per 1000 atoms: 0.24 Number of scatterers: 27662 At special positions: 0 Unit cell: (158.098, 150.412, 163.587, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 144 16.00 O 5472 8.00 N 4501 7.00 C 17545 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=50, symmetry=0 Simple disulfide: pdb=" SG CYS A 34 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 182 " - pdb=" SG CYS A 220 " distance=2.03 Simple disulfide: pdb=" SG CYS A 191 " - pdb=" SG CYS A 242 " distance=2.06 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 354 " distance=2.02 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 412 " distance=2.03 Simple disulfide: pdb=" SG CYS A 430 " - pdb=" SG CYS A 483 " distance=2.03 Simple disulfide: pdb=" SG CYS A 442 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 507 " - pdb=" SG CYS A 531 " distance=2.03 Simple disulfide: pdb=" SG CYS A 608 " - pdb=" SG CYS A 659 " distance=2.03 Simple disulfide: pdb=" SG CYS A 625 " - pdb=" SG CYS A 655 " distance=2.03 Simple disulfide: pdb=" SG CYS A 684 " - pdb=" SG CYS A 717 " distance=2.03 Simple disulfide: pdb=" SG CYS A 731 " - pdb=" SG CYS A 740 " distance=2.03 Simple disulfide: pdb=" SG CYS A 805 " - pdb=" SG CYS A 827 " distance=2.03 Simple disulfide: pdb=" SG CYS A 810 " - pdb=" SG CYS A 816 " distance=2.03 Simple disulfide: pdb=" SG CYS A 911 " - pdb=" SG CYS A 924 " distance=2.03 Simple disulfide: pdb=" SG CYS A1105 " - pdb=" SG CYS A1116 " distance=2.03 Simple disulfide: pdb=" SG CYS A1155 " - pdb=" SG CYS A1163 " distance=2.04 Simple disulfide: pdb=" SG CYS B 34 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 182 " - pdb=" SG CYS B 220 " distance=2.03 Simple disulfide: pdb=" SG CYS B 191 " - pdb=" SG CYS B 242 " distance=2.07 Simple disulfide: pdb=" SG CYS B 344 " - pdb=" SG CYS B 354 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 412 " distance=2.03 Simple disulfide: pdb=" SG CYS B 430 " - pdb=" SG CYS B 483 " distance=2.03 Simple disulfide: pdb=" SG CYS B 442 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 507 " - pdb=" SG CYS B 531 " distance=2.03 Simple disulfide: pdb=" SG CYS B 608 " - pdb=" SG CYS B 659 " distance=2.03 Simple disulfide: pdb=" SG CYS B 625 " - pdb=" SG CYS B 655 " distance=2.03 Simple disulfide: pdb=" SG CYS B 684 " - pdb=" SG CYS B 717 " distance=2.03 Simple disulfide: pdb=" SG CYS B 731 " - pdb=" SG CYS B 740 " distance=2.02 Simple disulfide: pdb=" SG CYS B 805 " - pdb=" SG CYS B 827 " distance=2.04 Simple disulfide: pdb=" SG CYS B 810 " - pdb=" SG CYS B 816 " distance=2.03 Simple disulfide: pdb=" SG CYS B 911 " - pdb=" SG CYS B 924 " distance=2.03 Simple disulfide: pdb=" SG CYS B1105 " - pdb=" SG CYS B1116 " distance=2.02 Simple disulfide: pdb=" SG CYS B1155 " - pdb=" SG CYS B1163 " distance=2.03 Simple disulfide: pdb=" SG CYS C 34 " - pdb=" SG CYS C 201 " distance=2.03 Simple disulfide: pdb=" SG CYS C 182 " - pdb=" SG CYS C 220 " distance=2.03 Simple disulfide: pdb=" SG CYS C 191 " - pdb=" SG CYS C 242 " distance=2.05 Simple disulfide: pdb=" SG CYS C 344 " - pdb=" SG CYS C 354 " distance=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 412 " distance=2.03 Simple disulfide: pdb=" SG CYS C 430 " - pdb=" SG CYS C 483 " distance=2.03 Simple disulfide: pdb=" SG CYS C 442 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 507 " - pdb=" SG CYS C 531 " distance=2.03 Simple disulfide: pdb=" SG CYS C 608 " - pdb=" SG CYS C 659 " distance=2.03 Simple disulfide: pdb=" SG CYS C 625 " - pdb=" SG CYS C 655 " distance=2.03 Simple disulfide: pdb=" SG CYS C 684 " - pdb=" SG CYS C 717 " distance=2.05 Simple disulfide: pdb=" SG CYS C 731 " - pdb=" SG CYS C 740 " distance=2.02 Simple disulfide: pdb=" SG CYS C 805 " - pdb=" SG CYS C 827 " distance=2.04 Simple disulfide: pdb=" SG CYS C 810 " - pdb=" SG CYS C 816 " distance=2.03 Simple disulfide: pdb=" SG CYS C 911 " - pdb=" SG CYS C 924 " distance=2.03 Simple disulfide: pdb=" SG CYS C1105 " - pdb=" SG CYS C1116 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " NAG I 3 " " NAG J 1 " - " NAG J 2 " BETA1-6 " NAG F 2 " - " FUC F 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A1301 " - " ASN A 71 " " NAG A1302 " - " ASN A 111 " " NAG A1303 " - " ASN A 162 " " NAG A1304 " - " ASN A 172 " " NAG A1305 " - " ASN A 241 " " NAG A1307 " - " ASN A 492 " " NAG A1308 " - " ASN A 723 " " NAG A1309 " - " ASN A 762 " " NAG A1310 " - " ASN A 784 " " NAG A1311 " - " ASN A 869 " " NAG B1301 " - " ASN B 71 " " NAG B1302 " - " ASN B 111 " " NAG B1303 " - " ASN B 162 " " NAG B1304 " - " ASN B 172 " " NAG B1305 " - " ASN B 241 " " NAG B1306 " - " ASN B 415 " " NAG B1307 " - " ASN B 624 " " NAG B1308 " - " ASN B 723 " " NAG B1309 " - " ASN B 762 " " NAG B1310 " - " ASN B 784 " " NAG B1311 " - " ASN B 869 " " NAG B1312 " - " ASN B1174 " " NAG C1301 " - " ASN C 71 " " NAG C1302 " - " ASN C 111 " " NAG C1303 " - " ASN C 172 " " NAG C1304 " - " ASN C 241 " " NAG C1305 " - " ASN C 415 " " NAG C1306 " - " ASN C 624 " " NAG C1307 " - " ASN C 723 " " NAG D 1 " - " ASN A 227 " " NAG E 1 " - " ASN A 132 " " NAG F 1 " - " ASN B 132 " " NAG G 1 " - " ASN C 162 " " NAG H 1 " - " ASN C 227 " " NAG I 1 " - " ASN C 132 " " NAG J 1 " - " ASN C 869 " NAG-THR " NAG A1306 " - " THR A 417 " Time building additional restraints: 2.47 Conformation dependent library (CDL) restraints added in 1.4 seconds 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6484 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 55 sheets defined 25.8% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 40 through 47 removed outlier: 3.655A pdb=" N PHE A 44 " --> pdb=" O ASP A 40 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU A 47 " --> pdb=" O ALA A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 115 removed outlier: 4.685A pdb=" N SER A 113 " --> pdb=" O SER A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 236 removed outlier: 3.897A pdb=" N PHE A 236 " --> pdb=" O SER A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 357 Processing helix chain 'A' and resid 390 through 395 removed outlier: 3.533A pdb=" N LYS A 395 " --> pdb=" O PRO A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 423 removed outlier: 3.543A pdb=" N LEU A 419 " --> pdb=" O ASN A 415 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER A 421 " --> pdb=" O THR A 417 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N PHE A 423 " --> pdb=" O LEU A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 439 Processing helix chain 'A' and resid 468 through 473 Processing helix chain 'A' and resid 531 through 535 removed outlier: 3.775A pdb=" N ALA A 535 " --> pdb=" O ARG A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 633 Processing helix chain 'A' and resid 683 through 690 Processing helix chain 'A' and resid 804 through 810 Processing helix chain 'A' and resid 813 through 824 removed outlier: 3.748A pdb=" N LEU A 819 " --> pdb=" O ARG A 815 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLU A 822 " --> pdb=" O LYS A 818 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N TYR A 823 " --> pdb=" O LEU A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 850 removed outlier: 3.507A pdb=" N VAL A 845 " --> pdb=" O GLN A 841 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER A 847 " --> pdb=" O GLU A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 874 Processing helix chain 'A' and resid 887 through 897 removed outlier: 3.512A pdb=" N ASP A 895 " --> pdb=" O ASP A 891 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS A 896 " --> pdb=" O LEU A 892 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL A 897 " --> pdb=" O LEU A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 913 removed outlier: 3.587A pdb=" N MET A 912 " --> pdb=" O TYR A 908 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS A 913 " --> pdb=" O ASP A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 930 removed outlier: 4.177A pdb=" N VAL A 928 " --> pdb=" O CYS A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 954 removed outlier: 3.504A pdb=" N TYR A 946 " --> pdb=" O MET A 942 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR A 947 " --> pdb=" O GLU A 943 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A 951 " --> pdb=" O THR A 947 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY A 952 " --> pdb=" O SER A 948 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE A 954 " --> pdb=" O LEU A 950 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 982 removed outlier: 3.615A pdb=" N ARG A 978 " --> pdb=" O SER A 974 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A 982 " --> pdb=" O ARG A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 991 Processing helix chain 'A' and resid 993 through 1006 removed outlier: 3.603A pdb=" N ALA A 997 " --> pdb=" O GLN A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1011 Processing helix chain 'A' and resid 1015 through 1038 removed outlier: 3.533A pdb=" N LEU A1032 " --> pdb=" O ASN A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1057 removed outlier: 3.592A pdb=" N LEU A1057 " --> pdb=" O ILE A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1072 removed outlier: 3.920A pdb=" N ASP A1063 " --> pdb=" O THR A1059 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ALA A1064 " --> pdb=" O ALA A1060 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN A1065 " --> pdb=" O GLU A1061 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP A1067 " --> pdb=" O ASP A1063 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG A1068 " --> pdb=" O ALA A1064 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1106 Processing helix chain 'A' and resid 1199 through 1201 No H-bonds generated for 'chain 'A' and resid 1199 through 1201' Processing helix chain 'A' and resid 1220 through 1224 Processing helix chain 'B' and resid 40 through 47 removed outlier: 4.010A pdb=" N PHE B 44 " --> pdb=" O ASP B 40 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU B 47 " --> pdb=" O ALA B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 115 Processing helix chain 'B' and resid 227 through 235 Processing helix chain 'B' and resid 347 through 356 Processing helix chain 'B' and resid 390 through 395 removed outlier: 3.741A pdb=" N LYS B 395 " --> pdb=" O PRO B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 404 removed outlier: 3.611A pdb=" N PHE B 404 " --> pdb=" O VAL B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 423 removed outlier: 3.591A pdb=" N LEU B 419 " --> pdb=" O ASN B 415 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE B 423 " --> pdb=" O LEU B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 441 Processing helix chain 'B' and resid 454 through 461 removed outlier: 3.772A pdb=" N MET B 457 " --> pdb=" O PRO B 454 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS B 458 " --> pdb=" O LEU B 455 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N SER B 459 " --> pdb=" O SER B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 473 Processing helix chain 'B' and resid 529 through 534 removed outlier: 4.173A pdb=" N ASP B 533 " --> pdb=" O ILE B 530 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE B 534 " --> pdb=" O CYS B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 633 Processing helix chain 'B' and resid 683 through 690 removed outlier: 3.626A pdb=" N VAL B 687 " --> pdb=" O ALA B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 804 through 809 Processing helix chain 'B' and resid 813 through 821 removed outlier: 3.981A pdb=" N LEU B 819 " --> pdb=" O ARG B 815 " (cutoff:3.500A) Processing helix chain 'B' and resid 824 through 852 removed outlier: 3.892A pdb=" N SER B 828 " --> pdb=" O GLY B 824 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS B 829 " --> pdb=" O GLN B 825 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE B 830 " --> pdb=" O PHE B 826 " (cutoff:3.500A) Processing helix chain 'B' and resid 870 through 874 Processing helix chain 'B' and resid 887 through 896 removed outlier: 3.625A pdb=" N LYS B 896 " --> pdb=" O LEU B 892 " (cutoff:3.500A) Processing helix chain 'B' and resid 906 through 914 Processing helix chain 'B' and resid 917 through 921 removed outlier: 4.056A pdb=" N ARG B 920 " --> pdb=" O GLN B 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 930 removed outlier: 3.537A pdb=" N GLY B 930 " --> pdb=" O GLN B 926 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 952 removed outlier: 3.884A pdb=" N THR B 947 " --> pdb=" O GLU B 943 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU B 950 " --> pdb=" O TYR B 946 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 951 " --> pdb=" O THR B 947 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY B 952 " --> pdb=" O SER B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 970 through 982 removed outlier: 3.717A pdb=" N VAL B 982 " --> pdb=" O ARG B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 991 No H-bonds generated for 'chain 'B' and resid 989 through 991' Processing helix chain 'B' and resid 992 through 1006 removed outlier: 6.523A pdb=" N ASN B 998 " --> pdb=" O LYS B 994 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS B 999 " --> pdb=" O LEU B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1011 removed outlier: 3.506A pdb=" N PHE B1011 " --> pdb=" O GLN B1008 " (cutoff:3.500A) Processing helix chain 'B' and resid 1015 through 1038 removed outlier: 3.578A pdb=" N LEU B1032 " --> pdb=" O ASN B1028 " (cutoff:3.500A) Processing helix chain 'B' and resid 1039 through 1041 No H-bonds generated for 'chain 'B' and resid 1039 through 1041' Processing helix chain 'B' and resid 1049 through 1057 removed outlier: 3.543A pdb=" N LEU B1057 " --> pdb=" O ILE B1053 " (cutoff:3.500A) Processing helix chain 'B' and resid 1058 through 1072 removed outlier: 3.823A pdb=" N ASP B1063 " --> pdb=" O THR B1059 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA B1064 " --> pdb=" O ALA B1060 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG B1068 " --> pdb=" O ALA B1064 " (cutoff:3.500A) Processing helix chain 'B' and resid 1074 through 1106 removed outlier: 3.623A pdb=" N GLN B1096 " --> pdb=" O ALA B1092 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU B1097 " --> pdb=" O ARG B1093 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 47 removed outlier: 3.956A pdb=" N PHE C 44 " --> pdb=" O ASP C 40 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU C 47 " --> pdb=" O ALA C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 115 removed outlier: 4.677A pdb=" N SER C 113 " --> pdb=" O SER C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 220 Processing helix chain 'C' and resid 227 through 236 removed outlier: 3.967A pdb=" N PHE C 236 " --> pdb=" O SER C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 356 Processing helix chain 'C' and resid 390 through 395 removed outlier: 3.690A pdb=" N PHE C 394 " --> pdb=" O PHE C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 423 removed outlier: 3.672A pdb=" N LEU C 419 " --> pdb=" O ASN C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 441 Processing helix chain 'C' and resid 454 through 462 removed outlier: 5.368A pdb=" N SER C 459 " --> pdb=" O SER C 456 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE C 461 " --> pdb=" O LYS C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 473 Processing helix chain 'C' and resid 531 through 535 removed outlier: 3.633A pdb=" N PHE C 534 " --> pdb=" O CYS C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 690 removed outlier: 3.500A pdb=" N VAL C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 810 Processing helix chain 'C' and resid 813 through 821 removed outlier: 3.590A pdb=" N LEU C 819 " --> pdb=" O ARG C 815 " (cutoff:3.500A) Processing helix chain 'C' and resid 824 through 851 removed outlier: 3.555A pdb=" N LYS C 829 " --> pdb=" O GLN C 825 " (cutoff:3.500A) Processing helix chain 'C' and resid 870 through 874 Processing helix chain 'C' and resid 887 through 897 Processing helix chain 'C' and resid 906 through 911 Processing helix chain 'C' and resid 912 through 918 removed outlier: 5.605A pdb=" N GLY C 915 " --> pdb=" O MET C 912 " (cutoff:3.500A) Proline residue: C 916 - end of helix No H-bonds generated for 'chain 'C' and resid 912 through 918' Processing helix chain 'C' and resid 925 through 930 Processing helix chain 'C' and resid 939 through 952 removed outlier: 3.793A pdb=" N TYR C 946 " --> pdb=" O MET C 942 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR C 947 " --> pdb=" O GLU C 943 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU C 951 " --> pdb=" O THR C 947 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLY C 952 " --> pdb=" O SER C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 953 through 958 removed outlier: 3.835A pdb=" N GLY C 958 " --> pdb=" O ILE C 954 " (cutoff:3.500A) Processing helix chain 'C' and resid 970 through 982 removed outlier: 3.512A pdb=" N PHE C 976 " --> pdb=" O ALA C 972 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL C 982 " --> pdb=" O ARG C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 992 through 1006 Processing helix chain 'C' and resid 1015 through 1038 removed outlier: 3.749A pdb=" N LEU C1032 " --> pdb=" O ASN C1028 " (cutoff:3.500A) Processing helix chain 'C' and resid 1039 through 1041 No H-bonds generated for 'chain 'C' and resid 1039 through 1041' Processing helix chain 'C' and resid 1049 through 1055 Processing helix chain 'C' and resid 1058 through 1072 removed outlier: 3.876A pdb=" N ASP C1063 " --> pdb=" O THR C1059 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA C1064 " --> pdb=" O ALA C1060 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG C1068 " --> pdb=" O ALA C1064 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU C1069 " --> pdb=" O GLN C1065 " (cutoff:3.500A) Processing helix chain 'C' and resid 1074 through 1106 removed outlier: 3.703A pdb=" N GLN C1096 " --> pdb=" O ALA C1092 " (cutoff:3.500A) Processing helix chain 'C' and resid 1220 through 1224 Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 39 Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 80 removed outlier: 4.036A pdb=" N ARG A 340 " --> pdb=" O ASP A 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 88 through 90 removed outlier: 3.646A pdb=" N ALA A 287 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N SER A 272 " --> pdb=" O ARG A 285 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ARG A 285 " --> pdb=" O SER A 272 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 117 through 118 removed outlier: 3.651A pdb=" N CYS A 191 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE A 244 " --> pdb=" O TYR A 190 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ILE A 192 " --> pdb=" O CYS A 242 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N CYS A 242 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LYS A 194 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N VAL A 240 " --> pdb=" O LYS A 194 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 134 through 136 removed outlier: 3.825A pdb=" N ALA A 314 " --> pdb=" O LYS A 146 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 159 through 162 removed outlier: 4.087A pdb=" N SER A 159 " --> pdb=" O ALA A 171 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 212 through 213 removed outlier: 6.467A pdb=" N ILE A 212 " --> pdb=" O SER A 304 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 364 through 368 removed outlier: 4.734A pdb=" N VAL A 664 " --> pdb=" O VAL A 368 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 378 through 381 removed outlier: 6.825A pdb=" N PHE A 379 " --> pdb=" O SER A 612 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N VAL A 644 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL A 636 " --> pdb=" O VAL A 644 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 405 through 409 removed outlier: 6.833A pdb=" N THR A 482 " --> pdb=" O CYS A 430 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N CYS A 430 " --> pdb=" O THR A 482 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ARG A 484 " --> pdb=" O PHE A 428 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N PHE A 428 " --> pdb=" O ARG A 484 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU A 486 " --> pdb=" O ASP A 426 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 412 through 414 removed outlier: 6.363A pdb=" N CYS A 412 " --> pdb=" O CYS A 590 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 517 through 520 removed outlier: 6.410A pdb=" N VAL A 562 " --> pdb=" O SER A 505 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N CYS A 507 " --> pdb=" O ILE A 560 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE A 560 " --> pdb=" O CYS A 507 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ARG A 509 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU A 558 " --> pdb=" O ARG A 509 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY A 557 " --> pdb=" O LEU A 550 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 722 through 727 removed outlier: 6.548A pdb=" N SER A 722 " --> pdb=" O LEU A 758 " (cutoff:3.500A) removed outlier: 9.089A pdb=" N VAL A 760 " --> pdb=" O SER A 722 " (cutoff:3.500A) removed outlier: 10.873A pdb=" N ASN A 724 " --> pdb=" O VAL A 760 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 767 through 768 removed outlier: 6.014A pdb=" N ILE A 767 " --> pdb=" O THR C 857 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1129 removed outlier: 6.451A pdb=" N HIS A1121 " --> pdb=" O TYR A1140 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N TYR A1140 " --> pdb=" O HIS A1121 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL A1123 " --> pdb=" O VAL A1138 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ASN A 784 " --> pdb=" O THR A1143 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N TYR A1145 " --> pdb=" O PRO A 782 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASN A1147 " --> pdb=" O ALA A 780 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ALA A 780 " --> pdb=" O ASN A1147 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 800 through 803 removed outlier: 4.479A pdb=" N LYS A 800 " --> pdb=" O LEU A 934 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 856 through 858 removed outlier: 6.668A pdb=" N THR A 857 " --> pdb=" O LEU B 769 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 966 through 967 removed outlier: 7.212A pdb=" N ALA B 780 " --> pdb=" O ASN B1147 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ASN B1147 " --> pdb=" O ALA B 780 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N TYR B1145 " --> pdb=" O PRO B 782 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASN B 784 " --> pdb=" O THR B1143 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N GLY B1132 " --> pdb=" O ASN B1128 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ASN B1128 " --> pdb=" O GLY B1132 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N TYR B1134 " --> pdb=" O VAL B1126 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL B1126 " --> pdb=" O TYR B1134 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N PHE B1136 " --> pdb=" O SER B1124 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N SER B1124 " --> pdb=" O PHE B1136 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VAL B1138 " --> pdb=" O ILE B1122 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1154 through 1156 Processing sheet with id=AC2, first strand: chain 'A' and resid 1163 through 1166 removed outlier: 3.846A pdb=" N CYS A1163 " --> pdb=" O VAL A1206 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1169 through 1172 Processing sheet with id=AC4, first strand: chain 'B' and resid 37 through 39 Processing sheet with id=AC5, first strand: chain 'B' and resid 68 through 69 removed outlier: 6.539A pdb=" N VAL C 636 " --> pdb=" O VAL C 644 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL C 644 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLY C 377 " --> pdb=" O ASP C 610 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N SER C 612 " --> pdb=" O GLY C 377 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N PHE C 379 " --> pdb=" O SER C 612 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 72 through 80 removed outlier: 4.201A pdb=" N ARG B 340 " --> pdb=" O ASP B 331 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 88 through 90 removed outlier: 6.029A pdb=" N VAL B 268 " --> pdb=" O THR B 288 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N THR B 288 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU B 270 " --> pdb=" O PHE B 286 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 93 through 94 removed outlier: 7.467A pdb=" N SER B 93 " --> pdb=" O PHE B 305 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE B 212 " --> pdb=" O SER B 304 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ARG B 306 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N GLU B 214 " --> pdb=" O ARG B 306 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 117 through 118 removed outlier: 3.602A pdb=" N TYR B 298 " --> pdb=" O ASN B 117 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE B 244 " --> pdb=" O TYR B 190 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 134 through 136 removed outlier: 4.131A pdb=" N ALA B 314 " --> pdb=" O LYS B 146 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 160 through 162 Processing sheet with id=AD3, first strand: chain 'B' and resid 364 through 367 Processing sheet with id=AD4, first strand: chain 'B' and resid 380 through 381 removed outlier: 3.622A pdb=" N GLU B 381 " --> pdb=" O SER B 612 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N TYR B 653 " --> pdb=" O CYS B 625 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N VAL B 644 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL B 636 " --> pdb=" O VAL B 644 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 405 through 409 removed outlier: 6.840A pdb=" N THR B 482 " --> pdb=" O CYS B 430 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N CYS B 430 " --> pdb=" O THR B 482 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ARG B 484 " --> pdb=" O PHE B 428 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N PHE B 428 " --> pdb=" O ARG B 484 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU B 486 " --> pdb=" O ASP B 426 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 412 through 414 removed outlier: 6.389A pdb=" N CYS B 412 " --> pdb=" O CYS B 590 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 517 through 520 removed outlier: 5.394A pdb=" N GLY B 502 " --> pdb=" O VAL B 566 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL B 566 " --> pdb=" O GLY B 502 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ILE B 504 " --> pdb=" O THR B 564 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N THR B 564 " --> pdb=" O ILE B 504 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS B 506 " --> pdb=" O VAL B 562 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 722 through 728 removed outlier: 6.598A pdb=" N SER B 722 " --> pdb=" O LEU B 758 " (cutoff:3.500A) removed outlier: 8.952A pdb=" N VAL B 760 " --> pdb=" O SER B 722 " (cutoff:3.500A) removed outlier: 10.989A pdb=" N ASN B 724 " --> pdb=" O VAL B 760 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 801 through 803 Processing sheet with id=AE1, first strand: chain 'B' and resid 856 through 857 Processing sheet with id=AE2, first strand: chain 'B' and resid 966 through 967 removed outlier: 6.997A pdb=" N ALA C 780 " --> pdb=" O ASN C1147 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ASN C1147 " --> pdb=" O ALA C 780 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N TYR C1145 " --> pdb=" O PRO C 782 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN C 784 " --> pdb=" O THR C1143 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N TYR C1140 " --> pdb=" O HIS C1121 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N HIS C1121 " --> pdb=" O TYR C1140 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 1203 through 1206 removed outlier: 4.129A pdb=" N CYS B1163 " --> pdb=" O VAL B1206 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 1169 through 1173 Processing sheet with id=AE5, first strand: chain 'C' and resid 37 through 39 removed outlier: 3.506A pdb=" N ILE C 109 " --> pdb=" O GLN C 38 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N HIS C 96 " --> pdb=" O THR C 105 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 72 through 81 removed outlier: 4.832A pdb=" N GLY C 122 " --> pdb=" O LEU C 323 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N VAL C 268 " --> pdb=" O THR C 288 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N THR C 288 " --> pdb=" O VAL C 268 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU C 270 " --> pdb=" O PHE C 286 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 89 through 90 removed outlier: 4.089A pdb=" N ARG C 340 " --> pdb=" O ASP C 331 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 134 through 136 Processing sheet with id=AE9, first strand: chain 'C' and resid 237 through 249 removed outlier: 6.936A pdb=" N VAL C 240 " --> pdb=" O LYS C 194 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LYS C 194 " --> pdb=" O VAL C 240 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N CYS C 242 " --> pdb=" O ILE C 192 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE C 192 " --> pdb=" O CYS C 242 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE C 244 " --> pdb=" O TYR C 190 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 160 through 162 Processing sheet with id=AF2, first strand: chain 'C' and resid 212 through 215 removed outlier: 6.504A pdb=" N ILE C 212 " --> pdb=" O SER C 304 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ARG C 306 " --> pdb=" O ILE C 212 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLU C 214 " --> pdb=" O ARG C 306 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'C' and resid 364 through 366 removed outlier: 3.710A pdb=" N GLY C 716 " --> pdb=" O THR C 713 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 405 through 409 removed outlier: 6.969A pdb=" N THR C 482 " --> pdb=" O CYS C 430 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N CYS C 430 " --> pdb=" O THR C 482 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ARG C 484 " --> pdb=" O PHE C 428 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE C 428 " --> pdb=" O ARG C 484 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU C 486 " --> pdb=" O ASP C 426 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 412 through 414 removed outlier: 6.492A pdb=" N CYS C 412 " --> pdb=" O CYS C 590 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'C' and resid 517 through 520 removed outlier: 5.263A pdb=" N GLY C 502 " --> pdb=" O VAL C 566 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL C 566 " --> pdb=" O GLY C 502 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ILE C 504 " --> pdb=" O THR C 564 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N THR C 564 " --> pdb=" O ILE C 504 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS C 506 " --> pdb=" O VAL C 562 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLY C 557 " --> pdb=" O LEU C 550 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 722 through 728 removed outlier: 6.446A pdb=" N SER C 722 " --> pdb=" O LEU C 758 " (cutoff:3.500A) removed outlier: 8.804A pdb=" N VAL C 760 " --> pdb=" O SER C 722 " (cutoff:3.500A) removed outlier: 11.066A pdb=" N ASN C 724 " --> pdb=" O VAL C 760 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N LEU C 739 " --> pdb=" O LEU C 735 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 800 through 803 removed outlier: 4.612A pdb=" N LYS C 800 " --> pdb=" O LEU C 934 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 1203 through 1206 removed outlier: 7.073A pdb=" N CYS C1155 " --> pdb=" O LEU C1215 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 1169 through 1173 996 hydrogen bonds defined for protein. 2640 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: 8.30 Time building geometry restraints manager: 3.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8467 1.33 - 1.46: 7370 1.46 - 1.59: 12269 1.59 - 1.72: 0 1.72 - 1.84: 186 Bond restraints: 28292 Sorted by residual: bond pdb=" CA SER B 965 " pdb=" CB SER B 965 " ideal model delta sigma weight residual 1.535 1.469 0.066 1.93e-02 2.68e+03 1.16e+01 bond pdb=" CA SER B 949 " pdb=" CB SER B 949 " ideal model delta sigma weight residual 1.529 1.476 0.053 1.64e-02 3.72e+03 1.03e+01 bond pdb=" N GLN B 917 " pdb=" CA GLN B 917 " ideal model delta sigma weight residual 1.455 1.497 -0.041 1.33e-02 5.65e+03 9.62e+00 bond pdb=" N GLY A 377 " pdb=" CA GLY A 377 " ideal model delta sigma weight residual 1.446 1.477 -0.032 1.02e-02 9.61e+03 9.60e+00 bond pdb=" N ASP B 921 " pdb=" CA ASP B 921 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.23e-02 6.61e+03 9.31e+00 ... (remaining 28287 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.95: 38444 4.95 - 9.89: 47 9.89 - 14.84: 6 14.84 - 19.79: 2 19.79 - 24.73: 1 Bond angle restraints: 38500 Sorted by residual: angle pdb=" C PRO C1160 " pdb=" CA PRO C1160 " pdb=" CB PRO C1160 " ideal model delta sigma weight residual 110.92 124.90 -13.98 1.22e+00 6.72e-01 1.31e+02 angle pdb=" CA CYS B 191 " pdb=" CB CYS B 191 " pdb=" SG CYS B 191 " ideal model delta sigma weight residual 114.40 139.13 -24.73 2.30e+00 1.89e-01 1.16e+02 angle pdb=" C GLY B 958 " pdb=" N TRP B 959 " pdb=" CA TRP B 959 " ideal model delta sigma weight residual 122.37 109.02 13.35 1.54e+00 4.22e-01 7.52e+01 angle pdb=" CA CYS C 191 " pdb=" CB CYS C 191 " pdb=" SG CYS C 191 " ideal model delta sigma weight residual 114.40 133.34 -18.94 2.30e+00 1.89e-01 6.78e+01 angle pdb=" CA PRO C1160 " pdb=" N PRO C1160 " pdb=" CD PRO C1160 " ideal model delta sigma weight residual 112.00 101.76 10.24 1.40e+00 5.10e-01 5.35e+01 ... (remaining 38495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.96: 16452 22.96 - 45.91: 793 45.91 - 68.87: 129 68.87 - 91.83: 29 91.83 - 114.79: 20 Dihedral angle restraints: 17423 sinusoidal: 7231 harmonic: 10192 Sorted by residual: dihedral pdb=" CA PRO B 195 " pdb=" C PRO B 195 " pdb=" N ARG B 196 " pdb=" CA ARG B 196 " ideal model delta harmonic sigma weight residual 180.00 116.32 63.68 0 5.00e+00 4.00e-02 1.62e+02 dihedral pdb=" CA ILE B 192 " pdb=" C ILE B 192 " pdb=" N LEU B 193 " pdb=" CA LEU B 193 " ideal model delta harmonic sigma weight residual 180.00 117.37 62.63 0 5.00e+00 4.00e-02 1.57e+02 dihedral pdb=" CA VAL C 240 " pdb=" C VAL C 240 " pdb=" N ASN C 241 " pdb=" CA ASN C 241 " ideal model delta harmonic sigma weight residual -180.00 -130.65 -49.35 0 5.00e+00 4.00e-02 9.74e+01 ... (remaining 17420 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 4321 0.118 - 0.235: 102 0.235 - 0.353: 11 0.353 - 0.470: 2 0.470 - 0.588: 1 Chirality restraints: 4437 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 227 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.81 -0.59 2.00e-01 2.50e+01 8.63e+00 chirality pdb=" CA TYR B 862 " pdb=" N TYR B 862 " pdb=" C TYR B 862 " pdb=" CB TYR B 862 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.86e+00 chirality pdb=" CA GLU B 991 " pdb=" N GLU B 991 " pdb=" C GLU B 991 " pdb=" CB GLU B 991 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.82e+00 ... (remaining 4434 not shown) Planarity restraints: 4979 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS B 191 " -0.026 2.00e-02 2.50e+03 5.27e-02 2.78e+01 pdb=" C CYS B 191 " 0.091 2.00e-02 2.50e+03 pdb=" O CYS B 191 " -0.034 2.00e-02 2.50e+03 pdb=" N ILE B 192 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 192 " -0.021 2.00e-02 2.50e+03 4.27e-02 1.82e+01 pdb=" C ILE B 192 " 0.074 2.00e-02 2.50e+03 pdb=" O ILE B 192 " -0.027 2.00e-02 2.50e+03 pdb=" N LEU B 193 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B1159 " 0.069 5.00e-02 4.00e+02 1.04e-01 1.74e+01 pdb=" N PRO B1160 " -0.181 5.00e-02 4.00e+02 pdb=" CA PRO B1160 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO B1160 " 0.056 5.00e-02 4.00e+02 ... (remaining 4976 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 226 2.60 - 3.17: 23023 3.17 - 3.75: 39687 3.75 - 4.32: 60039 4.32 - 4.90: 99890 Nonbonded interactions: 222865 Sorted by model distance: nonbonded pdb=" O PRO A 81 " pdb=" OH TYR A 328 " model vdw 2.023 3.040 nonbonded pdb=" O PRO B 81 " pdb=" OH TYR B 328 " model vdw 2.041 3.040 nonbonded pdb=" OG SER A 744 " pdb=" OE1 GLN A 757 " model vdw 2.044 3.040 nonbonded pdb=" O PRO C 81 " pdb=" OH TYR C 328 " model vdw 2.079 3.040 nonbonded pdb=" OD2 ASP C 348 " pdb=" OG1 THR C 677 " model vdw 2.162 3.040 ... (remaining 222860 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 21 through 916 or (resid 917 and (name N or name CA or nam \ e C or name O or name CB )) or resid 918 through 1307)) selection = (chain 'B' and ((resid 21 and (name CA or name C or name O or name CB or name CG \ or name CD or name OE1 or name NE2)) or resid 22 through 1307)) selection = (chain 'C' and ((resid 21 and (name CA or name C or name O or name CB or name CG \ or name CD or name OE1 or name NE2)) or resid 22 through 916 or (resid 917 and \ (name N or name CA or name C or name O or name CB )) or resid 918 through 1307)) \ } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'J' } ncs_group { reference = (chain 'F' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 29.860 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.100 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:9.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 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 0.095 28388 Z= 0.254 Angle : 0.796 24.733 38737 Z= 0.449 Chirality : 0.052 0.588 4437 Planarity : 0.006 0.104 4943 Dihedral : 13.842 114.787 10789 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.22 % Favored : 95.49 % Rotamer: Outliers : 0.34 % Allowed : 0.64 % Favored : 99.03 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.18 % 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: -1.13 (0.13), residues: 3480 helix: -1.02 (0.18), residues: 710 sheet: 0.16 (0.17), residues: 831 loop : -1.04 (0.13), residues: 1939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 200 TYR 0.051 0.002 TYR C 328 PHE 0.048 0.002 PHE C 428 TRP 0.022 0.002 TRP C 959 HIS 0.007 0.001 HIS C1137 Details of bonding type rmsd covalent geometry : bond 0.00510 (28292) covalent geometry : angle 0.77509 (38500) SS BOND : bond 0.00783 ( 50) SS BOND : angle 1.86876 ( 100) hydrogen bonds : bond 0.20754 ( 996) hydrogen bonds : angle 7.68846 ( 2640) link_BETA1-4 : bond 0.00889 ( 8) link_BETA1-4 : angle 3.34071 ( 24) link_BETA1-6 : bond 0.00444 ( 1) link_BETA1-6 : angle 1.86578 ( 3) link_NAG-ASN : bond 0.00578 ( 36) link_NAG-ASN : angle 2.71221 ( 108) link_NAG-THR : bond 0.01913 ( 1) link_NAG-THR : angle 2.19357 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 418 time to evaluate : 1.044 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 39 VAL cc_start: 0.8355 (t) cc_final: 0.8087 (t) REVERT: A 418 LYS cc_start: 0.7740 (mtpt) cc_final: 0.7487 (mmtp) REVERT: A 818 LYS cc_start: 0.8248 (mmtp) cc_final: 0.7883 (ttpp) REVERT: A 843 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7187 (mm-30) REVERT: A 1100 ASP cc_start: 0.7360 (m-30) cc_final: 0.6809 (m-30) REVERT: A 1108 SER cc_start: 0.8571 (p) cc_final: 0.8286 (t) REVERT: A 1213 GLU cc_start: 0.8299 (mm-30) cc_final: 0.7976 (mm-30) REVERT: A 1220 PRO cc_start: 0.8386 (Cg_exo) cc_final: 0.7964 (Cg_endo) REVERT: B 47 LEU cc_start: 0.8550 (tp) cc_final: 0.7947 (pt) REVERT: B 148 LYS cc_start: 0.7938 (mttm) cc_final: 0.7649 (mttt) REVERT: B 348 ASP cc_start: 0.7776 (m-30) cc_final: 0.7552 (m-30) REVERT: B 574 MET cc_start: 0.8675 (mtp) cc_final: 0.8468 (mtp) REVERT: B 921 ASP cc_start: 0.6483 (OUTLIER) cc_final: 0.6053 (p0) REVERT: B 986 GLN cc_start: 0.7591 (tp40) cc_final: 0.7187 (tm130) REVERT: B 1216 GLU cc_start: 0.5906 (pm20) cc_final: 0.5652 (pm20) REVERT: C 33 GLU cc_start: 0.7619 (pt0) cc_final: 0.7144 (pm20) REVERT: C 47 LEU cc_start: 0.7542 (mm) cc_final: 0.7178 (mm) REVERT: C 426 ASP cc_start: 0.7851 (t70) cc_final: 0.7414 (m-30) REVERT: C 1075 THR cc_start: 0.9086 (m) cc_final: 0.8851 (m) REVERT: C 1209 ASP cc_start: 0.7035 (m-30) cc_final: 0.6670 (m-30) outliers start: 10 outliers final: 1 residues processed: 427 average time/residue: 0.6248 time to fit residues: 313.0883 Evaluate side-chains 220 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 218 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 921 ASP Chi-restraints excluded: chain C residue 1160 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 0.2980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 ASN A 652 ASN A 831 ASN A 835 HIS A 993 GLN A1128 ASN B 30 ASN B 623 GLN B 755 GLN ** B 865 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1008 GLN B1084 GLN C 144 GLN C 246 ASN C 282 ASN C 411 ASN C 632 GLN C 906 GLN C1030 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.140735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.109186 restraints weight = 36274.212| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.17 r_work: 0.3005 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 28388 Z= 0.125 Angle : 0.636 11.229 38737 Z= 0.324 Chirality : 0.046 0.422 4437 Planarity : 0.005 0.141 4943 Dihedral : 9.054 109.708 4786 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.97 % Favored : 95.83 % Rotamer: Outliers : 1.84 % Allowed : 7.78 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.15 % 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: -0.62 (0.13), residues: 3480 helix: -0.07 (0.18), residues: 748 sheet: 0.43 (0.18), residues: 787 loop : -0.88 (0.13), residues: 1945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 49 TYR 0.030 0.001 TYR C 328 PHE 0.029 0.001 PHE A 756 TRP 0.013 0.001 TRP A 959 HIS 0.005 0.001 HIS C 675 Details of bonding type rmsd covalent geometry : bond 0.00280 (28292) covalent geometry : angle 0.61992 (38500) SS BOND : bond 0.00587 ( 50) SS BOND : angle 0.98707 ( 100) hydrogen bonds : bond 0.04701 ( 996) hydrogen bonds : angle 5.51367 ( 2640) link_BETA1-4 : bond 0.00812 ( 8) link_BETA1-4 : angle 2.84168 ( 24) link_BETA1-6 : bond 0.01607 ( 1) link_BETA1-6 : angle 1.93830 ( 3) link_NAG-ASN : bond 0.00439 ( 36) link_NAG-ASN : angle 2.27580 ( 108) link_NAG-THR : bond 0.01280 ( 1) link_NAG-THR : angle 0.75204 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 251 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 ASN cc_start: 0.8300 (m-40) cc_final: 0.8073 (m110) REVERT: A 322 LYS cc_start: 0.9060 (mtpt) cc_final: 0.8624 (mmtp) REVERT: A 530 ILE cc_start: 0.9418 (tt) cc_final: 0.9131 (tt) REVERT: A 818 LYS cc_start: 0.8627 (mmtp) cc_final: 0.8277 (ttpp) REVERT: A 864 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7176 (tm) REVERT: A 1100 ASP cc_start: 0.8244 (m-30) cc_final: 0.7836 (m-30) REVERT: A 1108 SER cc_start: 0.8859 (p) cc_final: 0.8642 (t) REVERT: A 1213 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8071 (mm-30) REVERT: B 47 LEU cc_start: 0.8478 (tp) cc_final: 0.7864 (pt) REVERT: B 148 LYS cc_start: 0.7982 (mttm) cc_final: 0.7365 (mttt) REVERT: B 895 ASP cc_start: 0.7983 (m-30) cc_final: 0.7758 (m-30) REVERT: B 912 MET cc_start: 0.8440 (tpt) cc_final: 0.8209 (tpt) REVERT: B 986 GLN cc_start: 0.7914 (tp40) cc_final: 0.7569 (tm-30) REVERT: B 1111 LYS cc_start: 0.8930 (mtpp) cc_final: 0.8327 (mptp) REVERT: B 1216 GLU cc_start: 0.6063 (pm20) cc_final: 0.5679 (pm20) REVERT: C 33 GLU cc_start: 0.7602 (pt0) cc_final: 0.7350 (pm20) REVERT: C 246 ASN cc_start: 0.8440 (m-40) cc_final: 0.8143 (m110) REVERT: C 393 MET cc_start: 0.8903 (ttm) cc_final: 0.8565 (ttp) REVERT: C 407 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8911 (mt) REVERT: C 426 ASP cc_start: 0.8250 (t70) cc_final: 0.7926 (m-30) REVERT: C 730 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7617 (pm20) REVERT: C 761 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8840 (mp) REVERT: C 895 ASP cc_start: 0.7757 (m-30) cc_final: 0.7507 (m-30) REVERT: C 1016 GLN cc_start: 0.7686 (OUTLIER) cc_final: 0.7307 (tp40) REVERT: C 1209 ASP cc_start: 0.7543 (m-30) cc_final: 0.7270 (m-30) outliers start: 55 outliers final: 14 residues processed: 288 average time/residue: 0.5899 time to fit residues: 201.5498 Evaluate side-chains 224 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 205 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 552 GLN Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 1013 THR Chi-restraints excluded: chain B residue 1148 VAL Chi-restraints excluded: chain B residue 1224 LEU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 574 MET Chi-restraints excluded: chain C residue 672 THR Chi-restraints excluded: chain C residue 730 GLU Chi-restraints excluded: chain C residue 761 LEU Chi-restraints excluded: chain C residue 1016 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 180 optimal weight: 7.9990 chunk 281 optimal weight: 0.7980 chunk 262 optimal weight: 5.9990 chunk 272 optimal weight: 3.9990 chunk 279 optimal weight: 3.9990 chunk 306 optimal weight: 7.9990 chunk 314 optimal weight: 7.9990 chunk 198 optimal weight: 6.9990 chunk 156 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 333 optimal weight: 0.4980 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 GLN A 623 GLN A 724 ASN A 757 GLN ** A 865 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 993 GLN B 623 GLN ** B 865 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 632 GLN ** C 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.134868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.102978 restraints weight = 36196.412| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.20 r_work: 0.2883 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 28388 Z= 0.202 Angle : 0.662 11.773 38737 Z= 0.340 Chirality : 0.048 0.442 4437 Planarity : 0.005 0.136 4943 Dihedral : 7.630 114.054 4781 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.11 % Favored : 95.69 % Rotamer: Outliers : 2.18 % Allowed : 9.42 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.15 % 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: -0.52 (0.14), residues: 3480 helix: 0.25 (0.19), residues: 746 sheet: 0.32 (0.18), residues: 833 loop : -0.87 (0.13), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 49 TYR 0.030 0.002 TYR C 328 PHE 0.045 0.002 PHE A 756 TRP 0.018 0.002 TRP A 959 HIS 0.010 0.001 HIS B1137 Details of bonding type rmsd covalent geometry : bond 0.00486 (28292) covalent geometry : angle 0.64471 (38500) SS BOND : bond 0.00896 ( 50) SS BOND : angle 1.25740 ( 100) hydrogen bonds : bond 0.05178 ( 996) hydrogen bonds : angle 5.38789 ( 2640) link_BETA1-4 : bond 0.00696 ( 8) link_BETA1-4 : angle 2.94627 ( 24) link_BETA1-6 : bond 0.01911 ( 1) link_BETA1-6 : angle 1.16638 ( 3) link_NAG-ASN : bond 0.00397 ( 36) link_NAG-ASN : angle 2.34468 ( 108) link_NAG-THR : bond 0.01465 ( 1) link_NAG-THR : angle 1.42723 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 216 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8075 (tt0) cc_final: 0.7856 (pt0) REVERT: A 49 ARG cc_start: 0.7302 (ptm-80) cc_final: 0.6956 (ptm160) REVERT: A 67 ARG cc_start: 0.9346 (OUTLIER) cc_final: 0.7897 (ptm-80) REVERT: A 200 ARG cc_start: 0.7382 (mtp180) cc_final: 0.7129 (mtp180) REVERT: A 530 ILE cc_start: 0.9391 (tt) cc_final: 0.9107 (tt) REVERT: A 818 LYS cc_start: 0.8673 (mmtp) cc_final: 0.8217 (ttpp) REVERT: A 864 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7176 (tm) REVERT: A 1108 SER cc_start: 0.8892 (p) cc_final: 0.8653 (t) REVERT: B 47 LEU cc_start: 0.8500 (tp) cc_final: 0.7821 (pt) REVERT: B 48 MET cc_start: 0.7966 (pp-130) cc_final: 0.7746 (ppp) REVERT: B 148 LYS cc_start: 0.7770 (mttm) cc_final: 0.7336 (mttt) REVERT: B 730 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.7171 (pp20) REVERT: B 912 MET cc_start: 0.8551 (tpt) cc_final: 0.8282 (tpt) REVERT: B 921 ASP cc_start: 0.6803 (OUTLIER) cc_final: 0.5887 (p0) REVERT: B 986 GLN cc_start: 0.7943 (tp40) cc_final: 0.7569 (tm-30) REVERT: B 1111 LYS cc_start: 0.9054 (mtpp) cc_final: 0.8373 (mptp) REVERT: B 1216 GLU cc_start: 0.6045 (pm20) cc_final: 0.5677 (pm20) REVERT: C 33 GLU cc_start: 0.7754 (pt0) cc_final: 0.7458 (pm20) REVERT: C 91 LEU cc_start: 0.8786 (tp) cc_final: 0.8547 (tm) REVERT: C 214 GLU cc_start: 0.7061 (pt0) cc_final: 0.6531 (pm20) REVERT: C 393 MET cc_start: 0.8944 (ttm) cc_final: 0.8544 (ttp) REVERT: C 426 ASP cc_start: 0.8592 (t70) cc_final: 0.8180 (m-30) REVERT: C 761 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.8929 (mp) REVERT: C 895 ASP cc_start: 0.7895 (m-30) cc_final: 0.7642 (m-30) REVERT: C 987 GLN cc_start: 0.8057 (tt0) cc_final: 0.7438 (tp40) REVERT: C 1111 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8491 (mttm) REVERT: C 1209 ASP cc_start: 0.7625 (m-30) cc_final: 0.7396 (t0) outliers start: 65 outliers final: 25 residues processed: 262 average time/residue: 0.5740 time to fit residues: 179.3168 Evaluate side-chains 236 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 205 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ARG Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 552 GLN Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain A residue 1148 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 730 GLU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 921 ASP Chi-restraints excluded: chain B residue 1013 THR Chi-restraints excluded: chain B residue 1224 LEU Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 574 MET Chi-restraints excluded: chain C residue 610 ASP Chi-restraints excluded: chain C residue 672 THR Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 761 LEU Chi-restraints excluded: chain C residue 770 THR Chi-restraints excluded: chain C residue 1093 ARG Chi-restraints excluded: chain C residue 1111 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 43 optimal weight: 0.0070 chunk 254 optimal weight: 8.9990 chunk 255 optimal weight: 0.9980 chunk 204 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 290 optimal weight: 2.9990 chunk 307 optimal weight: 3.9990 chunk 279 optimal weight: 0.9990 chunk 236 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 overall best weight: 1.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 ASN A 623 GLN A 686 HIS A 724 ASN A 993 GLN B 865 ASN ** B1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 632 GLN ** C 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.135879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.103713 restraints weight = 36214.440| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.24 r_work: 0.2911 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 28388 Z= 0.128 Angle : 0.590 12.174 38737 Z= 0.301 Chirality : 0.045 0.406 4437 Planarity : 0.005 0.132 4943 Dihedral : 7.167 105.001 4781 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.79 % Favored : 96.03 % Rotamer: Outliers : 1.78 % Allowed : 10.83 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.09 % 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: -0.36 (0.14), residues: 3480 helix: 0.57 (0.19), residues: 734 sheet: 0.41 (0.18), residues: 817 loop : -0.83 (0.13), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 200 TYR 0.013 0.001 TYR A 927 PHE 0.025 0.001 PHE A 756 TRP 0.014 0.001 TRP A 959 HIS 0.004 0.001 HIS B1137 Details of bonding type rmsd covalent geometry : bond 0.00296 (28292) covalent geometry : angle 0.57228 (38500) SS BOND : bond 0.00552 ( 50) SS BOND : angle 1.36009 ( 100) hydrogen bonds : bond 0.04101 ( 996) hydrogen bonds : angle 5.13560 ( 2640) link_BETA1-4 : bond 0.00797 ( 8) link_BETA1-4 : angle 2.84991 ( 24) link_BETA1-6 : bond 0.01642 ( 1) link_BETA1-6 : angle 1.16703 ( 3) link_NAG-ASN : bond 0.00366 ( 36) link_NAG-ASN : angle 2.16741 ( 108) link_NAG-THR : bond 0.01092 ( 1) link_NAG-THR : angle 1.23388 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 228 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7725 (pm20) cc_final: 0.7365 (pm20) REVERT: A 38 GLN cc_start: 0.8268 (tt0) cc_final: 0.8052 (pt0) REVERT: A 49 ARG cc_start: 0.7293 (ptm-80) cc_final: 0.6985 (ptm160) REVERT: A 180 ASP cc_start: 0.8141 (OUTLIER) cc_final: 0.7737 (m-30) REVERT: A 246 ASN cc_start: 0.8486 (m-40) cc_final: 0.8276 (m110) REVERT: A 530 ILE cc_start: 0.9378 (tt) cc_final: 0.9077 (tt) REVERT: A 545 VAL cc_start: 0.8699 (p) cc_final: 0.8419 (t) REVERT: A 818 LYS cc_start: 0.8644 (mmtp) cc_final: 0.8242 (ttpp) REVERT: A 942 MET cc_start: 0.9365 (OUTLIER) cc_final: 0.9077 (ttt) REVERT: A 1089 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8201 (mm-30) REVERT: A 1108 SER cc_start: 0.8901 (p) cc_final: 0.8677 (t) REVERT: B 47 LEU cc_start: 0.8475 (tp) cc_final: 0.7818 (pt) REVERT: B 148 LYS cc_start: 0.7816 (mttm) cc_final: 0.7384 (mttt) REVERT: B 690 MET cc_start: 0.6119 (tmm) cc_final: 0.5846 (ttp) REVERT: B 792 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8280 (tt0) REVERT: B 921 ASP cc_start: 0.6963 (OUTLIER) cc_final: 0.6568 (p0) REVERT: B 986 GLN cc_start: 0.7966 (tp40) cc_final: 0.7620 (tm-30) REVERT: B 1111 LYS cc_start: 0.9063 (mtpp) cc_final: 0.8456 (mptp) REVERT: B 1216 GLU cc_start: 0.6007 (pm20) cc_final: 0.5670 (pm20) REVERT: C 47 LEU cc_start: 0.7279 (OUTLIER) cc_final: 0.6841 (mm) REVERT: C 246 ASN cc_start: 0.8517 (m-40) cc_final: 0.8222 (m110) REVERT: C 393 MET cc_start: 0.8890 (ttm) cc_final: 0.8485 (ttp) REVERT: C 426 ASP cc_start: 0.8450 (t70) cc_final: 0.8048 (m-30) REVERT: C 761 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8903 (mp) REVERT: C 818 LYS cc_start: 0.8664 (ttpp) cc_final: 0.8368 (ttpp) REVERT: C 895 ASP cc_start: 0.7934 (m-30) cc_final: 0.7681 (m-30) REVERT: C 987 GLN cc_start: 0.8067 (tt0) cc_final: 0.7587 (tp40) outliers start: 53 outliers final: 22 residues processed: 264 average time/residue: 0.5627 time to fit residues: 177.5414 Evaluate side-chains 228 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 200 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 552 GLN Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 942 MET Chi-restraints excluded: chain A residue 1148 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain B residue 843 GLU Chi-restraints excluded: chain B residue 875 VAL Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 921 ASP Chi-restraints excluded: chain B residue 1013 THR Chi-restraints excluded: chain B residue 1224 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 574 MET Chi-restraints excluded: chain C residue 672 THR Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 761 LEU Chi-restraints excluded: chain C residue 1093 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 149 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 341 optimal weight: 0.9990 chunk 173 optimal weight: 7.9990 chunk 250 optimal weight: 2.9990 chunk 201 optimal weight: 0.6980 chunk 2 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 279 optimal weight: 0.6980 chunk 86 optimal weight: 0.0670 chunk 215 optimal weight: 4.9990 overall best weight: 0.8922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 623 GLN A1008 GLN A1159 ASN B 623 GLN ** B1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 632 GLN C 686 HIS ** C 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.137426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.105682 restraints weight = 35970.312| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.16 r_work: 0.2973 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 28388 Z= 0.113 Angle : 0.564 9.699 38737 Z= 0.288 Chirality : 0.044 0.379 4437 Planarity : 0.004 0.128 4943 Dihedral : 6.840 99.234 4781 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.88 % Favored : 95.95 % Rotamer: Outliers : 2.04 % Allowed : 11.03 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.14), residues: 3480 helix: 0.74 (0.19), residues: 748 sheet: 0.37 (0.18), residues: 835 loop : -0.76 (0.13), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 49 TYR 0.011 0.001 TYR C1140 PHE 0.021 0.001 PHE A 756 TRP 0.010 0.001 TRP A 959 HIS 0.004 0.001 HIS B1137 Details of bonding type rmsd covalent geometry : bond 0.00262 (28292) covalent geometry : angle 0.54722 (38500) SS BOND : bond 0.00491 ( 50) SS BOND : angle 1.26765 ( 100) hydrogen bonds : bond 0.03753 ( 996) hydrogen bonds : angle 4.93768 ( 2640) link_BETA1-4 : bond 0.00812 ( 8) link_BETA1-4 : angle 2.82579 ( 24) link_BETA1-6 : bond 0.01332 ( 1) link_BETA1-6 : angle 0.95702 ( 3) link_NAG-ASN : bond 0.00336 ( 36) link_NAG-ASN : angle 2.02442 ( 108) link_NAG-THR : bond 0.01739 ( 1) link_NAG-THR : angle 1.67313 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 217 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7678 (pm20) cc_final: 0.7345 (pm20) REVERT: A 38 GLN cc_start: 0.8226 (tt0) cc_final: 0.7960 (pt0) REVERT: A 246 ASN cc_start: 0.8461 (m-40) cc_final: 0.8260 (m110) REVERT: A 322 LYS cc_start: 0.9046 (mtpt) cc_final: 0.8742 (mmtm) REVERT: A 530 ILE cc_start: 0.9356 (tt) cc_final: 0.9050 (tt) REVERT: A 545 VAL cc_start: 0.8654 (p) cc_final: 0.8389 (t) REVERT: A 632 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8488 (pt0) REVERT: A 818 LYS cc_start: 0.8564 (mmtp) cc_final: 0.8124 (ttpp) REVERT: A 920 ARG cc_start: 0.6291 (OUTLIER) cc_final: 0.4559 (tpm170) REVERT: A 1108 SER cc_start: 0.8881 (p) cc_final: 0.8664 (t) REVERT: B 47 LEU cc_start: 0.8496 (tp) cc_final: 0.7844 (pt) REVERT: B 148 LYS cc_start: 0.7808 (mttm) cc_final: 0.7436 (mttp) REVERT: B 690 MET cc_start: 0.6084 (tmm) cc_final: 0.5853 (ttp) REVERT: B 792 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8235 (tt0) REVERT: B 921 ASP cc_start: 0.6867 (OUTLIER) cc_final: 0.6104 (p0) REVERT: B 986 GLN cc_start: 0.7860 (tp40) cc_final: 0.7584 (tm-30) REVERT: B 1089 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8369 (mm-30) REVERT: B 1111 LYS cc_start: 0.9049 (mtpp) cc_final: 0.8444 (mptp) REVERT: B 1158 ASN cc_start: 0.7851 (t0) cc_final: 0.7528 (t0) REVERT: B 1216 GLU cc_start: 0.5989 (pm20) cc_final: 0.5664 (pm20) REVERT: C 180 ASP cc_start: 0.7815 (OUTLIER) cc_final: 0.7589 (m-30) REVERT: C 246 ASN cc_start: 0.8439 (m-40) cc_final: 0.8153 (m110) REVERT: C 393 MET cc_start: 0.8846 (ttm) cc_final: 0.8425 (ttp) REVERT: C 426 ASP cc_start: 0.8387 (t70) cc_final: 0.7997 (m-30) REVERT: C 552 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.8070 (tm-30) REVERT: C 761 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8995 (tp) REVERT: C 818 LYS cc_start: 0.8619 (ttpp) cc_final: 0.8293 (ttpp) REVERT: C 895 ASP cc_start: 0.7905 (m-30) cc_final: 0.7651 (m-30) REVERT: C 987 GLN cc_start: 0.7952 (tt0) cc_final: 0.7543 (tp40) outliers start: 61 outliers final: 28 residues processed: 261 average time/residue: 0.5438 time to fit residues: 171.2313 Evaluate side-chains 237 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 202 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 552 GLN Chi-restraints excluded: chain A residue 632 GLN Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain A residue 920 ARG Chi-restraints excluded: chain A residue 1148 VAL Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 843 GLU Chi-restraints excluded: chain B residue 875 VAL Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 921 ASP Chi-restraints excluded: chain B residue 985 THR Chi-restraints excluded: chain B residue 1013 THR Chi-restraints excluded: chain B residue 1224 LEU Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 552 GLN Chi-restraints excluded: chain C residue 574 MET Chi-restraints excluded: chain C residue 672 THR Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 761 LEU Chi-restraints excluded: chain C residue 770 THR Chi-restraints excluded: chain C residue 1093 ARG Chi-restraints excluded: chain C residue 1148 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 344 optimal weight: 10.0000 chunk 258 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 249 optimal weight: 0.7980 chunk 160 optimal weight: 3.9990 chunk 291 optimal weight: 9.9990 chunk 330 optimal weight: 7.9990 chunk 198 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 43 optimal weight: 0.0770 chunk 13 optimal weight: 7.9990 overall best weight: 1.5542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 623 GLN A1008 GLN B 221 ASN ** B1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 632 GLN ** C 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.134946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.102748 restraints weight = 36217.591| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.24 r_work: 0.2903 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 28388 Z= 0.149 Angle : 0.590 9.874 38737 Z= 0.301 Chirality : 0.045 0.390 4437 Planarity : 0.004 0.125 4943 Dihedral : 6.785 95.866 4781 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.85 % Favored : 95.98 % Rotamer: Outliers : 2.04 % Allowed : 11.73 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.14), residues: 3480 helix: 0.78 (0.20), residues: 739 sheet: 0.33 (0.18), residues: 853 loop : -0.74 (0.13), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 200 TYR 0.014 0.001 TYR C 474 PHE 0.024 0.001 PHE A 756 TRP 0.013 0.001 TRP A 959 HIS 0.006 0.001 HIS B1137 Details of bonding type rmsd covalent geometry : bond 0.00355 (28292) covalent geometry : angle 0.57234 (38500) SS BOND : bond 0.00593 ( 50) SS BOND : angle 1.28822 ( 100) hydrogen bonds : bond 0.04134 ( 996) hydrogen bonds : angle 4.96295 ( 2640) link_BETA1-4 : bond 0.00788 ( 8) link_BETA1-4 : angle 2.88591 ( 24) link_BETA1-6 : bond 0.01174 ( 1) link_BETA1-6 : angle 0.95847 ( 3) link_NAG-ASN : bond 0.00323 ( 36) link_NAG-ASN : angle 2.12529 ( 108) link_NAG-THR : bond 0.01657 ( 1) link_NAG-THR : angle 1.42176 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 210 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7708 (pm20) cc_final: 0.7345 (pm20) REVERT: A 49 ARG cc_start: 0.7228 (ptm-80) cc_final: 0.6961 (ptm160) REVERT: A 120 ASP cc_start: 0.7541 (OUTLIER) cc_final: 0.7210 (m-30) REVERT: A 530 ILE cc_start: 0.9355 (tt) cc_final: 0.9073 (tt) REVERT: A 545 VAL cc_start: 0.8684 (p) cc_final: 0.8417 (t) REVERT: A 632 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8635 (pt0) REVERT: A 818 LYS cc_start: 0.8576 (mmtp) cc_final: 0.8128 (ttpp) REVERT: A 920 ARG cc_start: 0.6370 (OUTLIER) cc_final: 0.4566 (tpm170) REVERT: A 942 MET cc_start: 0.9350 (OUTLIER) cc_final: 0.9059 (ttt) REVERT: A 1108 SER cc_start: 0.8894 (p) cc_final: 0.8669 (t) REVERT: B 47 LEU cc_start: 0.8438 (tp) cc_final: 0.7710 (pt) REVERT: B 148 LYS cc_start: 0.7816 (mttm) cc_final: 0.7442 (mttp) REVERT: B 690 MET cc_start: 0.6176 (tmm) cc_final: 0.5916 (ttp) REVERT: B 921 ASP cc_start: 0.6842 (OUTLIER) cc_final: 0.6055 (p0) REVERT: B 1089 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8350 (mm-30) REVERT: B 1111 LYS cc_start: 0.9060 (mtpp) cc_final: 0.8595 (mmpt) REVERT: B 1158 ASN cc_start: 0.7866 (t0) cc_final: 0.7530 (t0) REVERT: B 1216 GLU cc_start: 0.5985 (pm20) cc_final: 0.5681 (pm20) REVERT: C 246 ASN cc_start: 0.8488 (m-40) cc_final: 0.8167 (m110) REVERT: C 393 MET cc_start: 0.8930 (ttm) cc_final: 0.8511 (ttp) REVERT: C 426 ASP cc_start: 0.8487 (t70) cc_final: 0.8067 (m-30) REVERT: C 552 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.8089 (tm-30) REVERT: C 761 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8981 (tp) REVERT: C 895 ASP cc_start: 0.7932 (m-30) cc_final: 0.7684 (m-30) REVERT: C 987 GLN cc_start: 0.8063 (tt0) cc_final: 0.7618 (tp40) REVERT: C 1111 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8452 (mttm) outliers start: 61 outliers final: 32 residues processed: 253 average time/residue: 0.5586 time to fit residues: 169.7099 Evaluate side-chains 242 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 202 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 552 GLN Chi-restraints excluded: chain A residue 632 GLN Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain A residue 920 ARG Chi-restraints excluded: chain A residue 942 MET Chi-restraints excluded: chain A residue 1148 VAL Chi-restraints excluded: chain B residue 51 TYR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 843 GLU Chi-restraints excluded: chain B residue 875 VAL Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 921 ASP Chi-restraints excluded: chain B residue 985 THR Chi-restraints excluded: chain B residue 1013 THR Chi-restraints excluded: chain B residue 1224 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 552 GLN Chi-restraints excluded: chain C residue 574 MET Chi-restraints excluded: chain C residue 672 THR Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 761 LEU Chi-restraints excluded: chain C residue 770 THR Chi-restraints excluded: chain C residue 1093 ARG Chi-restraints excluded: chain C residue 1111 LYS Chi-restraints excluded: chain C residue 1148 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 131 optimal weight: 0.9990 chunk 160 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 227 optimal weight: 0.9990 chunk 166 optimal weight: 5.9990 chunk 284 optimal weight: 0.2980 overall best weight: 0.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 ASN A 623 GLN B 623 GLN B1131 ASN C 632 GLN ** C 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.136496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.104369 restraints weight = 36136.767| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.18 r_work: 0.2939 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.092 28388 Z= 0.109 Angle : 0.561 11.882 38737 Z= 0.285 Chirality : 0.044 0.370 4437 Planarity : 0.004 0.123 4943 Dihedral : 6.648 93.560 4781 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.62 % Favored : 96.21 % Rotamer: Outliers : 1.91 % Allowed : 12.40 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.14), residues: 3480 helix: 0.85 (0.20), residues: 749 sheet: 0.47 (0.18), residues: 837 loop : -0.71 (0.13), residues: 1894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 49 TYR 0.012 0.001 TYR C1140 PHE 0.017 0.001 PHE A 756 TRP 0.010 0.001 TRP A 959 HIS 0.004 0.001 HIS C 675 Details of bonding type rmsd covalent geometry : bond 0.00247 (28292) covalent geometry : angle 0.54587 (38500) SS BOND : bond 0.00629 ( 50) SS BOND : angle 0.99588 ( 100) hydrogen bonds : bond 0.03668 ( 996) hydrogen bonds : angle 4.82686 ( 2640) link_BETA1-4 : bond 0.00813 ( 8) link_BETA1-4 : angle 2.78402 ( 24) link_BETA1-6 : bond 0.01101 ( 1) link_BETA1-6 : angle 0.89776 ( 3) link_NAG-ASN : bond 0.00334 ( 36) link_NAG-ASN : angle 2.00752 ( 108) link_NAG-THR : bond 0.01179 ( 1) link_NAG-THR : angle 1.09067 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 213 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7425 (pm20) cc_final: 0.7137 (pm20) REVERT: A 49 ARG cc_start: 0.7182 (ptm-80) cc_final: 0.6858 (ptp-170) REVERT: A 120 ASP cc_start: 0.7437 (OUTLIER) cc_final: 0.7061 (m-30) REVERT: A 393 MET cc_start: 0.9123 (ttm) cc_final: 0.8901 (mtm) REVERT: A 530 ILE cc_start: 0.9354 (tt) cc_final: 0.9051 (tt) REVERT: A 545 VAL cc_start: 0.8632 (p) cc_final: 0.8402 (t) REVERT: A 632 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.8568 (pt0) REVERT: A 818 LYS cc_start: 0.8517 (mmtp) cc_final: 0.8026 (ttpp) REVERT: A 920 ARG cc_start: 0.6341 (OUTLIER) cc_final: 0.4553 (tpm170) REVERT: A 942 MET cc_start: 0.9340 (OUTLIER) cc_final: 0.9044 (ttt) REVERT: A 1108 SER cc_start: 0.8843 (p) cc_final: 0.8625 (t) REVERT: B 47 LEU cc_start: 0.8470 (tp) cc_final: 0.7799 (pt) REVERT: B 148 LYS cc_start: 0.7827 (mttm) cc_final: 0.7457 (mttp) REVERT: B 623 GLN cc_start: 0.6932 (OUTLIER) cc_final: 0.6697 (mm110) REVERT: B 690 MET cc_start: 0.6131 (tmm) cc_final: 0.5888 (ttp) REVERT: B 1111 LYS cc_start: 0.9041 (mtpp) cc_final: 0.8446 (mptp) REVERT: B 1158 ASN cc_start: 0.7865 (t0) cc_final: 0.7483 (t0) REVERT: B 1216 GLU cc_start: 0.5928 (pm20) cc_final: 0.5666 (pm20) REVERT: C 148 LYS cc_start: 0.8056 (mttt) cc_final: 0.7831 (mttt) REVERT: C 180 ASP cc_start: 0.7835 (OUTLIER) cc_final: 0.7625 (m-30) REVERT: C 393 MET cc_start: 0.8861 (ttm) cc_final: 0.8455 (ttp) REVERT: C 407 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8956 (mt) REVERT: C 426 ASP cc_start: 0.8384 (t70) cc_final: 0.8033 (m-30) REVERT: C 690 MET cc_start: 0.5378 (tmm) cc_final: 0.5163 (mmt) REVERT: C 761 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8993 (tp) REVERT: C 895 ASP cc_start: 0.7895 (m-30) cc_final: 0.7641 (m-30) REVERT: C 987 GLN cc_start: 0.7977 (tt0) cc_final: 0.7532 (tp40) outliers start: 57 outliers final: 34 residues processed: 253 average time/residue: 0.5409 time to fit residues: 164.9702 Evaluate side-chains 235 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 193 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 632 GLN Chi-restraints excluded: chain A residue 665 SER Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain A residue 920 ARG Chi-restraints excluded: chain A residue 942 MET Chi-restraints excluded: chain A residue 1148 VAL Chi-restraints excluded: chain B residue 51 TYR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 623 GLN Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 843 GLU Chi-restraints excluded: chain B residue 875 VAL Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 985 THR Chi-restraints excluded: chain B residue 1013 THR Chi-restraints excluded: chain B residue 1148 VAL Chi-restraints excluded: chain B residue 1224 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 574 MET Chi-restraints excluded: chain C residue 672 THR Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 761 LEU Chi-restraints excluded: chain C residue 770 THR Chi-restraints excluded: chain C residue 1093 ARG Chi-restraints excluded: chain C residue 1148 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 143 optimal weight: 3.9990 chunk 279 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 290 optimal weight: 0.7980 chunk 175 optimal weight: 7.9990 chunk 284 optimal weight: 2.9990 chunk 259 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 285 optimal weight: 5.9990 chunk 314 optimal weight: 4.9990 chunk 240 optimal weight: 5.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 ASN C 167 GLN C 632 GLN C 906 GLN ** C 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.133846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.102084 restraints weight = 35979.347| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.17 r_work: 0.2895 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 28388 Z= 0.213 Angle : 0.646 11.200 38737 Z= 0.329 Chirality : 0.047 0.391 4437 Planarity : 0.005 0.121 4943 Dihedral : 6.777 90.712 4781 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.45 % Favored : 95.43 % Rotamer: Outliers : 2.01 % Allowed : 12.84 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.09 % 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: -0.26 (0.14), residues: 3480 helix: 0.73 (0.20), residues: 735 sheet: 0.41 (0.18), residues: 835 loop : -0.79 (0.13), residues: 1910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 67 TYR 0.021 0.002 TYR B 474 PHE 0.031 0.002 PHE B 622 TRP 0.016 0.001 TRP A 959 HIS 0.008 0.001 HIS B1137 Details of bonding type rmsd covalent geometry : bond 0.00517 (28292) covalent geometry : angle 0.62906 (38500) SS BOND : bond 0.00768 ( 50) SS BOND : angle 1.31844 ( 100) hydrogen bonds : bond 0.04692 ( 996) hydrogen bonds : angle 5.08061 ( 2640) link_BETA1-4 : bond 0.00766 ( 8) link_BETA1-4 : angle 2.98980 ( 24) link_BETA1-6 : bond 0.00761 ( 1) link_BETA1-6 : angle 0.99172 ( 3) link_NAG-ASN : bond 0.00352 ( 36) link_NAG-ASN : angle 2.18825 ( 108) link_NAG-THR : bond 0.01669 ( 1) link_NAG-THR : angle 1.37886 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 194 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ARG cc_start: 0.7196 (ptm-80) cc_final: 0.6861 (ptp-170) REVERT: A 120 ASP cc_start: 0.7426 (OUTLIER) cc_final: 0.7143 (m-30) REVERT: A 246 ASN cc_start: 0.8644 (m-40) cc_final: 0.8443 (m110) REVERT: A 530 ILE cc_start: 0.9382 (tt) cc_final: 0.9057 (tt) REVERT: A 545 VAL cc_start: 0.8704 (p) cc_final: 0.8440 (t) REVERT: A 818 LYS cc_start: 0.8676 (mmtp) cc_final: 0.8265 (ttpp) REVERT: A 920 ARG cc_start: 0.6325 (OUTLIER) cc_final: 0.4499 (tpm170) REVERT: A 942 MET cc_start: 0.9356 (OUTLIER) cc_final: 0.9074 (ttt) REVERT: B 47 LEU cc_start: 0.8450 (tp) cc_final: 0.7828 (pt) REVERT: B 148 LYS cc_start: 0.7895 (mttm) cc_final: 0.7522 (mttp) REVERT: B 690 MET cc_start: 0.6244 (tmm) cc_final: 0.5929 (ttp) REVERT: B 921 ASP cc_start: 0.6861 (OUTLIER) cc_final: 0.6521 (p0) REVERT: B 1111 LYS cc_start: 0.9058 (mtpp) cc_final: 0.8631 (mmpt) REVERT: B 1158 ASN cc_start: 0.7887 (t0) cc_final: 0.7402 (t0) REVERT: B 1216 GLU cc_start: 0.5899 (pm20) cc_final: 0.5652 (pm20) REVERT: C 148 LYS cc_start: 0.8124 (mttt) cc_final: 0.7896 (mttt) REVERT: C 246 ASN cc_start: 0.8606 (m-40) cc_final: 0.8270 (m110) REVERT: C 393 MET cc_start: 0.8936 (ttm) cc_final: 0.8484 (ttp) REVERT: C 426 ASP cc_start: 0.8575 (t70) cc_final: 0.8177 (m-30) REVERT: C 690 MET cc_start: 0.5366 (tmm) cc_final: 0.4128 (ttm) REVERT: C 761 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.8963 (mp) REVERT: C 895 ASP cc_start: 0.7910 (m-30) cc_final: 0.7674 (m-30) REVERT: C 987 GLN cc_start: 0.8038 (tt0) cc_final: 0.7631 (tp40) REVERT: C 1111 LYS cc_start: 0.8960 (OUTLIER) cc_final: 0.8462 (mttm) outliers start: 60 outliers final: 36 residues processed: 239 average time/residue: 0.5612 time to fit residues: 161.5911 Evaluate side-chains 231 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 189 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 665 SER Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain A residue 920 ARG Chi-restraints excluded: chain A residue 942 MET Chi-restraints excluded: chain A residue 1148 VAL Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain B residue 51 TYR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 843 GLU Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 875 VAL Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 921 ASP Chi-restraints excluded: chain B residue 985 THR Chi-restraints excluded: chain B residue 1013 THR Chi-restraints excluded: chain B residue 1148 VAL Chi-restraints excluded: chain B residue 1224 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 574 MET Chi-restraints excluded: chain C residue 672 THR Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 761 LEU Chi-restraints excluded: chain C residue 770 THR Chi-restraints excluded: chain C residue 1093 ARG Chi-restraints excluded: chain C residue 1111 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 309 optimal weight: 2.9990 chunk 317 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 chunk 133 optimal weight: 6.9990 chunk 173 optimal weight: 1.9990 chunk 296 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 302 optimal weight: 3.9990 chunk 260 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 623 GLN C 632 GLN ** C 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.134712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.102791 restraints weight = 36189.997| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.24 r_work: 0.2958 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 28388 Z= 0.135 Angle : 0.597 14.997 38737 Z= 0.303 Chirality : 0.045 0.374 4437 Planarity : 0.004 0.120 4943 Dihedral : 6.617 89.171 4781 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.97 % Favored : 95.95 % Rotamer: Outliers : 1.64 % Allowed : 13.38 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.09 % 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: -0.20 (0.14), residues: 3480 helix: 0.79 (0.20), residues: 739 sheet: 0.44 (0.18), residues: 841 loop : -0.75 (0.13), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 200 TYR 0.012 0.001 TYR C1140 PHE 0.018 0.001 PHE C 756 TRP 0.015 0.001 TRP A 959 HIS 0.005 0.001 HIS B1137 Details of bonding type rmsd covalent geometry : bond 0.00318 (28292) covalent geometry : angle 0.57934 (38500) SS BOND : bond 0.00628 ( 50) SS BOND : angle 1.53350 ( 100) hydrogen bonds : bond 0.04020 ( 996) hydrogen bonds : angle 4.95104 ( 2640) link_BETA1-4 : bond 0.00783 ( 8) link_BETA1-4 : angle 2.84897 ( 24) link_BETA1-6 : bond 0.00948 ( 1) link_BETA1-6 : angle 0.91381 ( 3) link_NAG-ASN : bond 0.00324 ( 36) link_NAG-ASN : angle 2.08758 ( 108) link_NAG-THR : bond 0.01351 ( 1) link_NAG-THR : angle 1.34838 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 195 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ARG cc_start: 0.7168 (ptm-80) cc_final: 0.6872 (ptp-170) REVERT: A 120 ASP cc_start: 0.7378 (OUTLIER) cc_final: 0.7061 (m-30) REVERT: A 246 ASN cc_start: 0.8620 (m-40) cc_final: 0.8410 (m110) REVERT: A 530 ILE cc_start: 0.9372 (tt) cc_final: 0.9049 (tt) REVERT: A 545 VAL cc_start: 0.8682 (p) cc_final: 0.8430 (t) REVERT: A 818 LYS cc_start: 0.8689 (mmtp) cc_final: 0.8250 (ttpp) REVERT: A 920 ARG cc_start: 0.6288 (OUTLIER) cc_final: 0.4488 (tpm170) REVERT: A 942 MET cc_start: 0.9347 (OUTLIER) cc_final: 0.9065 (ttt) REVERT: A 1108 SER cc_start: 0.8861 (p) cc_final: 0.8638 (t) REVERT: B 47 LEU cc_start: 0.8445 (tp) cc_final: 0.7800 (pt) REVERT: B 148 LYS cc_start: 0.7881 (mttm) cc_final: 0.7491 (mttp) REVERT: B 690 MET cc_start: 0.6099 (tmm) cc_final: 0.5775 (ttp) REVERT: B 921 ASP cc_start: 0.6844 (OUTLIER) cc_final: 0.6155 (p0) REVERT: B 1111 LYS cc_start: 0.9056 (mtpp) cc_final: 0.8631 (mmpt) REVERT: B 1158 ASN cc_start: 0.7880 (t0) cc_final: 0.7373 (t0) REVERT: B 1216 GLU cc_start: 0.5910 (pm20) cc_final: 0.5709 (pm20) REVERT: C 393 MET cc_start: 0.8895 (ttm) cc_final: 0.8537 (ttp) REVERT: C 407 LEU cc_start: 0.9210 (mp) cc_final: 0.8961 (mt) REVERT: C 426 ASP cc_start: 0.8469 (t70) cc_final: 0.8057 (m-30) REVERT: C 690 MET cc_start: 0.5307 (tmm) cc_final: 0.4131 (ttm) REVERT: C 761 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.9022 (tp) REVERT: C 895 ASP cc_start: 0.7856 (m-30) cc_final: 0.7596 (m-30) REVERT: C 987 GLN cc_start: 0.8044 (tt0) cc_final: 0.7705 (mm-40) outliers start: 49 outliers final: 36 residues processed: 234 average time/residue: 0.5440 time to fit residues: 153.4979 Evaluate side-chains 231 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 190 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 665 SER Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain A residue 920 ARG Chi-restraints excluded: chain A residue 942 MET Chi-restraints excluded: chain A residue 1148 VAL Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain B residue 51 TYR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 843 GLU Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 875 VAL Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 921 ASP Chi-restraints excluded: chain B residue 985 THR Chi-restraints excluded: chain B residue 1013 THR Chi-restraints excluded: chain B residue 1148 VAL Chi-restraints excluded: chain B residue 1224 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 574 MET Chi-restraints excluded: chain C residue 672 THR Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 761 LEU Chi-restraints excluded: chain C residue 770 THR Chi-restraints excluded: chain C residue 1093 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 141 optimal weight: 1.9990 chunk 213 optimal weight: 0.0470 chunk 234 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 251 optimal weight: 3.9990 chunk 349 optimal weight: 10.0000 chunk 220 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 226 optimal weight: 4.9990 chunk 253 optimal weight: 5.9990 overall best weight: 1.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 632 GLN ** C 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.135526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.103935 restraints weight = 36021.014| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.21 r_work: 0.2931 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 28388 Z= 0.139 Angle : 0.589 13.487 38737 Z= 0.300 Chirality : 0.045 0.373 4437 Planarity : 0.004 0.118 4943 Dihedral : 6.491 86.096 4781 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.40 % Favored : 95.52 % Rotamer: Outliers : 1.58 % Allowed : 13.48 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.14), residues: 3480 helix: 0.86 (0.20), residues: 735 sheet: 0.47 (0.18), residues: 833 loop : -0.76 (0.13), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 196 TYR 0.012 0.001 TYR C 474 PHE 0.020 0.001 PHE C 756 TRP 0.014 0.001 TRP A 959 HIS 0.005 0.001 HIS B1137 Details of bonding type rmsd covalent geometry : bond 0.00329 (28292) covalent geometry : angle 0.57198 (38500) SS BOND : bond 0.00615 ( 50) SS BOND : angle 1.38150 ( 100) hydrogen bonds : bond 0.04002 ( 996) hydrogen bonds : angle 4.92525 ( 2640) link_BETA1-4 : bond 0.00792 ( 8) link_BETA1-4 : angle 2.85170 ( 24) link_BETA1-6 : bond 0.00875 ( 1) link_BETA1-6 : angle 0.94663 ( 3) link_NAG-ASN : bond 0.00315 ( 36) link_NAG-ASN : angle 2.08318 ( 108) link_NAG-THR : bond 0.01340 ( 1) link_NAG-THR : angle 1.27637 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 200 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ARG cc_start: 0.7125 (ptm-80) cc_final: 0.6834 (ptp-170) REVERT: A 120 ASP cc_start: 0.7366 (OUTLIER) cc_final: 0.7072 (m-30) REVERT: A 530 ILE cc_start: 0.9371 (tt) cc_final: 0.9072 (tt) REVERT: A 545 VAL cc_start: 0.8676 (p) cc_final: 0.8430 (t) REVERT: A 818 LYS cc_start: 0.8676 (mmtp) cc_final: 0.8242 (ttpp) REVERT: A 920 ARG cc_start: 0.6324 (OUTLIER) cc_final: 0.4580 (tpm170) REVERT: A 942 MET cc_start: 0.9347 (OUTLIER) cc_final: 0.9076 (ttt) REVERT: A 1108 SER cc_start: 0.8852 (p) cc_final: 0.8629 (t) REVERT: B 148 LYS cc_start: 0.7894 (mttm) cc_final: 0.7503 (mttp) REVERT: B 690 MET cc_start: 0.5977 (tmm) cc_final: 0.5643 (ttp) REVERT: B 792 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8275 (tt0) REVERT: B 1111 LYS cc_start: 0.9037 (mtpp) cc_final: 0.8612 (mmpt) REVERT: B 1158 ASN cc_start: 0.7861 (t0) cc_final: 0.7381 (t0) REVERT: C 91 LEU cc_start: 0.8910 (tp) cc_final: 0.8681 (tp) REVERT: C 393 MET cc_start: 0.8900 (ttm) cc_final: 0.8524 (ttp) REVERT: C 426 ASP cc_start: 0.8406 (t70) cc_final: 0.8003 (m-30) REVERT: C 690 MET cc_start: 0.5305 (tmm) cc_final: 0.4094 (ttm) REVERT: C 761 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.9027 (tp) REVERT: C 895 ASP cc_start: 0.7917 (m-30) cc_final: 0.7649 (m-30) REVERT: C 987 GLN cc_start: 0.8013 (tt0) cc_final: 0.7724 (mm-40) REVERT: C 1111 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8394 (mttm) outliers start: 47 outliers final: 35 residues processed: 236 average time/residue: 0.5567 time to fit residues: 158.6604 Evaluate side-chains 230 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 189 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 665 SER Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain A residue 920 ARG Chi-restraints excluded: chain A residue 942 MET Chi-restraints excluded: chain A residue 1148 VAL Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain B residue 51 TYR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 843 GLU Chi-restraints excluded: chain B residue 875 VAL Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 985 THR Chi-restraints excluded: chain B residue 1013 THR Chi-restraints excluded: chain B residue 1148 VAL Chi-restraints excluded: chain B residue 1224 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 574 MET Chi-restraints excluded: chain C residue 672 THR Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 761 LEU Chi-restraints excluded: chain C residue 770 THR Chi-restraints excluded: chain C residue 1093 ARG Chi-restraints excluded: chain C residue 1111 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 98 optimal weight: 0.8980 chunk 319 optimal weight: 0.9980 chunk 220 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 339 optimal weight: 0.9980 chunk 315 optimal weight: 0.0970 chunk 96 optimal weight: 10.0000 chunk 58 optimal weight: 0.9980 chunk 272 optimal weight: 0.6980 chunk 221 optimal weight: 2.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 ASN A 623 GLN C 632 GLN ** C 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.137207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.105556 restraints weight = 35898.906| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.17 r_work: 0.2957 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.089 28388 Z= 0.104 Angle : 0.561 12.065 38737 Z= 0.284 Chirality : 0.044 0.361 4437 Planarity : 0.004 0.117 4943 Dihedral : 6.323 83.791 4781 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.79 % Favored : 96.12 % Rotamer: Outliers : 1.51 % Allowed : 13.74 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.14), residues: 3480 helix: 0.91 (0.20), residues: 747 sheet: 0.49 (0.18), residues: 839 loop : -0.72 (0.14), residues: 1894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 49 TYR 0.011 0.001 TYR C1140 PHE 0.016 0.001 PHE B 119 TRP 0.010 0.001 TRP A 959 HIS 0.003 0.001 HIS C 675 Details of bonding type rmsd covalent geometry : bond 0.00237 (28292) covalent geometry : angle 0.54530 (38500) SS BOND : bond 0.00516 ( 50) SS BOND : angle 1.11646 ( 100) hydrogen bonds : bond 0.03542 ( 996) hydrogen bonds : angle 4.79156 ( 2640) link_BETA1-4 : bond 0.00723 ( 8) link_BETA1-4 : angle 2.75090 ( 24) link_BETA1-6 : bond 0.00886 ( 1) link_BETA1-6 : angle 0.85556 ( 3) link_NAG-ASN : bond 0.00332 ( 36) link_NAG-ASN : angle 1.99967 ( 108) link_NAG-THR : bond 0.01096 ( 1) link_NAG-THR : angle 1.10634 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8822.40 seconds wall clock time: 151 minutes 25.85 seconds (9085.85 seconds total)