Starting phenix.real_space_refine on Fri Mar 6 13:23:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bam_12124/03_2026/7bam_12124.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bam_12124/03_2026/7bam_12124.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7bam_12124/03_2026/7bam_12124.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bam_12124/03_2026/7bam_12124.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7bam_12124/03_2026/7bam_12124.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bam_12124/03_2026/7bam_12124.map" } resolution = 3.5 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= 0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 6 9.91 5 S 146 5.16 5 C 19270 2.51 5 N 5280 2.21 5 O 5910 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30612 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 15093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1904, 15093 Classifications: {'peptide': 1904} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 74, 'TRANS': 1829} Chain breaks: 4 Chain: "B" Number of atoms: 15093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1904, 15093 Classifications: {'peptide': 1904} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 74, 'TRANS': 1829} Chain breaks: 4 Chain: "C" 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: "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: 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: "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: 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: "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: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 101 Unusual residues: {' CA': 3, 'NAG': 7} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 101 Unusual residues: {' CA': 3, 'NAG': 7} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 5.49, per 1000 atoms: 0.18 Number of scatterers: 30612 At special positions: 0 Unit cell: (192.282, 169.454, 122.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 6 19.99 S 146 16.00 O 5910 8.00 N 5280 7.00 C 19270 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS A 838 " - pdb=" SG CYS A 857 " distance=2.04 Simple disulfide: pdb=" SG CYS A 852 " - pdb=" SG CYS A 863 " distance=2.04 Simple disulfide: pdb=" SG CYS A 858 " - pdb=" SG CYS A 869 " distance=2.04 Simple disulfide: pdb=" SG CYS A1011 " - pdb=" SG CYS A1145 " distance=2.02 Simple disulfide: pdb=" SG CYS A1035 " - pdb=" SG CYS A2524 " distance=2.03 Simple disulfide: pdb=" SG CYS A1217 " - pdb=" SG CYS A1220 " distance=2.03 Simple disulfide: pdb=" SG CYS A1237 " - pdb=" SG CYS A1545 " distance=2.03 Simple disulfide: pdb=" SG CYS A1328 " - pdb=" SG CYS A1336 " distance=2.03 Simple disulfide: pdb=" SG CYS A1395 " - pdb=" SG CYS A1448 " distance=2.03 Simple disulfide: pdb=" SG CYS A1513 " - pdb=" SG CYS A1521 " distance=2.03 Simple disulfide: pdb=" SG CYS A1515 " - pdb=" SG CYS A1523 " distance=2.04 Simple disulfide: pdb=" SG CYS B 838 " - pdb=" SG CYS B 857 " distance=2.04 Simple disulfide: pdb=" SG CYS B 852 " - pdb=" SG CYS B 863 " distance=2.04 Simple disulfide: pdb=" SG CYS B 858 " - pdb=" SG CYS B 869 " distance=2.04 Simple disulfide: pdb=" SG CYS B1011 " - pdb=" SG CYS B1145 " distance=2.02 Simple disulfide: pdb=" SG CYS B1035 " - pdb=" SG CYS B2524 " distance=2.03 Simple disulfide: pdb=" SG CYS B1217 " - pdb=" SG CYS B1220 " distance=2.03 Simple disulfide: pdb=" SG CYS B1237 " - pdb=" SG CYS B1545 " distance=2.03 Simple disulfide: pdb=" SG CYS B1328 " - pdb=" SG CYS B1336 " distance=2.03 Simple disulfide: pdb=" SG CYS B1395 " - pdb=" SG CYS B1448 " distance=2.03 Simple disulfide: pdb=" SG CYS B1513 " - pdb=" SG CYS B1521 " distance=2.03 Simple disulfide: pdb=" SG CYS B1515 " - pdb=" SG CYS B1523 " distance=2.04 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 C 1 " - " NAG C 2 " " 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 J 1 " - " NAG J 2 " NAG-ASN " NAG A2801 " - " ASN A1705 " " NAG A2802 " - " ASN A1799 " " NAG A2803 " - " ASN A1884 " " NAG A2804 " - " ASN A1259 " " NAG A2805 " - " ASN A1741 " " NAG A2806 " - " ASN A1985 " " NAG A2807 " - " ASN A2188 " " NAG B2801 " - " ASN B1705 " " NAG B2802 " - " ASN B1799 " " NAG B2803 " - " ASN B1884 " " NAG B2804 " - " ASN B1259 " " NAG B2805 " - " ASN B1741 " " NAG B2806 " - " ASN B1985 " " NAG B2807 " - " ASN B2188 " " NAG C 1 " - " ASN A1609 " " NAG D 1 " - " ASN A2328 " " NAG E 1 " - " ASN A2646 " " NAG F 1 " - " ASN A 940 " " NAG G 1 " - " ASN B1609 " " NAG H 1 " - " ASN B2328 " " NAG I 1 " - " ASN B2646 " " NAG J 1 " - " ASN B 940 " Time building additional restraints: 2.35 Conformation dependent library (CDL) restraints added in 1.2 seconds 7576 Ramachandran restraints generated. 3788 Oldfield, 0 Emsley, 3788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7016 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 44 sheets defined 10.2% alpha, 47.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.50 Creating SS restraints... Processing helix chain 'A' and resid 850 through 860 Proline residue: A 855 - end of helix removed outlier: 3.706A pdb=" N LEU A 859 " --> pdb=" O ASP A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 881 Processing helix chain 'A' and resid 895 through 902 removed outlier: 4.701A pdb=" N PHE A 900 " --> pdb=" O ARG A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 949 Processing helix chain 'A' and resid 1043 through 1046 Processing helix chain 'A' and resid 1197 through 1199 No H-bonds generated for 'chain 'A' and resid 1197 through 1199' Processing helix chain 'A' and resid 1271 through 1280 removed outlier: 4.310A pdb=" N HIS A1275 " --> pdb=" O ARG A1272 " (cutoff:3.500A) Proline residue: A1277 - end of helix Processing helix chain 'A' and resid 1402 through 1404 No H-bonds generated for 'chain 'A' and resid 1402 through 1404' Processing helix chain 'A' and resid 1530 through 1534 Processing helix chain 'A' and resid 2401 through 2405 Processing helix chain 'A' and resid 2434 through 2438 Processing helix chain 'A' and resid 2452 through 2456 Processing helix chain 'A' and resid 2464 through 2470 removed outlier: 3.771A pdb=" N MET A2468 " --> pdb=" O ILE A2464 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR A2469 " --> pdb=" O LYS A2465 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP A2470 " --> pdb=" O CYS A2466 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2464 through 2470' Processing helix chain 'A' and resid 2471 through 2479 Processing helix chain 'A' and resid 2481 through 2485 removed outlier: 3.542A pdb=" N VAL A2485 " --> pdb=" O LEU A2482 " (cutoff:3.500A) Processing helix chain 'A' and resid 2500 through 2506 Processing helix chain 'A' and resid 2506 through 2511 removed outlier: 4.059A pdb=" N GLN A2511 " --> pdb=" O GLN A2507 " (cutoff:3.500A) Processing helix chain 'A' and resid 2520 through 2533 removed outlier: 3.731A pdb=" N CYS A2524 " --> pdb=" O LEU A2520 " (cutoff:3.500A) Processing helix chain 'A' and resid 2539 through 2543 Processing helix chain 'A' and resid 2588 through 2599 removed outlier: 3.704A pdb=" N ARG A2592 " --> pdb=" O ASN A2588 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ARG A2593 " --> pdb=" O GLU A2589 " (cutoff:3.500A) Processing helix chain 'A' and resid 2625 through 2632 Processing helix chain 'A' and resid 2682 through 2712 removed outlier: 3.739A pdb=" N GLU A2712 " --> pdb=" O GLN A2708 " (cutoff:3.500A) Processing helix chain 'A' and resid 2721 through 2732 Processing helix chain 'A' and resid 2748 through 2752 Processing helix chain 'A' and resid 2754 through 2756 No H-bonds generated for 'chain 'A' and resid 2754 through 2756' Processing helix chain 'B' and resid 850 through 860 Proline residue: B 855 - end of helix removed outlier: 3.707A pdb=" N LEU B 859 " --> pdb=" O ASP B 856 " (cutoff:3.500A) Processing helix chain 'B' and resid 874 through 881 Processing helix chain 'B' and resid 895 through 902 removed outlier: 4.701A pdb=" N PHE B 900 " --> pdb=" O ARG B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 949 Processing helix chain 'B' and resid 1043 through 1046 Processing helix chain 'B' and resid 1197 through 1199 No H-bonds generated for 'chain 'B' and resid 1197 through 1199' Processing helix chain 'B' and resid 1271 through 1280 removed outlier: 4.310A pdb=" N HIS B1275 " --> pdb=" O ARG B1272 " (cutoff:3.500A) Proline residue: B1277 - end of helix Processing helix chain 'B' and resid 1402 through 1404 No H-bonds generated for 'chain 'B' and resid 1402 through 1404' Processing helix chain 'B' and resid 1530 through 1534 Processing helix chain 'B' and resid 2401 through 2405 Processing helix chain 'B' and resid 2434 through 2438 Processing helix chain 'B' and resid 2452 through 2456 Processing helix chain 'B' and resid 2464 through 2470 removed outlier: 3.772A pdb=" N MET B2468 " --> pdb=" O ILE B2464 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR B2469 " --> pdb=" O LYS B2465 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP B2470 " --> pdb=" O CYS B2466 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2464 through 2470' Processing helix chain 'B' and resid 2471 through 2479 Processing helix chain 'B' and resid 2481 through 2485 removed outlier: 3.542A pdb=" N VAL B2485 " --> pdb=" O LEU B2482 " (cutoff:3.500A) Processing helix chain 'B' and resid 2500 through 2506 Processing helix chain 'B' and resid 2506 through 2511 removed outlier: 4.059A pdb=" N GLN B2511 " --> pdb=" O GLN B2507 " (cutoff:3.500A) Processing helix chain 'B' and resid 2520 through 2533 removed outlier: 3.732A pdb=" N CYS B2524 " --> pdb=" O LEU B2520 " (cutoff:3.500A) Processing helix chain 'B' and resid 2539 through 2543 Processing helix chain 'B' and resid 2588 through 2599 removed outlier: 3.705A pdb=" N ARG B2592 " --> pdb=" O ASN B2588 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ARG B2593 " --> pdb=" O GLU B2589 " (cutoff:3.500A) Processing helix chain 'B' and resid 2625 through 2632 Processing helix chain 'B' and resid 2682 through 2712 removed outlier: 3.739A pdb=" N GLU B2712 " --> pdb=" O GLN B2708 " (cutoff:3.500A) Processing helix chain 'B' and resid 2721 through 2732 Processing helix chain 'B' and resid 2748 through 2752 Processing helix chain 'B' and resid 2754 through 2756 No H-bonds generated for 'chain 'B' and resid 2754 through 2756' Processing sheet with id=AA1, first strand: chain 'A' and resid 959 through 965 removed outlier: 8.423A pdb=" N PHE A 994 " --> pdb=" O ALA A 921 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VAL A 923 " --> pdb=" O PHE A 994 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 959 through 965 Processing sheet with id=AA3, first strand: chain 'A' and resid 951 through 953 removed outlier: 3.656A pdb=" N GLU A 975 " --> pdb=" O ASN A 940 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1022 through 1025 Processing sheet with id=AA5, first strand: chain 'A' and resid 1041 through 1042 Processing sheet with id=AA6, first strand: chain 'A' and resid 1100 through 1107 removed outlier: 3.520A pdb=" N LYS A1090 " --> pdb=" O GLU A1141 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR A1140 " --> pdb=" O LEU A1150 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A1150 " --> pdb=" O TYR A1140 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1178 through 1180 Processing sheet with id=AA8, first strand: chain 'A' and resid 1202 through 1203 removed outlier: 3.537A pdb=" N ARG A1559 " --> pdb=" O ASP A1554 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA A1553 " --> pdb=" O SER A1541 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N SER A1541 " --> pdb=" O ALA A1553 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1222 through 1223 removed outlier: 6.694A pdb=" N ILE A1251 " --> pdb=" O ILE A1263 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1283 through 1285 removed outlier: 4.206A pdb=" N VAL A1292 " --> pdb=" O ILE A1305 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A1294 " --> pdb=" O PHE A1303 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA A1322 " --> pdb=" O VAL A1302 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1350 through 1355 removed outlier: 4.975A pdb=" N GLY A1352 " --> pdb=" O VAL A1364 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1399 through 1400 removed outlier: 3.533A pdb=" N ARG A1439 " --> pdb=" O GLN A1431 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL A1441 " --> pdb=" O VAL A1429 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N VAL A1429 " --> pdb=" O VAL A1441 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER A1420 " --> pdb=" O ASN A1415 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASP A1411 " --> pdb=" O LEU A1424 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1470 through 1475 removed outlier: 5.528A pdb=" N ALA A1470 " --> pdb=" O THR A1486 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N THR A1486 " --> pdb=" O ALA A1470 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE A1494 " --> pdb=" O VAL A1506 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1569 through 1570 removed outlier: 4.260A pdb=" N PHE A1569 " --> pdb=" O GLU A1577 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N LEU A1596 " --> pdb=" O ASN A1609 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ASN A1609 " --> pdb=" O LEU A1596 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N THR A1598 " --> pdb=" O LEU A1607 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU A1607 " --> pdb=" O ASP A1623 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ASP A1623 " --> pdb=" O LEU A1607 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASN A1609 " --> pdb=" O ILE A1621 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ILE A1621 " --> pdb=" O ASN A1609 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR A1611 " --> pdb=" O THR A1619 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N THR A1619 " --> pdb=" O VAL A1631 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ASN A1630 " --> pdb=" O LEU A1642 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU A1642 " --> pdb=" O ASN A1630 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ARG A1632 " --> pdb=" O LEU A1640 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N LEU A1640 " --> pdb=" O VAL A1652 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A1652 " --> pdb=" O LEU A1640 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LYS A1661 " --> pdb=" O MET A1673 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA A1671 " --> pdb=" O VAL A1663 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N MET A1672 " --> pdb=" O LYS A1685 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LYS A1685 " --> pdb=" O MET A1672 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N THR A1674 " --> pdb=" O ALA A1683 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ALA A1683 " --> pdb=" O TYR A1695 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N PHE A1694 " --> pdb=" O VAL A1706 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VAL A1706 " --> pdb=" O PHE A1694 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLU A1696 " --> pdb=" O THR A1704 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N THR A1704 " --> pdb=" O PHE A1716 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL A1724 " --> pdb=" O THR A1740 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR A1740 " --> pdb=" O VAL A1724 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A1800 " --> pdb=" O ASN A1809 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL A1826 " --> pdb=" O GLU A1818 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL A1833 " --> pdb=" O ASN A1837 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ASN A1837 " --> pdb=" O VAL A1833 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N SER A1872 " --> pdb=" O VAL A1885 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN A1884 " --> pdb=" O ILE A1896 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ILE A1896 " --> pdb=" O ASN A1884 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N THR A1886 " --> pdb=" O ALA A1894 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ALA A1894 " --> pdb=" O MET A1905 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET A1905 " --> pdb=" O ALA A1894 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N SER A1902 " --> pdb=" O PHE A1918 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N PHE A1918 " --> pdb=" O SER A1902 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ARG A1904 " --> pdb=" O ARG A1916 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ARG A1916 " --> pdb=" O ARG A1904 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLU A1906 " --> pdb=" O THR A1914 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N THR A1914 " --> pdb=" O TYR A1926 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N SER A1954 " --> pdb=" O LEU A1966 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N HIS A2000 " --> pdb=" O ASP A1991 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N LEU A1999 " --> pdb=" O TYR A2012 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE A2011 " --> pdb=" O THR A2023 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N THR A2023 " --> pdb=" O ILE A2011 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LYS A2013 " --> pdb=" O ALA A2021 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ALA A2021 " --> pdb=" O PHE A2032 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS A2029 " --> pdb=" O GLN A2047 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N LYS A2042 " --> pdb=" O TYR A2057 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N THR A2052 " --> pdb=" O PHE A2071 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N PHE A2071 " --> pdb=" O THR A2052 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR A2054 " --> pdb=" O PHE A2069 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N PHE A2069 " --> pdb=" O THR A2054 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ARG A2056 " --> pdb=" O GLN A2067 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLN A2067 " --> pdb=" O ARG A2056 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ARG A2058 " --> pdb=" O ASP A2065 " (cutoff:3.500A) removed outlier: 10.634A pdb=" N LEU A2063 " --> pdb=" O TYR A2085 " (cutoff:3.500A) removed outlier: 8.933A pdb=" N TYR A2085 " --> pdb=" O LEU A2063 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ASP A2065 " --> pdb=" O TYR A2083 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ARG A2080 " --> pdb=" O ALA A2096 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ALA A2096 " --> pdb=" O ARG A2080 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ASP A2082 " --> pdb=" O MET A2094 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N MET A2094 " --> pdb=" O ASP A2082 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ASN A2084 " --> pdb=" O THR A2092 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1569 through 1570 removed outlier: 4.260A pdb=" N PHE A1569 " --> pdb=" O GLU A1577 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N LEU A1596 " --> pdb=" O ASN A1609 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ASN A1609 " --> pdb=" O LEU A1596 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N THR A1598 " --> pdb=" O LEU A1607 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU A1607 " --> pdb=" O ASP A1623 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ASP A1623 " --> pdb=" O LEU A1607 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASN A1609 " --> pdb=" O ILE A1621 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ILE A1621 " --> pdb=" O ASN A1609 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR A1611 " --> pdb=" O THR A1619 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N THR A1619 " --> pdb=" O VAL A1631 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ASN A1630 " --> pdb=" O LEU A1642 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU A1642 " --> pdb=" O ASN A1630 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ARG A1632 " --> pdb=" O LEU A1640 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N LEU A1640 " --> pdb=" O VAL A1652 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A1652 " --> pdb=" O LEU A1640 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LYS A1661 " --> pdb=" O MET A1673 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA A1671 " --> pdb=" O VAL A1663 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N MET A1672 " --> pdb=" O LYS A1685 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LYS A1685 " --> pdb=" O MET A1672 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N THR A1674 " --> pdb=" O ALA A1683 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ALA A1683 " --> pdb=" O TYR A1695 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N PHE A1694 " --> pdb=" O VAL A1706 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VAL A1706 " --> pdb=" O PHE A1694 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLU A1696 " --> pdb=" O THR A1704 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N THR A1704 " --> pdb=" O PHE A1716 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL A1724 " --> pdb=" O THR A1740 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR A1740 " --> pdb=" O VAL A1724 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A1800 " --> pdb=" O ASN A1809 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL A1826 " --> pdb=" O GLU A1818 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL A1833 " --> pdb=" O ASN A1837 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ASN A1837 " --> pdb=" O VAL A1833 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N SER A1872 " --> pdb=" O VAL A1885 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN A1884 " --> pdb=" O ILE A1896 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ILE A1896 " --> pdb=" O ASN A1884 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N THR A1886 " --> pdb=" O ALA A1894 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ALA A1894 " --> pdb=" O MET A1905 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET A1905 " --> pdb=" O ALA A1894 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N SER A1902 " --> pdb=" O PHE A1918 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N PHE A1918 " --> pdb=" O SER A1902 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ARG A1904 " --> pdb=" O ARG A1916 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ARG A1916 " --> pdb=" O ARG A1904 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLU A1906 " --> pdb=" O THR A1914 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N THR A1914 " --> pdb=" O TYR A1926 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N SER A1954 " --> pdb=" O LEU A1966 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N HIS A2000 " --> pdb=" O ASP A1991 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N LEU A1999 " --> pdb=" O TYR A2012 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE A2011 " --> pdb=" O THR A2023 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N THR A2023 " --> pdb=" O ILE A2011 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LYS A2013 " --> pdb=" O ALA A2021 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ALA A2021 " --> pdb=" O PHE A2032 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS A2029 " --> pdb=" O GLN A2047 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N LYS A2042 " --> pdb=" O TYR A2057 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N THR A2052 " --> pdb=" O PHE A2071 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N PHE A2071 " --> pdb=" O THR A2052 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR A2054 " --> pdb=" O PHE A2069 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N PHE A2069 " --> pdb=" O THR A2054 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ARG A2056 " --> pdb=" O GLN A2067 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLN A2067 " --> pdb=" O ARG A2056 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ARG A2058 " --> pdb=" O ASP A2065 " (cutoff:3.500A) removed outlier: 10.634A pdb=" N LEU A2063 " --> pdb=" O TYR A2085 " (cutoff:3.500A) removed outlier: 8.933A pdb=" N TYR A2085 " --> pdb=" O LEU A2063 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ASP A2065 " --> pdb=" O TYR A2083 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ARG A2080 " --> pdb=" O ALA A2096 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ALA A2096 " --> pdb=" O ARG A2080 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ASP A2082 " --> pdb=" O MET A2094 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N MET A2094 " --> pdb=" O ASP A2082 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ASN A2084 " --> pdb=" O THR A2092 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N THR A2092 " --> pdb=" O TYR A2108 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LEU A2107 " --> pdb=" O PHE A2120 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N PHE A2120 " --> pdb=" O LEU A2107 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ARG A2109 " --> pdb=" O GLU A2118 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N GLU A2118 " --> pdb=" O VAL A2125 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL A2125 " --> pdb=" O GLU A2118 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN A2132 " --> pdb=" O LYS A2143 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU A2153 " --> pdb=" O HIS A2144 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N LYS A2152 " --> pdb=" O VAL A2168 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR A2164 " --> pdb=" O TYR A2156 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE A2158 " --> pdb=" O LEU A2162 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N LEU A2162 " --> pdb=" O ILE A2158 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS A2178 " --> pdb=" O GLN A2169 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N VAL A2177 " --> pdb=" O TYR A2194 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TRP A2213 " --> pdb=" O VAL A2205 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ILE A2207 " --> pdb=" O PRO A2211 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1782 through 1784 Processing sheet with id=AB8, first strand: chain 'A' and resid 2216 through 2217 removed outlier: 6.687A pdb=" N SER A2216 " --> pdb=" O HIS A2224 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N HIS A2224 " --> pdb=" O LEU A2237 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU A2248 " --> pdb=" O PRO A2236 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ARG A2238 " --> pdb=" O THR A2246 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N THR A2246 " --> pdb=" O TYR A2253 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLN A2252 " --> pdb=" O ARG A2264 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ARG A2264 " --> pdb=" O GLN A2252 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LYS A2254 " --> pdb=" O ARG A2262 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ARG A2262 " --> pdb=" O PHE A2269 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS A2279 " --> pdb=" O GLU A2270 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N ILE A2278 " --> pdb=" O TYR A2291 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ARG A2290 " --> pdb=" O SER A2302 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N SER A2302 " --> pdb=" O ARG A2290 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ARG A2292 " --> pdb=" O VAL A2300 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N VAL A2300 " --> pdb=" O PHE A2312 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE A2312 " --> pdb=" O VAL A2300 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU A2333 " --> pdb=" O ASN A2328 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA A2347 " --> pdb=" O TYR A2338 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N PHE A2346 " --> pdb=" O ILE A2358 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA A2368 " --> pdb=" O ALA A2359 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL A2369 " --> pdb=" O ILE A2377 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N MET A2390 " --> pdb=" O LEU A2381 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 2406 through 2408 removed outlier: 3.966A pdb=" N LEU A2413 " --> pdb=" O ASP A2408 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG A2427 " --> pdb=" O ASP A2422 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 2570 through 2574 Processing sheet with id=AC2, first strand: chain 'A' and resid 2602 through 2603 Processing sheet with id=AC3, first strand: chain 'A' and resid 2602 through 2603 removed outlier: 5.970A pdb=" N ASP A2615 " --> pdb=" O CYS A2674 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ASN A2676 " --> pdb=" O ASP A2615 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N HIS A2617 " --> pdb=" O ASN A2676 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ARG A2678 " --> pdb=" O HIS A2617 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N PHE A2619 " --> pdb=" O ARG A2678 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 2737 through 2741 Processing sheet with id=AC5, first strand: chain 'B' and resid 959 through 965 removed outlier: 8.423A pdb=" N PHE B 994 " --> pdb=" O ALA B 921 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VAL B 923 " --> pdb=" O PHE B 994 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 959 through 965 Processing sheet with id=AC7, first strand: chain 'B' and resid 951 through 953 removed outlier: 3.656A pdb=" N GLU B 975 " --> pdb=" O ASN B 940 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 1022 through 1025 Processing sheet with id=AC9, first strand: chain 'B' and resid 1041 through 1042 Processing sheet with id=AD1, first strand: chain 'B' and resid 1100 through 1107 removed outlier: 3.520A pdb=" N LYS B1090 " --> pdb=" O GLU B1141 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR B1140 " --> pdb=" O LEU B1150 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU B1150 " --> pdb=" O TYR B1140 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1178 through 1180 Processing sheet with id=AD3, first strand: chain 'B' and resid 1202 through 1203 removed outlier: 3.537A pdb=" N ARG B1559 " --> pdb=" O ASP B1554 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA B1553 " --> pdb=" O SER B1541 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N SER B1541 " --> pdb=" O ALA B1553 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1222 through 1223 removed outlier: 6.693A pdb=" N ILE B1251 " --> pdb=" O ILE B1263 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1283 through 1285 removed outlier: 4.206A pdb=" N VAL B1292 " --> pdb=" O ILE B1305 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU B1294 " --> pdb=" O PHE B1303 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA B1322 " --> pdb=" O VAL B1302 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1350 through 1355 removed outlier: 4.975A pdb=" N GLY B1352 " --> pdb=" O VAL B1364 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1399 through 1400 removed outlier: 3.533A pdb=" N ARG B1439 " --> pdb=" O GLN B1431 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL B1441 " --> pdb=" O VAL B1429 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N VAL B1429 " --> pdb=" O VAL B1441 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER B1420 " --> pdb=" O ASN B1415 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP B1411 " --> pdb=" O LEU B1424 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1470 through 1475 removed outlier: 5.527A pdb=" N ALA B1470 " --> pdb=" O THR B1486 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N THR B1486 " --> pdb=" O ALA B1470 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE B1494 " --> pdb=" O VAL B1506 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1569 through 1570 removed outlier: 4.260A pdb=" N PHE B1569 " --> pdb=" O GLU B1577 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N LEU B1596 " --> pdb=" O ASN B1609 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ASN B1609 " --> pdb=" O LEU B1596 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N THR B1598 " --> pdb=" O LEU B1607 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU B1607 " --> pdb=" O ASP B1623 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ASP B1623 " --> pdb=" O LEU B1607 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASN B1609 " --> pdb=" O ILE B1621 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ILE B1621 " --> pdb=" O ASN B1609 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR B1611 " --> pdb=" O THR B1619 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N THR B1619 " --> pdb=" O VAL B1631 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ASN B1630 " --> pdb=" O LEU B1642 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU B1642 " --> pdb=" O ASN B1630 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ARG B1632 " --> pdb=" O LEU B1640 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N LEU B1640 " --> pdb=" O VAL B1652 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL B1652 " --> pdb=" O LEU B1640 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N LYS B1661 " --> pdb=" O MET B1673 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA B1671 " --> pdb=" O VAL B1663 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N MET B1672 " --> pdb=" O LYS B1685 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LYS B1685 " --> pdb=" O MET B1672 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N THR B1674 " --> pdb=" O ALA B1683 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ALA B1683 " --> pdb=" O TYR B1695 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N PHE B1694 " --> pdb=" O VAL B1706 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL B1706 " --> pdb=" O PHE B1694 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N GLU B1696 " --> pdb=" O THR B1704 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N THR B1704 " --> pdb=" O PHE B1716 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL B1724 " --> pdb=" O THR B1740 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR B1740 " --> pdb=" O VAL B1724 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL B1800 " --> pdb=" O ASN B1809 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL B1826 " --> pdb=" O GLU B1818 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL B1833 " --> pdb=" O ASN B1837 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ASN B1837 " --> pdb=" O VAL B1833 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N SER B1872 " --> pdb=" O VAL B1885 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN B1884 " --> pdb=" O ILE B1896 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ILE B1896 " --> pdb=" O ASN B1884 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N THR B1886 " --> pdb=" O ALA B1894 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ALA B1894 " --> pdb=" O MET B1905 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET B1905 " --> pdb=" O ALA B1894 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N SER B1902 " --> pdb=" O PHE B1918 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N PHE B1918 " --> pdb=" O SER B1902 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ARG B1904 " --> pdb=" O ARG B1916 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ARG B1916 " --> pdb=" O ARG B1904 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLU B1906 " --> pdb=" O THR B1914 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N THR B1914 " --> pdb=" O TYR B1926 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N SER B1954 " --> pdb=" O LEU B1966 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N HIS B2000 " --> pdb=" O ASP B1991 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N LEU B1999 " --> pdb=" O TYR B2012 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE B2011 " --> pdb=" O THR B2023 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N THR B2023 " --> pdb=" O ILE B2011 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LYS B2013 " --> pdb=" O ALA B2021 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N ALA B2021 " --> pdb=" O PHE B2032 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS B2029 " --> pdb=" O GLN B2047 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N LYS B2042 " --> pdb=" O TYR B2057 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N THR B2052 " --> pdb=" O PHE B2071 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N PHE B2071 " --> pdb=" O THR B2052 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR B2054 " --> pdb=" O PHE B2069 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N PHE B2069 " --> pdb=" O THR B2054 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ARG B2056 " --> pdb=" O GLN B2067 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLN B2067 " --> pdb=" O ARG B2056 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ARG B2058 " --> pdb=" O ASP B2065 " (cutoff:3.500A) removed outlier: 10.634A pdb=" N LEU B2063 " --> pdb=" O TYR B2085 " (cutoff:3.500A) removed outlier: 8.933A pdb=" N TYR B2085 " --> pdb=" O LEU B2063 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ASP B2065 " --> pdb=" O TYR B2083 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ARG B2080 " --> pdb=" O ALA B2096 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ALA B2096 " --> pdb=" O ARG B2080 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ASP B2082 " --> pdb=" O MET B2094 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N MET B2094 " --> pdb=" O ASP B2082 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ASN B2084 " --> pdb=" O THR B2092 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 1569 through 1570 removed outlier: 4.260A pdb=" N PHE B1569 " --> pdb=" O GLU B1577 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N LEU B1596 " --> pdb=" O ASN B1609 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ASN B1609 " --> pdb=" O LEU B1596 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N THR B1598 " --> pdb=" O LEU B1607 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU B1607 " --> pdb=" O ASP B1623 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ASP B1623 " --> pdb=" O LEU B1607 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASN B1609 " --> pdb=" O ILE B1621 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ILE B1621 " --> pdb=" O ASN B1609 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR B1611 " --> pdb=" O THR B1619 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N THR B1619 " --> pdb=" O VAL B1631 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ASN B1630 " --> pdb=" O LEU B1642 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU B1642 " --> pdb=" O ASN B1630 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ARG B1632 " --> pdb=" O LEU B1640 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N LEU B1640 " --> pdb=" O VAL B1652 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL B1652 " --> pdb=" O LEU B1640 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N LYS B1661 " --> pdb=" O MET B1673 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA B1671 " --> pdb=" O VAL B1663 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N MET B1672 " --> pdb=" O LYS B1685 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LYS B1685 " --> pdb=" O MET B1672 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N THR B1674 " --> pdb=" O ALA B1683 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ALA B1683 " --> pdb=" O TYR B1695 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N PHE B1694 " --> pdb=" O VAL B1706 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL B1706 " --> pdb=" O PHE B1694 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N GLU B1696 " --> pdb=" O THR B1704 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N THR B1704 " --> pdb=" O PHE B1716 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL B1724 " --> pdb=" O THR B1740 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR B1740 " --> pdb=" O VAL B1724 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL B1800 " --> pdb=" O ASN B1809 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL B1826 " --> pdb=" O GLU B1818 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL B1833 " --> pdb=" O ASN B1837 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ASN B1837 " --> pdb=" O VAL B1833 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N SER B1872 " --> pdb=" O VAL B1885 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN B1884 " --> pdb=" O ILE B1896 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ILE B1896 " --> pdb=" O ASN B1884 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N THR B1886 " --> pdb=" O ALA B1894 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ALA B1894 " --> pdb=" O MET B1905 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET B1905 " --> pdb=" O ALA B1894 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N SER B1902 " --> pdb=" O PHE B1918 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N PHE B1918 " --> pdb=" O SER B1902 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ARG B1904 " --> pdb=" O ARG B1916 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ARG B1916 " --> pdb=" O ARG B1904 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLU B1906 " --> pdb=" O THR B1914 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N THR B1914 " --> pdb=" O TYR B1926 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N SER B1954 " --> pdb=" O LEU B1966 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N HIS B2000 " --> pdb=" O ASP B1991 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N LEU B1999 " --> pdb=" O TYR B2012 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE B2011 " --> pdb=" O THR B2023 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N THR B2023 " --> pdb=" O ILE B2011 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LYS B2013 " --> pdb=" O ALA B2021 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N ALA B2021 " --> pdb=" O PHE B2032 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS B2029 " --> pdb=" O GLN B2047 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N LYS B2042 " --> pdb=" O TYR B2057 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N THR B2052 " --> pdb=" O PHE B2071 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N PHE B2071 " --> pdb=" O THR B2052 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR B2054 " --> pdb=" O PHE B2069 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N PHE B2069 " --> pdb=" O THR B2054 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ARG B2056 " --> pdb=" O GLN B2067 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLN B2067 " --> pdb=" O ARG B2056 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ARG B2058 " --> pdb=" O ASP B2065 " (cutoff:3.500A) removed outlier: 10.634A pdb=" N LEU B2063 " --> pdb=" O TYR B2085 " (cutoff:3.500A) removed outlier: 8.933A pdb=" N TYR B2085 " --> pdb=" O LEU B2063 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ASP B2065 " --> pdb=" O TYR B2083 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ARG B2080 " --> pdb=" O ALA B2096 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ALA B2096 " --> pdb=" O ARG B2080 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ASP B2082 " --> pdb=" O MET B2094 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N MET B2094 " --> pdb=" O ASP B2082 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ASN B2084 " --> pdb=" O THR B2092 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N THR B2092 " --> pdb=" O TYR B2108 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LEU B2107 " --> pdb=" O PHE B2120 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N PHE B2120 " --> pdb=" O LEU B2107 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ARG B2109 " --> pdb=" O GLU B2118 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N GLU B2118 " --> pdb=" O VAL B2125 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL B2125 " --> pdb=" O GLU B2118 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN B2132 " --> pdb=" O LYS B2143 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU B2153 " --> pdb=" O HIS B2144 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N LYS B2152 " --> pdb=" O VAL B2168 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR B2164 " --> pdb=" O TYR B2156 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE B2158 " --> pdb=" O LEU B2162 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N LEU B2162 " --> pdb=" O ILE B2158 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS B2178 " --> pdb=" O GLN B2169 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N VAL B2177 " --> pdb=" O TYR B2194 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TRP B2213 " --> pdb=" O VAL B2205 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ILE B2207 " --> pdb=" O PRO B2211 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 1782 through 1784 Processing sheet with id=AE3, first strand: chain 'B' and resid 2216 through 2217 removed outlier: 6.687A pdb=" N SER B2216 " --> pdb=" O HIS B2224 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N HIS B2224 " --> pdb=" O LEU B2237 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU B2248 " --> pdb=" O PRO B2236 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ARG B2238 " --> pdb=" O THR B2246 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N THR B2246 " --> pdb=" O TYR B2253 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLN B2252 " --> pdb=" O ARG B2264 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ARG B2264 " --> pdb=" O GLN B2252 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LYS B2254 " --> pdb=" O ARG B2262 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ARG B2262 " --> pdb=" O PHE B2269 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS B2279 " --> pdb=" O GLU B2270 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N ILE B2278 " --> pdb=" O TYR B2291 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ARG B2290 " --> pdb=" O SER B2302 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N SER B2302 " --> pdb=" O ARG B2290 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ARG B2292 " --> pdb=" O VAL B2300 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N VAL B2300 " --> pdb=" O PHE B2312 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE B2312 " --> pdb=" O VAL B2300 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU B2333 " --> pdb=" O ASN B2328 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA B2347 " --> pdb=" O TYR B2338 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N PHE B2346 " --> pdb=" O ILE B2358 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA B2368 " --> pdb=" O ALA B2359 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL B2369 " --> pdb=" O ILE B2377 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N MET B2390 " --> pdb=" O LEU B2381 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 2406 through 2408 removed outlier: 3.966A pdb=" N LEU B2413 " --> pdb=" O ASP B2408 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG B2427 " --> pdb=" O ASP B2422 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 2570 through 2574 Processing sheet with id=AE6, first strand: chain 'B' and resid 2602 through 2603 Processing sheet with id=AE7, first strand: chain 'B' and resid 2602 through 2603 removed outlier: 5.970A pdb=" N ASP B2615 " --> pdb=" O CYS B2674 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ASN B2676 " --> pdb=" O ASP B2615 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N HIS B2617 " --> pdb=" O ASN B2676 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N ARG B2678 " --> pdb=" O HIS B2617 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N PHE B2619 " --> pdb=" O ARG B2678 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 2737 through 2741 1360 hydrogen bonds defined for protein. 3546 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: 14.22 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 10096 1.34 - 1.47: 7608 1.47 - 1.59: 13330 1.59 - 1.72: 0 1.72 - 1.84: 236 Bond restraints: 31270 Sorted by residual: bond pdb=" N LEU B 862 " pdb=" CA LEU B 862 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.23e-02 6.61e+03 1.02e+01 bond pdb=" N LEU A 862 " pdb=" CA LEU A 862 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.23e-02 6.61e+03 1.01e+01 bond pdb=" N LEU A 859 " pdb=" CA LEU A 859 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.35e-02 5.49e+03 6.26e+00 bond pdb=" C1 NAG A2807 " pdb=" O5 NAG A2807 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.24e+00 bond pdb=" C1 NAG B2807 " pdb=" O5 NAG B2807 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.24e+00 ... (remaining 31265 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 39698 1.51 - 3.02: 2313 3.02 - 4.53: 313 4.53 - 6.04: 60 6.04 - 7.55: 14 Bond angle restraints: 42398 Sorted by residual: angle pdb=" CA ASP B 847 " pdb=" CB ASP B 847 " pdb=" CG ASP B 847 " ideal model delta sigma weight residual 112.60 116.56 -3.96 1.00e+00 1.00e+00 1.57e+01 angle pdb=" CA ASP A 847 " pdb=" CB ASP A 847 " pdb=" CG ASP A 847 " ideal model delta sigma weight residual 112.60 116.55 -3.95 1.00e+00 1.00e+00 1.56e+01 angle pdb=" N MET A 853 " pdb=" CA MET A 853 " pdb=" C MET A 853 " ideal model delta sigma weight residual 112.54 108.03 4.51 1.22e+00 6.72e-01 1.37e+01 angle pdb=" CA HIS A 864 " pdb=" C HIS A 864 " pdb=" O HIS A 864 " ideal model delta sigma weight residual 120.55 116.73 3.82 1.06e+00 8.90e-01 1.30e+01 angle pdb=" CA HIS B 864 " pdb=" C HIS B 864 " pdb=" O HIS B 864 " ideal model delta sigma weight residual 120.55 116.74 3.81 1.06e+00 8.90e-01 1.29e+01 ... (remaining 42393 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 17378 17.79 - 35.57: 1318 35.57 - 53.36: 254 53.36 - 71.15: 58 71.15 - 88.94: 32 Dihedral angle restraints: 19040 sinusoidal: 8040 harmonic: 11000 Sorted by residual: dihedral pdb=" CA TYR B2025 " pdb=" C TYR B2025 " pdb=" N ASP B2026 " pdb=" CA ASP B2026 " ideal model delta harmonic sigma weight residual -180.00 -145.36 -34.64 0 5.00e+00 4.00e-02 4.80e+01 dihedral pdb=" CA TYR A2025 " pdb=" C TYR A2025 " pdb=" N ASP A2026 " pdb=" CA ASP A2026 " ideal model delta harmonic sigma weight residual -180.00 -145.37 -34.63 0 5.00e+00 4.00e-02 4.80e+01 dihedral pdb=" CB CYS A1011 " pdb=" SG CYS A1011 " pdb=" SG CYS A1145 " pdb=" CB CYS A1145 " ideal model delta sinusoidal sigma weight residual 93.00 45.29 47.71 1 1.00e+01 1.00e-02 3.14e+01 ... (remaining 19037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.241: 4738 0.241 - 0.482: 4 0.482 - 0.723: 0 0.723 - 0.965: 2 0.965 - 1.206: 2 Chirality restraints: 4746 Sorted by residual: chirality pdb=" C1 NAG A2806 " pdb=" ND2 ASN A1985 " pdb=" C2 NAG A2806 " pdb=" O5 NAG A2806 " both_signs ideal model delta sigma weight residual False -2.40 -1.19 -1.21 2.00e-01 2.50e+01 3.63e+01 chirality pdb=" C1 NAG B2806 " pdb=" ND2 ASN B1985 " pdb=" C2 NAG B2806 " pdb=" O5 NAG B2806 " both_signs ideal model delta sigma weight residual False -2.40 -1.20 -1.20 2.00e-01 2.50e+01 3.63e+01 chirality pdb=" C1 NAG A2807 " pdb=" ND2 ASN A2188 " pdb=" C2 NAG A2807 " pdb=" O5 NAG A2807 " both_signs ideal model delta sigma weight residual False -2.40 -1.50 -0.90 2.00e-01 2.50e+01 2.01e+01 ... (remaining 4743 not shown) Planarity restraints: 5496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A1286 " 0.076 5.00e-02 4.00e+02 1.17e-01 2.21e+01 pdb=" N PRO A1287 " -0.203 5.00e-02 4.00e+02 pdb=" CA PRO A1287 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO A1287 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B1286 " 0.076 5.00e-02 4.00e+02 1.17e-01 2.21e+01 pdb=" N PRO B1287 " -0.203 5.00e-02 4.00e+02 pdb=" CA PRO B1287 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO B1287 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B2128 " -0.030 2.00e-02 2.50e+03 1.99e-02 7.91e+00 pdb=" CG TYR B2128 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR B2128 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR B2128 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR B2128 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B2128 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B2128 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR B2128 " -0.007 2.00e-02 2.50e+03 ... (remaining 5493 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 206 2.48 - 3.08: 21735 3.08 - 3.69: 42470 3.69 - 4.29: 63868 4.29 - 4.90: 110868 Nonbonded interactions: 239147 Sorted by model distance: nonbonded pdb=" OD1 ASP A2470 " pdb=" OG SER A2473 " model vdw 1.869 3.040 nonbonded pdb=" OD1 ASP B2470 " pdb=" OG SER B2473 " model vdw 1.870 3.040 nonbonded pdb=" OG1 THR A2006 " pdb=" OD2 ASP A2258 " model vdw 1.942 3.040 nonbonded pdb=" OG1 THR B2006 " pdb=" OD2 ASP B2258 " model vdw 1.943 3.040 nonbonded pdb=" OG1 THR B 985 " pdb=" NZ LYS B1357 " model vdw 2.021 3.120 ... (remaining 239142 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 35.360 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 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 : 0.007 0.051 31322 Z= 0.325 Angle : 0.832 18.074 42532 Z= 0.455 Chirality : 0.059 1.206 4746 Planarity : 0.006 0.117 5474 Dihedral : 13.403 88.937 11958 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 24.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.24 % Allowed : 0.60 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.70 (0.13), residues: 3788 helix: -1.92 (0.30), residues: 220 sheet: -0.27 (0.15), residues: 1182 loop : -1.56 (0.12), residues: 2386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A2150 TYR 0.045 0.003 TYR B2128 PHE 0.035 0.002 PHE B1031 TRP 0.034 0.002 TRP A 990 HIS 0.011 0.002 HIS B 864 Details of bonding type rmsd covalent geometry : bond 0.00699 (31270) covalent geometry : angle 0.79326 (42398) SS BOND : bond 0.00683 ( 22) SS BOND : angle 2.36410 ( 44) hydrogen bonds : bond 0.24314 ( 1002) hydrogen bonds : angle 9.09162 ( 3546) link_BETA1-4 : bond 0.00581 ( 8) link_BETA1-4 : angle 1.56040 ( 24) link_NAG-ASN : bond 0.00852 ( 22) link_NAG-ASN : angle 6.07505 ( 66) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7576 Ramachandran restraints generated. 3788 Oldfield, 0 Emsley, 3788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7576 Ramachandran restraints generated. 3788 Oldfield, 0 Emsley, 3788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 344 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 879 ILE cc_start: 0.9057 (tp) cc_final: 0.8790 (tp) REVERT: A 907 THR cc_start: 0.8486 (t) cc_final: 0.8204 (p) REVERT: A 1304 LYS cc_start: 0.8527 (tmtt) cc_final: 0.8199 (tmtt) REVERT: B 879 ILE cc_start: 0.8992 (tp) cc_final: 0.8719 (tp) REVERT: B 907 THR cc_start: 0.8569 (t) cc_final: 0.8298 (p) REVERT: B 1255 PHE cc_start: 0.7858 (m-10) cc_final: 0.7607 (m-80) REVERT: B 1304 LYS cc_start: 0.8484 (tmtt) cc_final: 0.8187 (tmtt) outliers start: 8 outliers final: 0 residues processed: 346 average time/residue: 0.1889 time to fit residues: 105.9889 Evaluate side-chains 248 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 197 optimal weight: 0.0970 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 50.0000 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 30.0000 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 0.7980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 890 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 945 ASN A 956 GLN A1249 ASN A1262 ASN A1819 GLN A2000 HIS A2201 GLN A2208 ASN A2224 HIS A2342 GLN A2523 GLN ** B 890 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 945 ASN B 956 GLN B1125 ASN B1249 ASN B1262 ASN B1819 GLN B2000 HIS B2067 GLN B2201 GLN B2208 ASN B2224 HIS B2342 GLN B2523 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.150520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.114513 restraints weight = 52445.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.113137 restraints weight = 36000.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.114274 restraints weight = 35040.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.114517 restraints weight = 26597.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.114835 restraints weight = 23992.890| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31322 Z= 0.145 Angle : 0.713 12.600 42532 Z= 0.367 Chirality : 0.050 0.463 4746 Planarity : 0.005 0.074 5474 Dihedral : 6.327 58.494 4842 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.99 % Allowed : 6.31 % Favored : 92.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.98 (0.13), residues: 3788 helix: 0.08 (0.36), residues: 208 sheet: 0.17 (0.14), residues: 1266 loop : -1.24 (0.12), residues: 2314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B2233 TYR 0.025 0.002 TYR B1140 PHE 0.018 0.001 PHE A1106 TRP 0.018 0.001 TRP B 990 HIS 0.005 0.001 HIS B2483 Details of bonding type rmsd covalent geometry : bond 0.00322 (31270) covalent geometry : angle 0.69399 (42398) SS BOND : bond 0.00339 ( 22) SS BOND : angle 1.56517 ( 44) hydrogen bonds : bond 0.04572 ( 1002) hydrogen bonds : angle 5.79721 ( 3546) link_BETA1-4 : bond 0.00627 ( 8) link_BETA1-4 : angle 1.15387 ( 24) link_NAG-ASN : bond 0.00488 ( 22) link_NAG-ASN : angle 4.02726 ( 66) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7576 Ramachandran restraints generated. 3788 Oldfield, 0 Emsley, 3788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7576 Ramachandran restraints generated. 3788 Oldfield, 0 Emsley, 3788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 312 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 879 ILE cc_start: 0.9073 (tp) cc_final: 0.8846 (tp) REVERT: A 1112 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7941 (mm) REVERT: A 1230 LEU cc_start: 0.7708 (mt) cc_final: 0.7469 (mt) REVERT: A 1304 LYS cc_start: 0.8592 (tmtt) cc_final: 0.8244 (tmtt) REVERT: A 1482 TYR cc_start: 0.8271 (m-80) cc_final: 0.8000 (m-80) REVERT: A 1853 TYR cc_start: 0.8312 (p90) cc_final: 0.8084 (p90) REVERT: A 2468 MET cc_start: 0.7706 (tmt) cc_final: 0.7195 (tmt) REVERT: B 879 ILE cc_start: 0.9035 (tp) cc_final: 0.8814 (tp) REVERT: B 907 THR cc_start: 0.8432 (t) cc_final: 0.8206 (m) REVERT: B 1105 TRP cc_start: 0.6827 (p-90) cc_final: 0.6584 (p-90) REVERT: B 1304 LYS cc_start: 0.8501 (tmtt) cc_final: 0.8142 (tmtt) REVERT: B 1549 GLU cc_start: 0.7092 (pt0) cc_final: 0.6634 (tt0) REVERT: B 1853 TYR cc_start: 0.8305 (p90) cc_final: 0.8067 (p90) REVERT: B 2468 MET cc_start: 0.7680 (tmt) cc_final: 0.7163 (tmt) REVERT: B 2531 LYS cc_start: 0.8190 (tppt) cc_final: 0.7938 (tptp) outliers start: 33 outliers final: 17 residues processed: 331 average time/residue: 0.1783 time to fit residues: 97.8887 Evaluate side-chains 275 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 257 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 945 ASN Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1077 ILE Chi-restraints excluded: chain A residue 1112 LEU Chi-restraints excluded: chain A residue 1794 THR Chi-restraints excluded: chain A residue 2460 ASN Chi-restraints excluded: chain A residue 2494 MET Chi-restraints excluded: chain A residue 2750 GLU Chi-restraints excluded: chain B residue 945 ASN Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain B residue 1077 ILE Chi-restraints excluded: chain B residue 1555 LEU Chi-restraints excluded: chain B residue 1742 LEU Chi-restraints excluded: chain B residue 1794 THR Chi-restraints excluded: chain B residue 1968 THR Chi-restraints excluded: chain B residue 2460 ASN Chi-restraints excluded: chain B residue 2494 MET Chi-restraints excluded: chain B residue 2750 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 46 optimal weight: 20.0000 chunk 107 optimal weight: 4.9990 chunk 253 optimal weight: 8.9990 chunk 89 optimal weight: 8.9990 chunk 12 optimal weight: 0.0770 chunk 332 optimal weight: 0.0970 chunk 266 optimal weight: 3.9990 chunk 295 optimal weight: 7.9990 chunk 201 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 205 optimal weight: 8.9990 overall best weight: 2.8342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 890 ASN A 927 GLN ** A1785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1938 HIS A2067 GLN B 890 ASN B 927 GLN B1187 HIS ** B1785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1938 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.148007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.111731 restraints weight = 52929.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.109478 restraints weight = 38001.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.110507 restraints weight = 36657.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.111259 restraints weight = 26473.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.111537 restraints weight = 24346.454| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 31322 Z= 0.200 Angle : 0.688 10.525 42532 Z= 0.355 Chirality : 0.049 0.398 4746 Planarity : 0.005 0.055 5474 Dihedral : 6.062 58.583 4842 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.41 % Allowed : 10.13 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.13), residues: 3788 helix: 0.88 (0.37), residues: 208 sheet: 0.39 (0.15), residues: 1234 loop : -1.15 (0.12), residues: 2346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B2233 TYR 0.021 0.002 TYR A1140 PHE 0.022 0.002 PHE B1106 TRP 0.014 0.001 TRP B 990 HIS 0.007 0.001 HIS A1668 Details of bonding type rmsd covalent geometry : bond 0.00470 (31270) covalent geometry : angle 0.67143 (42398) SS BOND : bond 0.00262 ( 22) SS BOND : angle 1.76523 ( 44) hydrogen bonds : bond 0.04541 ( 1002) hydrogen bonds : angle 5.27792 ( 3546) link_BETA1-4 : bond 0.00410 ( 8) link_BETA1-4 : angle 1.39533 ( 24) link_NAG-ASN : bond 0.00548 ( 22) link_NAG-ASN : angle 3.58417 ( 66) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7576 Ramachandran restraints generated. 3788 Oldfield, 0 Emsley, 3788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7576 Ramachandran restraints generated. 3788 Oldfield, 0 Emsley, 3788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 281 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1112 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7876 (mm) REVERT: A 1371 ARG cc_start: 0.6736 (mpp-170) cc_final: 0.6433 (mpp80) REVERT: A 1477 HIS cc_start: 0.8407 (t-90) cc_final: 0.8174 (t-170) REVERT: A 1482 TYR cc_start: 0.8351 (m-80) cc_final: 0.8141 (m-80) REVERT: A 1549 GLU cc_start: 0.7002 (pt0) cc_final: 0.6613 (tt0) REVERT: A 1853 TYR cc_start: 0.8371 (p90) cc_final: 0.8082 (p90) REVERT: A 2468 MET cc_start: 0.7665 (tmt) cc_final: 0.7139 (tmt) REVERT: A 2531 LYS cc_start: 0.8231 (tppt) cc_final: 0.7942 (ttpt) REVERT: B 907 THR cc_start: 0.8540 (t) cc_final: 0.8233 (p) REVERT: B 1059 MET cc_start: 0.6991 (mmt) cc_final: 0.6726 (mmm) REVERT: B 1304 LYS cc_start: 0.8426 (tmtt) cc_final: 0.8221 (tmtt) REVERT: B 1371 ARG cc_start: 0.6724 (mpp-170) cc_final: 0.6510 (mpp80) REVERT: B 1482 TYR cc_start: 0.8409 (m-80) cc_final: 0.8149 (m-80) REVERT: B 1498 THR cc_start: 0.9034 (m) cc_final: 0.8777 (p) REVERT: B 1549 GLU cc_start: 0.7045 (pt0) cc_final: 0.6686 (tt0) REVERT: B 1853 TYR cc_start: 0.8393 (p90) cc_final: 0.8110 (p90) REVERT: B 2468 MET cc_start: 0.7648 (tmt) cc_final: 0.7122 (tmt) REVERT: B 2531 LYS cc_start: 0.8250 (tppt) cc_final: 0.7976 (tptp) outliers start: 47 outliers final: 30 residues processed: 317 average time/residue: 0.1800 time to fit residues: 94.0836 Evaluate side-chains 280 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 249 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 984 HIS Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1077 ILE Chi-restraints excluded: chain A residue 1112 LEU Chi-restraints excluded: chain A residue 1750 THR Chi-restraints excluded: chain A residue 1934 VAL Chi-restraints excluded: chain A residue 2224 HIS Chi-restraints excluded: chain A residue 2248 LEU Chi-restraints excluded: chain A residue 2460 ASN Chi-restraints excluded: chain A residue 2494 MET Chi-restraints excluded: chain A residue 2542 LEU Chi-restraints excluded: chain A residue 2652 ILE Chi-restraints excluded: chain A residue 2750 GLU Chi-restraints excluded: chain B residue 964 THR Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain B residue 1077 ILE Chi-restraints excluded: chain B residue 1467 LEU Chi-restraints excluded: chain B residue 1742 LEU Chi-restraints excluded: chain B residue 1750 THR Chi-restraints excluded: chain B residue 1794 THR Chi-restraints excluded: chain B residue 1934 VAL Chi-restraints excluded: chain B residue 1968 THR Chi-restraints excluded: chain B residue 2224 HIS Chi-restraints excluded: chain B residue 2248 LEU Chi-restraints excluded: chain B residue 2334 ILE Chi-restraints excluded: chain B residue 2460 ASN Chi-restraints excluded: chain B residue 2494 MET Chi-restraints excluded: chain B residue 2542 LEU Chi-restraints excluded: chain B residue 2750 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 142 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 207 optimal weight: 50.0000 chunk 157 optimal weight: 0.6980 chunk 235 optimal weight: 10.0000 chunk 181 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 126 optimal weight: 0.9980 chunk 186 optimal weight: 7.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 956 GLN ** A1419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1648 GLN ** A1950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2224 HIS B 956 GLN ** B1419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1648 GLN ** B1668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2224 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.149925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.113442 restraints weight = 52109.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.112881 restraints weight = 36307.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.113272 restraints weight = 37581.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.114127 restraints weight = 26333.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.115235 restraints weight = 22560.648| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 31322 Z= 0.116 Angle : 0.625 11.429 42532 Z= 0.319 Chirality : 0.046 0.367 4746 Planarity : 0.004 0.055 5474 Dihedral : 5.625 58.581 4842 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.50 % Allowed : 11.64 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.14), residues: 3788 helix: 1.58 (0.38), residues: 206 sheet: 0.59 (0.15), residues: 1254 loop : -1.02 (0.13), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1002 TYR 0.019 0.001 TYR A1140 PHE 0.019 0.001 PHE B1106 TRP 0.015 0.001 TRP A2165 HIS 0.007 0.001 HIS B2438 Details of bonding type rmsd covalent geometry : bond 0.00261 (31270) covalent geometry : angle 0.60880 (42398) SS BOND : bond 0.00223 ( 22) SS BOND : angle 1.78983 ( 44) hydrogen bonds : bond 0.03618 ( 1002) hydrogen bonds : angle 4.83305 ( 3546) link_BETA1-4 : bond 0.00438 ( 8) link_BETA1-4 : angle 1.28966 ( 24) link_NAG-ASN : bond 0.00519 ( 22) link_NAG-ASN : angle 3.32010 ( 66) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7576 Ramachandran restraints generated. 3788 Oldfield, 0 Emsley, 3788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7576 Ramachandran restraints generated. 3788 Oldfield, 0 Emsley, 3788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 280 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1112 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7871 (mm) REVERT: A 1482 TYR cc_start: 0.8296 (m-80) cc_final: 0.8009 (m-80) REVERT: A 1549 GLU cc_start: 0.6939 (pt0) cc_final: 0.6641 (tt0) REVERT: A 1853 TYR cc_start: 0.8322 (p90) cc_final: 0.8079 (p90) REVERT: A 1958 MET cc_start: 0.8407 (mtm) cc_final: 0.8041 (mtm) REVERT: A 2468 MET cc_start: 0.7624 (tmt) cc_final: 0.7106 (tmt) REVERT: A 2531 LYS cc_start: 0.8195 (tppt) cc_final: 0.7899 (tptp) REVERT: B 907 THR cc_start: 0.8493 (t) cc_final: 0.8162 (p) REVERT: B 1059 MET cc_start: 0.6929 (mmt) cc_final: 0.6674 (mmm) REVERT: B 1371 ARG cc_start: 0.6612 (mpp-170) cc_final: 0.6394 (mpp80) REVERT: B 1482 TYR cc_start: 0.8383 (m-80) cc_final: 0.8181 (m-80) REVERT: B 1498 THR cc_start: 0.9031 (m) cc_final: 0.8778 (p) REVERT: B 1853 TYR cc_start: 0.8294 (p90) cc_final: 0.8046 (p90) REVERT: B 2468 MET cc_start: 0.7612 (tmt) cc_final: 0.7092 (tmt) REVERT: B 2531 LYS cc_start: 0.8185 (tppt) cc_final: 0.7914 (tptp) outliers start: 50 outliers final: 25 residues processed: 320 average time/residue: 0.1799 time to fit residues: 95.0126 Evaluate side-chains 278 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 252 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 984 HIS Chi-restraints excluded: chain A residue 1077 ILE Chi-restraints excluded: chain A residue 1112 LEU Chi-restraints excluded: chain A residue 1770 LEU Chi-restraints excluded: chain A residue 2224 HIS Chi-restraints excluded: chain A residue 2248 LEU Chi-restraints excluded: chain A residue 2460 ASN Chi-restraints excluded: chain A residue 2494 MET Chi-restraints excluded: chain A residue 2542 LEU Chi-restraints excluded: chain A residue 2582 ASP Chi-restraints excluded: chain A residue 2750 GLU Chi-restraints excluded: chain B residue 1077 ILE Chi-restraints excluded: chain B residue 1079 LEU Chi-restraints excluded: chain B residue 1467 LEU Chi-restraints excluded: chain B residue 1742 LEU Chi-restraints excluded: chain B residue 1750 THR Chi-restraints excluded: chain B residue 1770 LEU Chi-restraints excluded: chain B residue 1794 THR Chi-restraints excluded: chain B residue 2224 HIS Chi-restraints excluded: chain B residue 2248 LEU Chi-restraints excluded: chain B residue 2460 ASN Chi-restraints excluded: chain B residue 2494 MET Chi-restraints excluded: chain B residue 2542 LEU Chi-restraints excluded: chain B residue 2582 ASP Chi-restraints excluded: chain B residue 2750 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 343 optimal weight: 8.9990 chunk 268 optimal weight: 6.9990 chunk 218 optimal weight: 10.0000 chunk 338 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 334 optimal weight: 8.9990 chunk 45 optimal weight: 20.0000 chunk 214 optimal weight: 9.9990 chunk 125 optimal weight: 5.9990 chunk 377 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 984 HIS A1049 GLN A1187 HIS ** A1419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1997 HIS A2141 HIS ** A2201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1003 HIS B1049 GLN ** B1419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1648 GLN ** B1725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1997 HIS B2141 HIS B2201 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.143843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.107040 restraints weight = 53531.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.106180 restraints weight = 37395.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.106369 restraints weight = 45706.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.107353 restraints weight = 29058.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.109011 restraints weight = 24132.473| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.094 31322 Z= 0.416 Angle : 0.860 11.820 42532 Z= 0.440 Chirality : 0.054 0.358 4746 Planarity : 0.006 0.059 5474 Dihedral : 6.514 59.015 4842 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 2.65 % Allowed : 12.75 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.01 (0.13), residues: 3788 helix: 0.85 (0.36), residues: 208 sheet: 0.06 (0.14), residues: 1244 loop : -1.27 (0.12), residues: 2336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A2538 TYR 0.026 0.003 TYR A2389 PHE 0.028 0.003 PHE A2559 TRP 0.018 0.002 TRP B2720 HIS 0.018 0.002 HIS A2224 Details of bonding type rmsd covalent geometry : bond 0.00991 (31270) covalent geometry : angle 0.84641 (42398) SS BOND : bond 0.00312 ( 22) SS BOND : angle 1.86123 ( 44) hydrogen bonds : bond 0.05465 ( 1002) hydrogen bonds : angle 5.43458 ( 3546) link_BETA1-4 : bond 0.00317 ( 8) link_BETA1-4 : angle 1.67481 ( 24) link_NAG-ASN : bond 0.00725 ( 22) link_NAG-ASN : angle 3.63208 ( 66) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7576 Ramachandran restraints generated. 3788 Oldfield, 0 Emsley, 3788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7576 Ramachandran restraints generated. 3788 Oldfield, 0 Emsley, 3788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 269 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1371 ARG cc_start: 0.6831 (mpp-170) cc_final: 0.6519 (mpp80) REVERT: A 1482 TYR cc_start: 0.8422 (m-80) cc_final: 0.8120 (m-80) REVERT: A 1498 THR cc_start: 0.9042 (OUTLIER) cc_final: 0.8826 (p) REVERT: A 1563 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8359 (mp) REVERT: A 2209 ASP cc_start: 0.7227 (t70) cc_final: 0.6911 (t70) REVERT: A 2445 MET cc_start: 0.7696 (ptt) cc_final: 0.7440 (ptt) REVERT: A 2531 LYS cc_start: 0.8334 (tppt) cc_final: 0.7985 (ttpt) REVERT: B 877 ASP cc_start: 0.8331 (t0) cc_final: 0.8019 (t0) REVERT: B 1371 ARG cc_start: 0.6814 (mpp-170) cc_final: 0.6566 (mpp80) REVERT: B 1482 TYR cc_start: 0.8570 (m-80) cc_final: 0.8357 (m-80) REVERT: B 1498 THR cc_start: 0.9098 (m) cc_final: 0.8845 (p) REVERT: B 1504 SER cc_start: 0.7909 (m) cc_final: 0.7596 (p) REVERT: B 1563 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8291 (mp) REVERT: B 2209 ASP cc_start: 0.7241 (t70) cc_final: 0.6942 (t70) REVERT: B 2531 LYS cc_start: 0.8331 (tppt) cc_final: 0.8047 (tptp) outliers start: 88 outliers final: 54 residues processed: 340 average time/residue: 0.1761 time to fit residues: 101.0389 Evaluate side-chains 293 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 236 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 961 ASP Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 984 HIS Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1077 ILE Chi-restraints excluded: chain A residue 1112 LEU Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain A residue 1174 ASP Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1498 THR Chi-restraints excluded: chain A residue 1563 ILE Chi-restraints excluded: chain A residue 1652 VAL Chi-restraints excluded: chain A residue 1684 THR Chi-restraints excluded: chain A residue 1692 THR Chi-restraints excluded: chain A residue 1750 THR Chi-restraints excluded: chain A residue 1770 LEU Chi-restraints excluded: chain A residue 1786 LEU Chi-restraints excluded: chain A residue 1855 ASP Chi-restraints excluded: chain A residue 1934 VAL Chi-restraints excluded: chain A residue 1968 THR Chi-restraints excluded: chain A residue 2248 LEU Chi-restraints excluded: chain A residue 2334 ILE Chi-restraints excluded: chain A residue 2460 ASN Chi-restraints excluded: chain A residue 2494 MET Chi-restraints excluded: chain A residue 2542 LEU Chi-restraints excluded: chain A residue 2648 THR Chi-restraints excluded: chain A residue 2750 GLU Chi-restraints excluded: chain B residue 964 THR Chi-restraints excluded: chain B residue 1003 HIS Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain B residue 1074 VAL Chi-restraints excluded: chain B residue 1077 ILE Chi-restraints excluded: chain B residue 1079 LEU Chi-restraints excluded: chain B residue 1136 VAL Chi-restraints excluded: chain B residue 1236 THR Chi-restraints excluded: chain B residue 1467 LEU Chi-restraints excluded: chain B residue 1563 ILE Chi-restraints excluded: chain B residue 1684 THR Chi-restraints excluded: chain B residue 1692 THR Chi-restraints excluded: chain B residue 1704 THR Chi-restraints excluded: chain B residue 1742 LEU Chi-restraints excluded: chain B residue 1750 THR Chi-restraints excluded: chain B residue 1770 LEU Chi-restraints excluded: chain B residue 1786 LEU Chi-restraints excluded: chain B residue 1794 THR Chi-restraints excluded: chain B residue 1855 ASP Chi-restraints excluded: chain B residue 1934 VAL Chi-restraints excluded: chain B residue 2040 MET Chi-restraints excluded: chain B residue 2248 LEU Chi-restraints excluded: chain B residue 2460 ASN Chi-restraints excluded: chain B residue 2494 MET Chi-restraints excluded: chain B residue 2542 LEU Chi-restraints excluded: chain B residue 2648 THR Chi-restraints excluded: chain B residue 2750 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 141 optimal weight: 0.7980 chunk 225 optimal weight: 0.8980 chunk 243 optimal weight: 6.9990 chunk 159 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 209 optimal weight: 2.9990 chunk 329 optimal weight: 0.7980 chunk 160 optimal weight: 0.7980 chunk 375 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 59 optimal weight: 8.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2132 GLN A2222 ASN A2342 GLN A2757 ASN B1477 HIS B1648 GLN ** B1668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2132 GLN B2201 GLN B2342 GLN B2757 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.148089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.111841 restraints weight = 52265.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.111014 restraints weight = 36221.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.111540 restraints weight = 37898.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.112240 restraints weight = 26643.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.113587 restraints weight = 22968.427| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 31322 Z= 0.112 Angle : 0.636 11.583 42532 Z= 0.326 Chirality : 0.047 0.335 4746 Planarity : 0.004 0.057 5474 Dihedral : 5.802 59.045 4842 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.01 % Allowed : 14.31 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.13), residues: 3788 helix: 1.70 (0.38), residues: 206 sheet: 0.32 (0.15), residues: 1194 loop : -1.02 (0.13), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B1857 TYR 0.020 0.001 TYR B2025 PHE 0.011 0.001 PHE B2002 TRP 0.025 0.001 TRP B1105 HIS 0.022 0.001 HIS A 984 Details of bonding type rmsd covalent geometry : bond 0.00247 (31270) covalent geometry : angle 0.62062 (42398) SS BOND : bond 0.00183 ( 22) SS BOND : angle 1.85052 ( 44) hydrogen bonds : bond 0.03645 ( 1002) hydrogen bonds : angle 4.82556 ( 3546) link_BETA1-4 : bond 0.00443 ( 8) link_BETA1-4 : angle 1.32227 ( 24) link_NAG-ASN : bond 0.00548 ( 22) link_NAG-ASN : angle 3.27503 ( 66) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7576 Ramachandran restraints generated. 3788 Oldfield, 0 Emsley, 3788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7576 Ramachandran restraints generated. 3788 Oldfield, 0 Emsley, 3788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 269 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1089 MET cc_start: 0.7686 (ptp) cc_final: 0.7475 (pmm) REVERT: A 1356 ASP cc_start: 0.8270 (t70) cc_final: 0.7691 (p0) REVERT: A 1371 ARG cc_start: 0.6707 (mpp-170) cc_final: 0.6458 (mpp80) REVERT: A 1549 GLU cc_start: 0.6913 (pt0) cc_final: 0.6710 (tt0) REVERT: A 1853 TYR cc_start: 0.8309 (p90) cc_final: 0.7990 (p90) REVERT: A 1958 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.8078 (mtm) REVERT: A 2209 ASP cc_start: 0.6916 (t70) cc_final: 0.6597 (t70) REVERT: A 2301 SER cc_start: 0.7798 (p) cc_final: 0.7462 (m) REVERT: A 2468 MET cc_start: 0.7502 (tmt) cc_final: 0.7045 (tmt) REVERT: A 2531 LYS cc_start: 0.8205 (tppt) cc_final: 0.7905 (tptp) REVERT: B 1371 ARG cc_start: 0.6702 (mpp-170) cc_final: 0.6489 (mpp80) REVERT: B 1498 THR cc_start: 0.9040 (OUTLIER) cc_final: 0.8815 (p) REVERT: B 1504 SER cc_start: 0.7795 (m) cc_final: 0.7563 (p) REVERT: B 1853 TYR cc_start: 0.8314 (p90) cc_final: 0.8013 (p90) REVERT: B 2209 ASP cc_start: 0.6832 (t70) cc_final: 0.6504 (t70) REVERT: B 2301 SER cc_start: 0.7799 (p) cc_final: 0.7463 (m) REVERT: B 2468 MET cc_start: 0.7549 (tmt) cc_final: 0.7105 (tmt) REVERT: B 2531 LYS cc_start: 0.8203 (tppt) cc_final: 0.7943 (tptp) outliers start: 67 outliers final: 41 residues processed: 323 average time/residue: 0.1773 time to fit residues: 95.6725 Evaluate side-chains 291 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 248 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 961 ASP Chi-restraints excluded: chain A residue 984 HIS Chi-restraints excluded: chain A residue 1077 ILE Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1555 LEU Chi-restraints excluded: chain A residue 1750 THR Chi-restraints excluded: chain A residue 1770 LEU Chi-restraints excluded: chain A residue 1934 VAL Chi-restraints excluded: chain A residue 1958 MET Chi-restraints excluded: chain A residue 2248 LEU Chi-restraints excluded: chain A residue 2334 ILE Chi-restraints excluded: chain A residue 2460 ASN Chi-restraints excluded: chain A residue 2494 MET Chi-restraints excluded: chain A residue 2542 LEU Chi-restraints excluded: chain A residue 2582 ASP Chi-restraints excluded: chain A residue 2659 ARG Chi-restraints excluded: chain A residue 2750 GLU Chi-restraints excluded: chain B residue 1003 HIS Chi-restraints excluded: chain B residue 1077 ILE Chi-restraints excluded: chain B residue 1079 LEU Chi-restraints excluded: chain B residue 1094 MET Chi-restraints excluded: chain B residue 1136 VAL Chi-restraints excluded: chain B residue 1236 THR Chi-restraints excluded: chain B residue 1467 LEU Chi-restraints excluded: chain B residue 1498 THR Chi-restraints excluded: chain B residue 1742 LEU Chi-restraints excluded: chain B residue 1750 THR Chi-restraints excluded: chain B residue 1770 LEU Chi-restraints excluded: chain B residue 1794 THR Chi-restraints excluded: chain B residue 1900 ILE Chi-restraints excluded: chain B residue 1934 VAL Chi-restraints excluded: chain B residue 2040 MET Chi-restraints excluded: chain B residue 2181 LEU Chi-restraints excluded: chain B residue 2248 LEU Chi-restraints excluded: chain B residue 2460 ASN Chi-restraints excluded: chain B residue 2494 MET Chi-restraints excluded: chain B residue 2542 LEU Chi-restraints excluded: chain B residue 2582 ASP Chi-restraints excluded: chain B residue 2659 ARG Chi-restraints excluded: chain B residue 2750 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 172 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 229 optimal weight: 20.0000 chunk 143 optimal weight: 2.9990 chunk 201 optimal weight: 0.5980 chunk 242 optimal weight: 20.0000 chunk 155 optimal weight: 0.5980 chunk 299 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 319 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1125 ASN ** A1668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2222 ASN B1221 ASN ** B1668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2222 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.146618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.110195 restraints weight = 52381.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.109129 restraints weight = 36889.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.109454 restraints weight = 40909.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.110543 restraints weight = 27796.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.111780 restraints weight = 23345.109| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 31322 Z= 0.165 Angle : 0.650 11.388 42532 Z= 0.331 Chirality : 0.047 0.323 4746 Planarity : 0.004 0.050 5474 Dihedral : 5.719 58.688 4842 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 1.95 % Allowed : 14.85 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.13), residues: 3788 helix: 1.73 (0.38), residues: 208 sheet: 0.31 (0.15), residues: 1218 loop : -1.01 (0.13), residues: 2362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2233 TYR 0.018 0.001 TYR A2025 PHE 0.013 0.001 PHE B1106 TRP 0.021 0.001 TRP A1105 HIS 0.007 0.001 HIS B2438 Details of bonding type rmsd covalent geometry : bond 0.00387 (31270) covalent geometry : angle 0.63534 (42398) SS BOND : bond 0.00189 ( 22) SS BOND : angle 1.82159 ( 44) hydrogen bonds : bond 0.03895 ( 1002) hydrogen bonds : angle 4.76809 ( 3546) link_BETA1-4 : bond 0.00314 ( 8) link_BETA1-4 : angle 1.37239 ( 24) link_NAG-ASN : bond 0.00542 ( 22) link_NAG-ASN : angle 3.20334 ( 66) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7576 Ramachandran restraints generated. 3788 Oldfield, 0 Emsley, 3788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7576 Ramachandran restraints generated. 3788 Oldfield, 0 Emsley, 3788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 260 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1089 MET cc_start: 0.7761 (ptp) cc_final: 0.7482 (pmm) REVERT: A 1112 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7457 (mm) REVERT: A 1356 ASP cc_start: 0.8281 (t70) cc_final: 0.7701 (p0) REVERT: A 1371 ARG cc_start: 0.6748 (mpp-170) cc_final: 0.6454 (mpp80) REVERT: A 1549 GLU cc_start: 0.6955 (pt0) cc_final: 0.6721 (tt0) REVERT: A 1563 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8376 (mp) REVERT: A 1853 TYR cc_start: 0.8316 (p90) cc_final: 0.8013 (p90) REVERT: A 2209 ASP cc_start: 0.6983 (t70) cc_final: 0.6651 (t70) REVERT: A 2301 SER cc_start: 0.7776 (p) cc_final: 0.7478 (m) REVERT: A 2531 LYS cc_start: 0.8272 (tppt) cc_final: 0.8054 (tmtt) REVERT: B 1125 ASN cc_start: 0.8369 (m-40) cc_final: 0.8104 (p0) REVERT: B 1370 ARG cc_start: 0.7325 (mmt90) cc_final: 0.6930 (mmt90) REVERT: B 1371 ARG cc_start: 0.6783 (mpp-170) cc_final: 0.6529 (mpp80) REVERT: B 1498 THR cc_start: 0.9056 (OUTLIER) cc_final: 0.8840 (p) REVERT: B 1504 SER cc_start: 0.7863 (m) cc_final: 0.7610 (p) REVERT: B 1853 TYR cc_start: 0.8333 (p90) cc_final: 0.8038 (p90) REVERT: B 2209 ASP cc_start: 0.6971 (t70) cc_final: 0.6644 (t70) REVERT: B 2301 SER cc_start: 0.7786 (p) cc_final: 0.7481 (m) REVERT: B 2468 MET cc_start: 0.7542 (tmt) cc_final: 0.7033 (tmt) REVERT: B 2531 LYS cc_start: 0.8231 (tppt) cc_final: 0.7954 (tptp) outliers start: 65 outliers final: 47 residues processed: 311 average time/residue: 0.1748 time to fit residues: 90.2006 Evaluate side-chains 297 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 247 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 961 ASP Chi-restraints excluded: chain A residue 984 HIS Chi-restraints excluded: chain A residue 1077 ILE Chi-restraints excluded: chain A residue 1112 LEU Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1486 THR Chi-restraints excluded: chain A residue 1563 ILE Chi-restraints excluded: chain A residue 1622 THR Chi-restraints excluded: chain A residue 1750 THR Chi-restraints excluded: chain A residue 1770 LEU Chi-restraints excluded: chain A residue 1855 ASP Chi-restraints excluded: chain A residue 1900 ILE Chi-restraints excluded: chain A residue 1934 VAL Chi-restraints excluded: chain A residue 2181 LEU Chi-restraints excluded: chain A residue 2224 HIS Chi-restraints excluded: chain A residue 2248 LEU Chi-restraints excluded: chain A residue 2334 ILE Chi-restraints excluded: chain A residue 2460 ASN Chi-restraints excluded: chain A residue 2494 MET Chi-restraints excluded: chain A residue 2542 LEU Chi-restraints excluded: chain A residue 2659 ARG Chi-restraints excluded: chain A residue 2750 GLU Chi-restraints excluded: chain B residue 961 ASP Chi-restraints excluded: chain B residue 1077 ILE Chi-restraints excluded: chain B residue 1079 LEU Chi-restraints excluded: chain B residue 1094 MET Chi-restraints excluded: chain B residue 1136 VAL Chi-restraints excluded: chain B residue 1236 THR Chi-restraints excluded: chain B residue 1438 VAL Chi-restraints excluded: chain B residue 1467 LEU Chi-restraints excluded: chain B residue 1498 THR Chi-restraints excluded: chain B residue 1742 LEU Chi-restraints excluded: chain B residue 1750 THR Chi-restraints excluded: chain B residue 1770 LEU Chi-restraints excluded: chain B residue 1794 THR Chi-restraints excluded: chain B residue 1900 ILE Chi-restraints excluded: chain B residue 1934 VAL Chi-restraints excluded: chain B residue 1958 MET Chi-restraints excluded: chain B residue 2040 MET Chi-restraints excluded: chain B residue 2181 LEU Chi-restraints excluded: chain B residue 2224 HIS Chi-restraints excluded: chain B residue 2248 LEU Chi-restraints excluded: chain B residue 2460 ASN Chi-restraints excluded: chain B residue 2494 MET Chi-restraints excluded: chain B residue 2542 LEU Chi-restraints excluded: chain B residue 2582 ASP Chi-restraints excluded: chain B residue 2659 ARG Chi-restraints excluded: chain B residue 2750 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 186 optimal weight: 7.9990 chunk 326 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 121 optimal weight: 6.9990 chunk 141 optimal weight: 4.9990 chunk 212 optimal weight: 2.9990 chunk 225 optimal weight: 5.9990 chunk 294 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 286 optimal weight: 0.1980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1221 ASN ** A1668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2222 ASN A2224 HIS ** B1668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1942 GLN B2222 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.147762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.111466 restraints weight = 52363.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.110665 restraints weight = 36735.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.111217 restraints weight = 37370.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.111765 restraints weight = 26736.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.112479 restraints weight = 23054.721| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31322 Z= 0.129 Angle : 0.621 11.348 42532 Z= 0.316 Chirality : 0.046 0.315 4746 Planarity : 0.004 0.052 5474 Dihedral : 5.518 58.847 4842 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.10 % Allowed : 15.03 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.14), residues: 3788 helix: 1.66 (0.38), residues: 218 sheet: 0.47 (0.15), residues: 1216 loop : -0.93 (0.13), residues: 2354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A2233 TYR 0.018 0.001 TYR B2025 PHE 0.013 0.001 PHE A2356 TRP 0.031 0.001 TRP A1105 HIS 0.006 0.001 HIS B2438 Details of bonding type rmsd covalent geometry : bond 0.00298 (31270) covalent geometry : angle 0.60781 (42398) SS BOND : bond 0.00148 ( 22) SS BOND : angle 1.38442 ( 44) hydrogen bonds : bond 0.03591 ( 1002) hydrogen bonds : angle 4.61084 ( 3546) link_BETA1-4 : bond 0.00340 ( 8) link_BETA1-4 : angle 1.29919 ( 24) link_NAG-ASN : bond 0.00540 ( 22) link_NAG-ASN : angle 3.07310 ( 66) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7576 Ramachandran restraints generated. 3788 Oldfield, 0 Emsley, 3788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7576 Ramachandran restraints generated. 3788 Oldfield, 0 Emsley, 3788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 277 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1089 MET cc_start: 0.7702 (ptp) cc_final: 0.7451 (pmm) REVERT: A 1112 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7578 (mm) REVERT: A 1356 ASP cc_start: 0.8275 (t70) cc_final: 0.7708 (p0) REVERT: A 1371 ARG cc_start: 0.6721 (mpp-170) cc_final: 0.6444 (mpp80) REVERT: A 1549 GLU cc_start: 0.6950 (pt0) cc_final: 0.6736 (tt0) REVERT: A 1563 ILE cc_start: 0.8600 (OUTLIER) cc_final: 0.8391 (mp) REVERT: A 1853 TYR cc_start: 0.8229 (p90) cc_final: 0.7973 (p90) REVERT: A 2209 ASP cc_start: 0.6984 (t70) cc_final: 0.6636 (t70) REVERT: A 2301 SER cc_start: 0.7710 (p) cc_final: 0.7442 (m) REVERT: A 2468 MET cc_start: 0.7521 (tmt) cc_final: 0.7062 (tmt) REVERT: A 2531 LYS cc_start: 0.8266 (tppt) cc_final: 0.8040 (tmtt) REVERT: B 1125 ASN cc_start: 0.8369 (m-40) cc_final: 0.8011 (p0) REVERT: B 1356 ASP cc_start: 0.8305 (t70) cc_final: 0.7708 (p0) REVERT: B 1370 ARG cc_start: 0.7362 (mmt90) cc_final: 0.6982 (mmt90) REVERT: B 1371 ARG cc_start: 0.6819 (mpp-170) cc_final: 0.6562 (mpp80) REVERT: B 1504 SER cc_start: 0.7850 (m) cc_final: 0.7617 (p) REVERT: B 1853 TYR cc_start: 0.8268 (p90) cc_final: 0.7986 (p90) REVERT: B 2209 ASP cc_start: 0.6963 (t70) cc_final: 0.6642 (t70) REVERT: B 2301 SER cc_start: 0.7723 (p) cc_final: 0.7441 (m) REVERT: B 2468 MET cc_start: 0.7531 (tmt) cc_final: 0.7062 (tmt) REVERT: B 2531 LYS cc_start: 0.8232 (tppt) cc_final: 0.7973 (tptp) outliers start: 70 outliers final: 53 residues processed: 331 average time/residue: 0.1735 time to fit residues: 96.0937 Evaluate side-chains 312 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 257 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 961 ASP Chi-restraints excluded: chain A residue 1077 ILE Chi-restraints excluded: chain A residue 1112 LEU Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain A residue 1260 VAL Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1486 THR Chi-restraints excluded: chain A residue 1563 ILE Chi-restraints excluded: chain A residue 1622 THR Chi-restraints excluded: chain A residue 1719 ASP Chi-restraints excluded: chain A residue 1750 THR Chi-restraints excluded: chain A residue 1770 LEU Chi-restraints excluded: chain A residue 1855 ASP Chi-restraints excluded: chain A residue 1900 ILE Chi-restraints excluded: chain A residue 1934 VAL Chi-restraints excluded: chain A residue 1958 MET Chi-restraints excluded: chain A residue 2181 LEU Chi-restraints excluded: chain A residue 2224 HIS Chi-restraints excluded: chain A residue 2248 LEU Chi-restraints excluded: chain A residue 2334 ILE Chi-restraints excluded: chain A residue 2460 ASN Chi-restraints excluded: chain A residue 2494 MET Chi-restraints excluded: chain A residue 2542 LEU Chi-restraints excluded: chain A residue 2582 ASP Chi-restraints excluded: chain A residue 2648 THR Chi-restraints excluded: chain A residue 2659 ARG Chi-restraints excluded: chain A residue 2750 GLU Chi-restraints excluded: chain B residue 961 ASP Chi-restraints excluded: chain B residue 1079 LEU Chi-restraints excluded: chain B residue 1094 MET Chi-restraints excluded: chain B residue 1136 VAL Chi-restraints excluded: chain B residue 1236 THR Chi-restraints excluded: chain B residue 1423 VAL Chi-restraints excluded: chain B residue 1438 VAL Chi-restraints excluded: chain B residue 1467 LEU Chi-restraints excluded: chain B residue 1486 THR Chi-restraints excluded: chain B residue 1742 LEU Chi-restraints excluded: chain B residue 1750 THR Chi-restraints excluded: chain B residue 1770 LEU Chi-restraints excluded: chain B residue 1794 THR Chi-restraints excluded: chain B residue 1801 THR Chi-restraints excluded: chain B residue 1900 ILE Chi-restraints excluded: chain B residue 1934 VAL Chi-restraints excluded: chain B residue 1958 MET Chi-restraints excluded: chain B residue 2040 MET Chi-restraints excluded: chain B residue 2181 LEU Chi-restraints excluded: chain B residue 2248 LEU Chi-restraints excluded: chain B residue 2460 ASN Chi-restraints excluded: chain B residue 2494 MET Chi-restraints excluded: chain B residue 2542 LEU Chi-restraints excluded: chain B residue 2582 ASP Chi-restraints excluded: chain B residue 2659 ARG Chi-restraints excluded: chain B residue 2750 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 327 optimal weight: 4.9990 chunk 176 optimal weight: 5.9990 chunk 225 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 68 optimal weight: 8.9990 chunk 45 optimal weight: 9.9990 chunk 175 optimal weight: 2.9990 chunk 92 optimal weight: 9.9990 chunk 378 optimal weight: 3.9990 chunk 326 optimal weight: 0.5980 chunk 57 optimal weight: 6.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1003 HIS ** B1785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.145902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.109544 restraints weight = 52624.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.107808 restraints weight = 35896.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.108444 restraints weight = 40243.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.109369 restraints weight = 27725.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.110643 restraints weight = 23880.685| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 31322 Z= 0.209 Angle : 0.674 11.722 42532 Z= 0.343 Chirality : 0.048 0.313 4746 Planarity : 0.004 0.049 5474 Dihedral : 5.704 58.922 4842 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.07 % Allowed : 15.60 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.14), residues: 3788 helix: 1.48 (0.37), residues: 220 sheet: 0.31 (0.15), residues: 1236 loop : -1.00 (0.13), residues: 2332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A2233 TYR 0.020 0.002 TYR B2025 PHE 0.015 0.001 PHE B1106 TRP 0.032 0.001 TRP A1105 HIS 0.014 0.001 HIS A2224 Details of bonding type rmsd covalent geometry : bond 0.00496 (31270) covalent geometry : angle 0.66171 (42398) SS BOND : bond 0.00219 ( 22) SS BOND : angle 1.11943 ( 44) hydrogen bonds : bond 0.04082 ( 1002) hydrogen bonds : angle 4.75628 ( 3546) link_BETA1-4 : bond 0.00322 ( 8) link_BETA1-4 : angle 1.43002 ( 24) link_NAG-ASN : bond 0.00561 ( 22) link_NAG-ASN : angle 3.10159 ( 66) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7576 Ramachandran restraints generated. 3788 Oldfield, 0 Emsley, 3788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7576 Ramachandran restraints generated. 3788 Oldfield, 0 Emsley, 3788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 257 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 973 ARG cc_start: 0.7407 (ttp-170) cc_final: 0.7130 (ttp-110) REVERT: A 1356 ASP cc_start: 0.8269 (t70) cc_final: 0.7703 (p0) REVERT: A 1371 ARG cc_start: 0.6850 (mpp-170) cc_final: 0.6498 (mpp80) REVERT: A 1549 GLU cc_start: 0.6980 (pt0) cc_final: 0.6774 (tt0) REVERT: A 1563 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8363 (mp) REVERT: A 1853 TYR cc_start: 0.8315 (p90) cc_final: 0.8032 (p90) REVERT: A 2094 MET cc_start: 0.8026 (ttp) cc_final: 0.7620 (ttp) REVERT: A 2209 ASP cc_start: 0.7103 (t70) cc_final: 0.6759 (t70) REVERT: A 2301 SER cc_start: 0.7780 (p) cc_final: 0.7502 (m) REVERT: A 2531 LYS cc_start: 0.8318 (tppt) cc_final: 0.7984 (ttpt) REVERT: B 1125 ASN cc_start: 0.8402 (m-40) cc_final: 0.8040 (p0) REVERT: B 1356 ASP cc_start: 0.8291 (t70) cc_final: 0.7687 (p0) REVERT: B 1370 ARG cc_start: 0.7488 (mmt90) cc_final: 0.6905 (mmt90) REVERT: B 1504 SER cc_start: 0.7936 (m) cc_final: 0.7636 (p) REVERT: B 1592 THR cc_start: 0.8079 (p) cc_final: 0.7816 (t) REVERT: B 1853 TYR cc_start: 0.8377 (p90) cc_final: 0.8061 (p90) REVERT: B 2209 ASP cc_start: 0.7053 (t70) cc_final: 0.6718 (t70) REVERT: B 2301 SER cc_start: 0.7873 (p) cc_final: 0.7623 (m) REVERT: B 2531 LYS cc_start: 0.8258 (tppt) cc_final: 0.7984 (tptp) outliers start: 69 outliers final: 59 residues processed: 312 average time/residue: 0.1755 time to fit residues: 91.0173 Evaluate side-chains 307 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 247 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 961 ASP Chi-restraints excluded: chain A residue 1077 ILE Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain A residue 1260 VAL Chi-restraints excluded: chain A residue 1423 VAL Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1486 THR Chi-restraints excluded: chain A residue 1563 ILE Chi-restraints excluded: chain A residue 1622 THR Chi-restraints excluded: chain A residue 1719 ASP Chi-restraints excluded: chain A residue 1750 THR Chi-restraints excluded: chain A residue 1770 LEU Chi-restraints excluded: chain A residue 1855 ASP Chi-restraints excluded: chain A residue 1900 ILE Chi-restraints excluded: chain A residue 1934 VAL Chi-restraints excluded: chain A residue 1958 MET Chi-restraints excluded: chain A residue 2181 LEU Chi-restraints excluded: chain A residue 2224 HIS Chi-restraints excluded: chain A residue 2248 LEU Chi-restraints excluded: chain A residue 2334 ILE Chi-restraints excluded: chain A residue 2460 ASN Chi-restraints excluded: chain A residue 2494 MET Chi-restraints excluded: chain A residue 2519 ILE Chi-restraints excluded: chain A residue 2542 LEU Chi-restraints excluded: chain A residue 2582 ASP Chi-restraints excluded: chain A residue 2648 THR Chi-restraints excluded: chain A residue 2659 ARG Chi-restraints excluded: chain A residue 2750 GLU Chi-restraints excluded: chain B residue 961 ASP Chi-restraints excluded: chain B residue 1003 HIS Chi-restraints excluded: chain B residue 1037 GLU Chi-restraints excluded: chain B residue 1079 LEU Chi-restraints excluded: chain B residue 1136 VAL Chi-restraints excluded: chain B residue 1236 THR Chi-restraints excluded: chain B residue 1260 VAL Chi-restraints excluded: chain B residue 1423 VAL Chi-restraints excluded: chain B residue 1438 VAL Chi-restraints excluded: chain B residue 1467 LEU Chi-restraints excluded: chain B residue 1486 THR Chi-restraints excluded: chain B residue 1742 LEU Chi-restraints excluded: chain B residue 1750 THR Chi-restraints excluded: chain B residue 1770 LEU Chi-restraints excluded: chain B residue 1794 THR Chi-restraints excluded: chain B residue 1801 THR Chi-restraints excluded: chain B residue 1900 ILE Chi-restraints excluded: chain B residue 1934 VAL Chi-restraints excluded: chain B residue 1958 MET Chi-restraints excluded: chain B residue 1968 THR Chi-restraints excluded: chain B residue 2040 MET Chi-restraints excluded: chain B residue 2181 LEU Chi-restraints excluded: chain B residue 2248 LEU Chi-restraints excluded: chain B residue 2460 ASN Chi-restraints excluded: chain B residue 2494 MET Chi-restraints excluded: chain B residue 2542 LEU Chi-restraints excluded: chain B residue 2582 ASP Chi-restraints excluded: chain B residue 2648 THR Chi-restraints excluded: chain B residue 2659 ARG Chi-restraints excluded: chain B residue 2750 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 167 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 201 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 163 optimal weight: 0.0370 chunk 365 optimal weight: 0.9990 chunk 368 optimal weight: 1.9990 chunk 151 optimal weight: 5.9990 chunk 189 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 overall best weight: 0.7862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1557 ASN ** A1668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2224 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.148627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.112281 restraints weight = 52017.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.111878 restraints weight = 35843.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.112184 restraints weight = 37624.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.113092 restraints weight = 25747.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.114138 restraints weight = 21742.956| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 31322 Z= 0.110 Angle : 0.631 12.276 42532 Z= 0.320 Chirality : 0.046 0.304 4746 Planarity : 0.004 0.052 5474 Dihedral : 5.452 58.872 4842 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.65 % Allowed : 16.27 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.14), residues: 3788 helix: 1.79 (0.38), residues: 218 sheet: 0.52 (0.15), residues: 1216 loop : -0.88 (0.13), residues: 2354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B1002 TYR 0.017 0.001 TYR B2025 PHE 0.017 0.001 PHE B1116 TRP 0.034 0.001 TRP A1105 HIS 0.015 0.001 HIS B1003 Details of bonding type rmsd covalent geometry : bond 0.00247 (31270) covalent geometry : angle 0.61904 (42398) SS BOND : bond 0.00323 ( 22) SS BOND : angle 1.23344 ( 44) hydrogen bonds : bond 0.03432 ( 1002) hydrogen bonds : angle 4.54607 ( 3546) link_BETA1-4 : bond 0.00388 ( 8) link_BETA1-4 : angle 1.27946 ( 24) link_NAG-ASN : bond 0.00550 ( 22) link_NAG-ASN : angle 3.00333 ( 66) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7576 Ramachandran restraints generated. 3788 Oldfield, 0 Emsley, 3788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7576 Ramachandran restraints generated. 3788 Oldfield, 0 Emsley, 3788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 270 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1356 ASP cc_start: 0.8250 (t70) cc_final: 0.7707 (p0) REVERT: A 1371 ARG cc_start: 0.6780 (mpp-170) cc_final: 0.6495 (mpp80) REVERT: A 1411 ASP cc_start: 0.7928 (m-30) cc_final: 0.7567 (m-30) REVERT: A 1549 GLU cc_start: 0.6966 (pt0) cc_final: 0.6749 (tt0) REVERT: A 1563 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8366 (mp) REVERT: A 1853 TYR cc_start: 0.8228 (p90) cc_final: 0.7981 (p90) REVERT: A 2209 ASP cc_start: 0.6937 (t70) cc_final: 0.6616 (t70) REVERT: A 2301 SER cc_start: 0.7746 (p) cc_final: 0.7535 (m) REVERT: A 2468 MET cc_start: 0.7468 (tmt) cc_final: 0.6994 (tmt) REVERT: A 2531 LYS cc_start: 0.8237 (tppt) cc_final: 0.8025 (tmtt) REVERT: B 1125 ASN cc_start: 0.8325 (m-40) cc_final: 0.8036 (p0) REVERT: B 1356 ASP cc_start: 0.8278 (t70) cc_final: 0.7708 (p0) REVERT: B 1370 ARG cc_start: 0.7460 (mmt90) cc_final: 0.7102 (mmt90) REVERT: B 1371 ARG cc_start: 0.6475 (mpp80) cc_final: 0.6215 (mpp80) REVERT: B 1504 SER cc_start: 0.7889 (m) cc_final: 0.7644 (p) REVERT: B 1592 THR cc_start: 0.8014 (p) cc_final: 0.7801 (t) REVERT: B 1853 TYR cc_start: 0.8291 (p90) cc_final: 0.8008 (p90) REVERT: B 2209 ASP cc_start: 0.6887 (t70) cc_final: 0.6554 (t70) REVERT: B 2301 SER cc_start: 0.7773 (p) cc_final: 0.7538 (m) REVERT: B 2468 MET cc_start: 0.7505 (tmt) cc_final: 0.6993 (tmt) REVERT: B 2531 LYS cc_start: 0.8220 (tppt) cc_final: 0.7962 (tptp) outliers start: 55 outliers final: 49 residues processed: 315 average time/residue: 0.1703 time to fit residues: 90.0157 Evaluate side-chains 306 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 256 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 961 ASP Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain A residue 1260 VAL Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1486 THR Chi-restraints excluded: chain A residue 1563 ILE Chi-restraints excluded: chain A residue 1622 THR Chi-restraints excluded: chain A residue 1719 ASP Chi-restraints excluded: chain A residue 1750 THR Chi-restraints excluded: chain A residue 1770 LEU Chi-restraints excluded: chain A residue 1801 THR Chi-restraints excluded: chain A residue 1900 ILE Chi-restraints excluded: chain A residue 1934 VAL Chi-restraints excluded: chain A residue 2181 LEU Chi-restraints excluded: chain A residue 2248 LEU Chi-restraints excluded: chain A residue 2334 ILE Chi-restraints excluded: chain A residue 2460 ASN Chi-restraints excluded: chain A residue 2494 MET Chi-restraints excluded: chain A residue 2542 LEU Chi-restraints excluded: chain A residue 2582 ASP Chi-restraints excluded: chain A residue 2648 THR Chi-restraints excluded: chain A residue 2659 ARG Chi-restraints excluded: chain A residue 2750 GLU Chi-restraints excluded: chain B residue 961 ASP Chi-restraints excluded: chain B residue 1003 HIS Chi-restraints excluded: chain B residue 1077 ILE Chi-restraints excluded: chain B residue 1136 VAL Chi-restraints excluded: chain B residue 1236 THR Chi-restraints excluded: chain B residue 1423 VAL Chi-restraints excluded: chain B residue 1438 VAL Chi-restraints excluded: chain B residue 1467 LEU Chi-restraints excluded: chain B residue 1486 THR Chi-restraints excluded: chain B residue 1742 LEU Chi-restraints excluded: chain B residue 1750 THR Chi-restraints excluded: chain B residue 1770 LEU Chi-restraints excluded: chain B residue 1794 THR Chi-restraints excluded: chain B residue 1801 THR Chi-restraints excluded: chain B residue 1900 ILE Chi-restraints excluded: chain B residue 1934 VAL Chi-restraints excluded: chain B residue 2181 LEU Chi-restraints excluded: chain B residue 2224 HIS Chi-restraints excluded: chain B residue 2248 LEU Chi-restraints excluded: chain B residue 2460 ASN Chi-restraints excluded: chain B residue 2494 MET Chi-restraints excluded: chain B residue 2542 LEU Chi-restraints excluded: chain B residue 2582 ASP Chi-restraints excluded: chain B residue 2648 THR Chi-restraints excluded: chain B residue 2659 ARG Chi-restraints excluded: chain B residue 2750 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 210 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 366 optimal weight: 1.9990 chunk 311 optimal weight: 6.9990 chunk 193 optimal weight: 0.0070 chunk 324 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 155 optimal weight: 3.9990 chunk 44 optimal weight: 20.0000 chunk 48 optimal weight: 7.9990 chunk 169 optimal weight: 3.9990 overall best weight: 1.5002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2155 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.148428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.112645 restraints weight = 52285.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.111923 restraints weight = 36263.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.112238 restraints weight = 39739.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.113151 restraints weight = 27012.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.114476 restraints weight = 22758.935| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31322 Z= 0.130 Angle : 0.631 13.067 42532 Z= 0.319 Chirality : 0.046 0.302 4746 Planarity : 0.004 0.051 5474 Dihedral : 5.418 58.745 4842 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.62 % Allowed : 16.30 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.14), residues: 3788 helix: 1.81 (0.38), residues: 218 sheet: 0.51 (0.15), residues: 1236 loop : -0.87 (0.13), residues: 2334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A2233 TYR 0.016 0.001 TYR A1140 PHE 0.016 0.001 PHE B1116 TRP 0.035 0.001 TRP A1105 HIS 0.011 0.001 HIS B2224 Details of bonding type rmsd covalent geometry : bond 0.00302 (31270) covalent geometry : angle 0.61912 (42398) SS BOND : bond 0.00350 ( 22) SS BOND : angle 1.01055 ( 44) hydrogen bonds : bond 0.03550 ( 1002) hydrogen bonds : angle 4.51395 ( 3546) link_BETA1-4 : bond 0.00324 ( 8) link_BETA1-4 : angle 1.29275 ( 24) link_NAG-ASN : bond 0.00527 ( 22) link_NAG-ASN : angle 2.96330 ( 66) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4393.50 seconds wall clock time: 77 minutes 5.09 seconds (4625.09 seconds total)