Starting phenix.real_space_refine on Fri Mar 6 13:28:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ban_12125/03_2026/7ban_12125.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ban_12125/03_2026/7ban_12125.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ban_12125/03_2026/7ban_12125.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ban_12125/03_2026/7ban_12125.map" model { file = "/net/cci-nas-00/data/ceres_data/7ban_12125/03_2026/7ban_12125.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ban_12125/03_2026/7ban_12125.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 148 5.16 5 C 19270 2.51 5 N 5280 2.21 5 O 5908 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: 7.96, per 1000 atoms: 0.26 Number of scatterers: 30612 At special positions: 0 Unit cell: (192.818, 169.242, 121.248, 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 148 16.00 O 5908 8.00 N 5280 7.00 C 19270 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=23, 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=2.03 Simple disulfide: pdb=" SG CYS A1035 " - pdb=" SG CYS A2524 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A2585 " - pdb=" SG CYS B2585 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B1035 " - pdb=" SG CYS B2524 " distance=2.04 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=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG 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: 2.75 Conformation dependent library (CDL) restraints added in 1.4 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 46 sheets defined 10.0% alpha, 40.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.42 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 894 through 900 removed outlier: 3.618A pdb=" N ILE A 898 " --> pdb=" O PHE A 894 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N PHE A 900 " --> pdb=" O ASP A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 949 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: 4.377A 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 1656 through 1658 No H-bonds generated for 'chain 'A' and resid 1656 through 1658' 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 2465 through 2470 removed outlier: 3.595A pdb=" N THR A2469 " --> pdb=" O LYS A2465 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP A2470 " --> pdb=" O CYS A2466 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2465 through 2470' Processing helix chain 'A' and resid 2471 through 2479 Processing helix chain 'A' and resid 2481 through 2485 Processing helix chain 'A' and resid 2500 through 2506 Processing helix chain 'A' and resid 2506 through 2511 removed outlier: 4.050A pdb=" N GLN A2511 " --> pdb=" O GLN A2507 " (cutoff:3.500A) Processing helix chain 'A' and resid 2520 through 2533 removed outlier: 3.674A 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: 3.641A pdb=" N ARG A2592 " --> pdb=" O ASN A2588 " (cutoff:3.500A) removed outlier: 3.905A 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: 3.579A pdb=" N GLU A2686 " --> pdb=" O THR A2682 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS A2687 " --> pdb=" O LEU A2683 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU A2712 " --> pdb=" O GLN A2708 " (cutoff:3.500A) Processing helix chain 'A' and resid 2721 through 2731 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: 3.706A 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 894 through 900 removed outlier: 3.618A pdb=" N ILE B 898 " --> pdb=" O PHE B 894 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N PHE B 900 " --> pdb=" O ASP B 896 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 949 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: 4.378A 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 1656 through 1658 No H-bonds generated for 'chain 'B' and resid 1656 through 1658' 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 2465 through 2470 removed outlier: 3.595A pdb=" N THR B2469 " --> pdb=" O LYS B2465 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP B2470 " --> pdb=" O CYS B2466 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2465 through 2470' Processing helix chain 'B' and resid 2471 through 2479 Processing helix chain 'B' and resid 2481 through 2485 Processing helix chain 'B' and resid 2500 through 2506 Processing helix chain 'B' and resid 2506 through 2511 removed outlier: 4.049A pdb=" N GLN B2511 " --> pdb=" O GLN B2507 " (cutoff:3.500A) Processing helix chain 'B' and resid 2520 through 2533 removed outlier: 3.674A 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: 3.641A pdb=" N ARG B2592 " --> pdb=" O ASN B2588 " (cutoff:3.500A) removed outlier: 3.905A 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: 3.579A pdb=" N GLU B2686 " --> pdb=" O THR B2682 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS B2687 " --> pdb=" O LEU B2683 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU B2712 " --> pdb=" O GLN B2708 " (cutoff:3.500A) Processing helix chain 'B' and resid 2721 through 2731 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: 8.373A pdb=" N PHE A 994 " --> pdb=" O ALA A 921 " (cutoff:3.500A) removed outlier: 6.190A 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 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 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: 3.522A pdb=" N ALA A1553 " --> pdb=" O SER A1541 " (cutoff:3.500A) removed outlier: 4.436A 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: 6.753A 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: 4.050A pdb=" N VAL A1292 " --> pdb=" O ILE A1305 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU A1294 " --> pdb=" O PHE A1303 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA A1322 " --> pdb=" O VAL A1302 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LYS A1304 " --> pdb=" O VAL A1320 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N VAL A1320 " --> pdb=" O LYS A1304 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1350 through 1355 removed outlier: 4.993A 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: 6.070A pdb=" N ILE A1440 " --> pdb=" O GLN A1431 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N GLN A1431 " --> pdb=" O ILE A1440 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA A1442 " --> pdb=" O VAL A1429 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER A1420 " --> pdb=" O ASN A1415 " (cutoff:3.500A) removed outlier: 3.729A 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: 5.389A pdb=" N ALA A1470 " --> pdb=" O THR A1486 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N THR A1486 " --> pdb=" O ALA A1470 " (cutoff:3.500A) removed outlier: 6.381A 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: 4.020A pdb=" N PHE A1569 " --> pdb=" O GLU A1577 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N LEU A1596 " --> pdb=" O ASN A1609 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ASN A1609 " --> pdb=" O LEU A1596 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N THR A1598 " --> pdb=" O LEU A1607 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LEU A1607 " --> pdb=" O ASP A1623 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ASP A1623 " --> pdb=" O LEU A1607 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASN A1609 " --> pdb=" O ILE A1621 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ILE A1621 " --> pdb=" O ASN A1609 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N THR A1611 " --> pdb=" O THR A1619 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP A1617 " --> pdb=" O THR A1613 " (cutoff:3.500A) removed outlier: 10.594A pdb=" N ASP A1617 " --> pdb=" O ARG A1633 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N ARG A1633 " --> pdb=" O ASP A1617 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N THR A1619 " --> pdb=" O VAL A1631 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ASN A1630 " --> pdb=" O LEU A1642 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LEU A1642 " --> pdb=" O ASN A1630 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ARG A1632 " --> pdb=" O LEU A1640 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N LEU A1640 " --> pdb=" O VAL A1652 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N TRP A1651 " --> pdb=" O VAL A1663 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N VAL A1663 " --> pdb=" O TRP A1651 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THR A1653 " --> pdb=" O LYS A1661 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N LYS A1661 " --> pdb=" O MET A1673 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N MET A1672 " --> pdb=" O LYS A1685 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LYS A1685 " --> pdb=" O MET A1672 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR A1674 " --> pdb=" O ALA A1683 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU A1681 " --> pdb=" O HIS A1676 " (cutoff:3.500A) removed outlier: 10.485A pdb=" N LEU A1681 " --> pdb=" O TYR A1697 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N TYR A1697 " --> pdb=" O LEU A1681 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ALA A1683 " --> pdb=" O TYR A1695 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N PHE A1694 " --> pdb=" O VAL A1706 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N VAL A1706 " --> pdb=" O PHE A1694 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLU A1696 " --> pdb=" O THR A1704 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N THR A1704 " --> pdb=" O PHE A1716 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N VAL A1724 " --> pdb=" O THR A1740 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR A1740 " --> pdb=" O VAL A1724 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL A1826 " --> pdb=" O GLU A1818 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N THR A1825 " --> pdb=" O ASP A1844 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASP A1844 " --> pdb=" O THR A1825 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N PHE A1827 " --> pdb=" O ASP A1842 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ASP A1842 " --> pdb=" O PHE A1827 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ARG A1829 " --> pdb=" O SER A1840 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N SER A1840 " --> pdb=" O ARG A1829 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU A1831 " --> pdb=" O LEU A1838 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N THR A1860 " --> pdb=" O PRO A1876 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ARG A1862 " --> pdb=" O TRP A1874 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TRP A1874 " --> pdb=" O ARG A1862 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU A1864 " --> pdb=" O SER A1872 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1782 through 1784 Processing sheet with id=AB7, first strand: chain 'A' and resid 1883 through 1887 removed outlier: 6.754A pdb=" N ASN A1884 " --> pdb=" O ILE A1896 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE A1896 " --> pdb=" O ASN A1884 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N THR A1886 " --> pdb=" O ALA A1894 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ALA A1894 " --> pdb=" O MET A1905 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N MET A1905 " --> pdb=" O ALA A1894 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N SER A1902 " --> pdb=" O PHE A1918 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N PHE A1918 " --> pdb=" O SER A1902 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARG A1904 " --> pdb=" O ARG A1916 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ARG A1916 " --> pdb=" O ARG A1904 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLU A1906 " --> pdb=" O THR A1914 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N THR A1914 " --> pdb=" O TYR A1926 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE A1944 " --> pdb=" O VAL A1956 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL A1956 " --> pdb=" O ILE A1944 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N GLU A1946 " --> pdb=" O SER A1954 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N SER A1954 " --> pdb=" O LEU A1966 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE A1989 " --> pdb=" O THR A2001 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N THR A2001 " --> pdb=" O ILE A1989 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ASP A1991 " --> pdb=" O LEU A1999 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N LEU A1999 " --> pdb=" O TYR A2012 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE A2011 " --> pdb=" O THR A2023 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N THR A2023 " --> pdb=" O ILE A2011 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LYS A2013 " --> pdb=" O ALA A2021 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ALA A2021 " --> pdb=" O PHE A2032 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LYS A2042 " --> pdb=" O TYR A2057 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N THR A2052 " --> pdb=" O PHE A2071 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N PHE A2071 " --> pdb=" O THR A2052 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N THR A2054 " --> pdb=" O PHE A2069 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N PHE A2069 " --> pdb=" O THR A2054 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ARG A2056 " --> pdb=" O GLN A2067 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLN A2067 " --> pdb=" O ARG A2056 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ARG A2058 " --> pdb=" O ASP A2065 " (cutoff:3.500A) removed outlier: 10.674A pdb=" N LEU A2063 " --> pdb=" O TYR A2085 " (cutoff:3.500A) removed outlier: 8.868A pdb=" N TYR A2085 " --> pdb=" O LEU A2063 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ASP A2065 " --> pdb=" O TYR A2083 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ARG A2080 " --> pdb=" O ALA A2096 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ALA A2096 " --> pdb=" O ARG A2080 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ASP A2082 " --> pdb=" O MET A2094 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N MET A2094 " --> pdb=" O ASP A2082 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ASN A2084 " --> pdb=" O THR A2092 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1883 through 1887 removed outlier: 6.754A pdb=" N ASN A1884 " --> pdb=" O ILE A1896 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE A1896 " --> pdb=" O ASN A1884 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N THR A1886 " --> pdb=" O ALA A1894 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ALA A1894 " --> pdb=" O MET A1905 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N MET A1905 " --> pdb=" O ALA A1894 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N SER A1902 " --> pdb=" O PHE A1918 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N PHE A1918 " --> pdb=" O SER A1902 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARG A1904 " --> pdb=" O ARG A1916 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ARG A1916 " --> pdb=" O ARG A1904 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLU A1906 " --> pdb=" O THR A1914 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N THR A1914 " --> pdb=" O TYR A1926 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE A1944 " --> pdb=" O VAL A1956 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL A1956 " --> pdb=" O ILE A1944 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N GLU A1946 " --> pdb=" O SER A1954 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N SER A1954 " --> pdb=" O LEU A1966 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE A1989 " --> pdb=" O THR A2001 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N THR A2001 " --> pdb=" O ILE A1989 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ASP A1991 " --> pdb=" O LEU A1999 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N LEU A1999 " --> pdb=" O TYR A2012 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE A2011 " --> pdb=" O THR A2023 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N THR A2023 " --> pdb=" O ILE A2011 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LYS A2013 " --> pdb=" O ALA A2021 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ALA A2021 " --> pdb=" O PHE A2032 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LYS A2042 " --> pdb=" O TYR A2057 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N THR A2052 " --> pdb=" O PHE A2071 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N PHE A2071 " --> pdb=" O THR A2052 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N THR A2054 " --> pdb=" O PHE A2069 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N PHE A2069 " --> pdb=" O THR A2054 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ARG A2056 " --> pdb=" O GLN A2067 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLN A2067 " --> pdb=" O ARG A2056 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ARG A2058 " --> pdb=" O ASP A2065 " (cutoff:3.500A) removed outlier: 10.674A pdb=" N LEU A2063 " --> pdb=" O TYR A2085 " (cutoff:3.500A) removed outlier: 8.868A pdb=" N TYR A2085 " --> pdb=" O LEU A2063 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ASP A2065 " --> pdb=" O TYR A2083 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ARG A2080 " --> pdb=" O ALA A2096 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ALA A2096 " --> pdb=" O ARG A2080 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ASP A2082 " --> pdb=" O MET A2094 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N MET A2094 " --> pdb=" O ASP A2082 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ASN A2084 " --> pdb=" O THR A2092 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N THR A2092 " --> pdb=" O TYR A2108 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU A2107 " --> pdb=" O PHE A2120 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N PHE A2120 " --> pdb=" O LEU A2107 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ARG A2109 " --> pdb=" O GLU A2118 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N GLU A2118 " --> pdb=" O VAL A2125 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN A2132 " --> pdb=" O LYS A2143 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU A2153 " --> pdb=" O HIS A2144 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N LYS A2152 " --> pdb=" O VAL A2168 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR A2164 " --> pdb=" O TYR A2156 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE A2158 " --> pdb=" O LEU A2162 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N LEU A2162 " --> pdb=" O ILE A2158 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS A2178 " --> pdb=" O GLN A2169 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N VAL A2177 " --> pdb=" O TYR A2194 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ARG A2191 " --> pdb=" O ILE A2207 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ILE A2207 " --> pdb=" O ARG A2191 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N SER A2193 " --> pdb=" O VAL A2205 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N VAL A2205 " --> pdb=" O SER A2193 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLU A2195 " --> pdb=" O GLN A2203 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE A2207 " --> pdb=" O PRO A2211 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 2216 through 2217 removed outlier: 6.786A pdb=" N SER A2216 " --> pdb=" O HIS A2224 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N HIS A2224 " --> pdb=" O LEU A2237 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LEU A2248 " --> pdb=" O PRO A2236 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ARG A2238 " --> pdb=" O THR A2246 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N THR A2246 " --> pdb=" O TYR A2253 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLN A2252 " --> pdb=" O ARG A2264 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ARG A2264 " --> pdb=" O GLN A2252 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LYS A2254 " --> pdb=" O ARG A2262 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ARG A2262 " --> pdb=" O PHE A2269 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS A2279 " --> pdb=" O GLU A2270 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ILE A2278 " --> pdb=" O TYR A2291 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N SER A2288 " --> pdb=" O SER A2304 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N SER A2304 " --> pdb=" O SER A2288 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ARG A2290 " --> pdb=" O SER A2302 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N SER A2302 " --> pdb=" O ARG A2290 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ARG A2292 " --> pdb=" O VAL A2300 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N VAL A2300 " --> pdb=" O PHE A2312 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A2347 " --> pdb=" O TYR A2338 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N PHE A2346 " --> pdb=" O ILE A2358 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N GLU A2355 " --> pdb=" O SER A2371 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N SER A2371 " --> pdb=" O GLU A2355 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N TYR A2357 " --> pdb=" O VAL A2369 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL A2369 " --> pdb=" O TYR A2357 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ALA A2359 " --> pdb=" O LEU A2367 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N LEU A2367 " --> pdb=" O ILE A2380 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS A2378 " --> pdb=" O VAL A2369 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N SER A2371 " --> pdb=" O MET A2376 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N MET A2376 " --> pdb=" O SER A2371 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N MET A2390 " --> pdb=" O LEU A2381 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 2406 through 2408 removed outlier: 3.858A pdb=" N LEU A2413 " --> pdb=" O ASP A2408 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 2570 through 2574 Processing sheet with id=AC3, first strand: chain 'A' and resid 2602 through 2603 Processing sheet with id=AC4, first strand: chain 'A' and resid 2602 through 2603 removed outlier: 6.183A pdb=" N ASP A2615 " --> pdb=" O CYS A2674 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N ASN A2676 " --> pdb=" O ASP A2615 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N HIS A2617 " --> pdb=" O ASN A2676 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N ARG A2678 " --> pdb=" O HIS A2617 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N PHE A2619 " --> pdb=" O ARG A2678 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 2737 through 2741 Processing sheet with id=AC6, first strand: chain 'B' and resid 959 through 965 removed outlier: 8.374A pdb=" N PHE B 994 " --> pdb=" O ALA B 921 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N VAL B 923 " --> pdb=" O PHE B 994 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 959 through 965 Processing sheet with id=AC8, first strand: chain 'B' and resid 951 through 953 Processing sheet with id=AC9, first strand: chain 'B' and resid 1022 through 1025 Processing sheet with id=AD1, first strand: chain 'B' and resid 1041 through 1042 Processing sheet with id=AD2, first strand: chain 'B' and resid 1100 through 1107 Processing sheet with id=AD3, first strand: chain 'B' and resid 1178 through 1180 Processing sheet with id=AD4, first strand: chain 'B' and resid 1202 through 1203 removed outlier: 3.522A pdb=" N ALA B1553 " --> pdb=" O SER B1541 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N SER B1541 " --> pdb=" O ALA B1553 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1222 through 1223 removed outlier: 6.753A pdb=" N ILE B1251 " --> pdb=" O ILE B1263 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1283 through 1285 removed outlier: 4.051A pdb=" N VAL B1292 " --> pdb=" O ILE B1305 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU B1294 " --> pdb=" O PHE B1303 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA B1322 " --> pdb=" O VAL B1302 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LYS B1304 " --> pdb=" O VAL B1320 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N VAL B1320 " --> pdb=" O LYS B1304 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1350 through 1355 removed outlier: 4.993A pdb=" N GLY B1352 " --> pdb=" O VAL B1364 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1399 through 1400 removed outlier: 6.070A pdb=" N ILE B1440 " --> pdb=" O GLN B1431 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N GLN B1431 " --> pdb=" O ILE B1440 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA B1442 " --> pdb=" O VAL B1429 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER B1420 " --> pdb=" O ASN B1415 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASP B1411 " --> pdb=" O LEU B1424 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1470 through 1475 removed outlier: 5.389A pdb=" N ALA B1470 " --> pdb=" O THR B1486 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N THR B1486 " --> pdb=" O ALA B1470 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE B1494 " --> pdb=" O VAL B1506 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 1569 through 1570 removed outlier: 4.020A pdb=" N PHE B1569 " --> pdb=" O GLU B1577 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N LEU B1596 " --> pdb=" O ASN B1609 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ASN B1609 " --> pdb=" O LEU B1596 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N THR B1598 " --> pdb=" O LEU B1607 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LEU B1607 " --> pdb=" O ASP B1623 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ASP B1623 " --> pdb=" O LEU B1607 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASN B1609 " --> pdb=" O ILE B1621 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ILE B1621 " --> pdb=" O ASN B1609 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N THR B1611 " --> pdb=" O THR B1619 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP B1617 " --> pdb=" O THR B1613 " (cutoff:3.500A) removed outlier: 10.594A pdb=" N ASP B1617 " --> pdb=" O ARG B1633 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N ARG B1633 " --> pdb=" O ASP B1617 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N THR B1619 " --> pdb=" O VAL B1631 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ASN B1630 " --> pdb=" O LEU B1642 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU B1642 " --> pdb=" O ASN B1630 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ARG B1632 " --> pdb=" O LEU B1640 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N LEU B1640 " --> pdb=" O VAL B1652 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N TRP B1651 " --> pdb=" O VAL B1663 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N VAL B1663 " --> pdb=" O TRP B1651 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THR B1653 " --> pdb=" O LYS B1661 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N LYS B1661 " --> pdb=" O MET B1673 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N MET B1672 " --> pdb=" O LYS B1685 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LYS B1685 " --> pdb=" O MET B1672 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR B1674 " --> pdb=" O ALA B1683 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU B1681 " --> pdb=" O HIS B1676 " (cutoff:3.500A) removed outlier: 10.485A pdb=" N LEU B1681 " --> pdb=" O TYR B1697 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N TYR B1697 " --> pdb=" O LEU B1681 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ALA B1683 " --> pdb=" O TYR B1695 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N PHE B1694 " --> pdb=" O VAL B1706 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N VAL B1706 " --> pdb=" O PHE B1694 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLU B1696 " --> pdb=" O THR B1704 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N THR B1704 " --> pdb=" O PHE B1716 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N VAL B1724 " --> pdb=" O THR B1740 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR B1740 " --> pdb=" O VAL B1724 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL B1826 " --> pdb=" O GLU B1818 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N THR B1825 " --> pdb=" O ASP B1844 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASP B1844 " --> pdb=" O THR B1825 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N PHE B1827 " --> pdb=" O ASP B1842 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ASP B1842 " --> pdb=" O PHE B1827 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ARG B1829 " --> pdb=" O SER B1840 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N SER B1840 " --> pdb=" O ARG B1829 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU B1831 " --> pdb=" O LEU B1838 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N THR B1860 " --> pdb=" O PRO B1876 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ARG B1862 " --> pdb=" O TRP B1874 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TRP B1874 " --> pdb=" O ARG B1862 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU B1864 " --> pdb=" O SER B1872 " (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 1883 through 1887 removed outlier: 6.754A pdb=" N ASN B1884 " --> pdb=" O ILE B1896 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ILE B1896 " --> pdb=" O ASN B1884 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N THR B1886 " --> pdb=" O ALA B1894 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ALA B1894 " --> pdb=" O MET B1905 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N MET B1905 " --> pdb=" O ALA B1894 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N SER B1902 " --> pdb=" O PHE B1918 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N PHE B1918 " --> pdb=" O SER B1902 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ARG B1904 " --> pdb=" O ARG B1916 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ARG B1916 " --> pdb=" O ARG B1904 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLU B1906 " --> pdb=" O THR B1914 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N THR B1914 " --> pdb=" O TYR B1926 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE B1944 " --> pdb=" O VAL B1956 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N VAL B1956 " --> pdb=" O ILE B1944 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLU B1946 " --> pdb=" O SER B1954 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N SER B1954 " --> pdb=" O LEU B1966 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE B1989 " --> pdb=" O THR B2001 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N THR B2001 " --> pdb=" O ILE B1989 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ASP B1991 " --> pdb=" O LEU B1999 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N LEU B1999 " --> pdb=" O TYR B2012 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE B2011 " --> pdb=" O THR B2023 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N THR B2023 " --> pdb=" O ILE B2011 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LYS B2013 " --> pdb=" O ALA B2021 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N ALA B2021 " --> pdb=" O PHE B2032 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N LYS B2042 " --> pdb=" O TYR B2057 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N THR B2052 " --> pdb=" O PHE B2071 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N PHE B2071 " --> pdb=" O THR B2052 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N THR B2054 " --> pdb=" O PHE B2069 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N PHE B2069 " --> pdb=" O THR B2054 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ARG B2056 " --> pdb=" O GLN B2067 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLN B2067 " --> pdb=" O ARG B2056 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ARG B2058 " --> pdb=" O ASP B2065 " (cutoff:3.500A) removed outlier: 10.674A pdb=" N LEU B2063 " --> pdb=" O TYR B2085 " (cutoff:3.500A) removed outlier: 8.868A pdb=" N TYR B2085 " --> pdb=" O LEU B2063 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ASP B2065 " --> pdb=" O TYR B2083 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ARG B2080 " --> pdb=" O ALA B2096 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ALA B2096 " --> pdb=" O ARG B2080 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ASP B2082 " --> pdb=" O MET B2094 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N MET B2094 " --> pdb=" O ASP B2082 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ASN B2084 " --> pdb=" O THR B2092 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 1883 through 1887 removed outlier: 6.754A pdb=" N ASN B1884 " --> pdb=" O ILE B1896 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ILE B1896 " --> pdb=" O ASN B1884 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N THR B1886 " --> pdb=" O ALA B1894 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ALA B1894 " --> pdb=" O MET B1905 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N MET B1905 " --> pdb=" O ALA B1894 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N SER B1902 " --> pdb=" O PHE B1918 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N PHE B1918 " --> pdb=" O SER B1902 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ARG B1904 " --> pdb=" O ARG B1916 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ARG B1916 " --> pdb=" O ARG B1904 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLU B1906 " --> pdb=" O THR B1914 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N THR B1914 " --> pdb=" O TYR B1926 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE B1944 " --> pdb=" O VAL B1956 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N VAL B1956 " --> pdb=" O ILE B1944 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLU B1946 " --> pdb=" O SER B1954 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N SER B1954 " --> pdb=" O LEU B1966 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE B1989 " --> pdb=" O THR B2001 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N THR B2001 " --> pdb=" O ILE B1989 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ASP B1991 " --> pdb=" O LEU B1999 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N LEU B1999 " --> pdb=" O TYR B2012 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE B2011 " --> pdb=" O THR B2023 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N THR B2023 " --> pdb=" O ILE B2011 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LYS B2013 " --> pdb=" O ALA B2021 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N ALA B2021 " --> pdb=" O PHE B2032 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N LYS B2042 " --> pdb=" O TYR B2057 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N THR B2052 " --> pdb=" O PHE B2071 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N PHE B2071 " --> pdb=" O THR B2052 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N THR B2054 " --> pdb=" O PHE B2069 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N PHE B2069 " --> pdb=" O THR B2054 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ARG B2056 " --> pdb=" O GLN B2067 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLN B2067 " --> pdb=" O ARG B2056 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ARG B2058 " --> pdb=" O ASP B2065 " (cutoff:3.500A) removed outlier: 10.674A pdb=" N LEU B2063 " --> pdb=" O TYR B2085 " (cutoff:3.500A) removed outlier: 8.868A pdb=" N TYR B2085 " --> pdb=" O LEU B2063 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ASP B2065 " --> pdb=" O TYR B2083 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ARG B2080 " --> pdb=" O ALA B2096 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ALA B2096 " --> pdb=" O ARG B2080 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ASP B2082 " --> pdb=" O MET B2094 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N MET B2094 " --> pdb=" O ASP B2082 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ASN B2084 " --> pdb=" O THR B2092 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N THR B2092 " --> pdb=" O TYR B2108 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU B2107 " --> pdb=" O PHE B2120 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N PHE B2120 " --> pdb=" O LEU B2107 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ARG B2109 " --> pdb=" O GLU B2118 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N GLU B2118 " --> pdb=" O VAL B2125 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN B2132 " --> pdb=" O LYS B2143 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU B2153 " --> pdb=" O HIS B2144 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N LYS B2152 " --> pdb=" O VAL B2168 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR B2164 " --> pdb=" O TYR B2156 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE B2158 " --> pdb=" O LEU B2162 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N LEU B2162 " --> pdb=" O ILE B2158 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS B2178 " --> pdb=" O GLN B2169 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N VAL B2177 " --> pdb=" O TYR B2194 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ARG B2191 " --> pdb=" O ILE B2207 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ILE B2207 " --> pdb=" O ARG B2191 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N SER B2193 " --> pdb=" O VAL B2205 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N VAL B2205 " --> pdb=" O SER B2193 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLU B2195 " --> pdb=" O GLN B2203 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE B2207 " --> pdb=" O PRO B2211 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 2216 through 2217 removed outlier: 6.786A pdb=" N SER B2216 " --> pdb=" O HIS B2224 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N HIS B2224 " --> pdb=" O LEU B2237 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LEU B2248 " --> pdb=" O PRO B2236 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ARG B2238 " --> pdb=" O THR B2246 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N THR B2246 " --> pdb=" O TYR B2253 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLN B2252 " --> pdb=" O ARG B2264 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ARG B2264 " --> pdb=" O GLN B2252 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LYS B2254 " --> pdb=" O ARG B2262 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ARG B2262 " --> pdb=" O PHE B2269 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS B2279 " --> pdb=" O GLU B2270 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ILE B2278 " --> pdb=" O TYR B2291 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N SER B2288 " --> pdb=" O SER B2304 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N SER B2304 " --> pdb=" O SER B2288 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ARG B2290 " --> pdb=" O SER B2302 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N SER B2302 " --> pdb=" O ARG B2290 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ARG B2292 " --> pdb=" O VAL B2300 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N VAL B2300 " --> pdb=" O PHE B2312 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA B2347 " --> pdb=" O TYR B2338 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N PHE B2346 " --> pdb=" O ILE B2358 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N GLU B2355 " --> pdb=" O SER B2371 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N SER B2371 " --> pdb=" O GLU B2355 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N TYR B2357 " --> pdb=" O VAL B2369 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL B2369 " --> pdb=" O TYR B2357 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ALA B2359 " --> pdb=" O LEU B2367 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N LEU B2367 " --> pdb=" O ILE B2380 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS B2378 " --> pdb=" O VAL B2369 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N SER B2371 " --> pdb=" O MET B2376 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N MET B2376 " --> pdb=" O SER B2371 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N MET B2390 " --> pdb=" O LEU B2381 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 2406 through 2408 removed outlier: 3.858A pdb=" N LEU B2413 " --> pdb=" O ASP B2408 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 2570 through 2574 Processing sheet with id=AE8, first strand: chain 'B' and resid 2602 through 2603 Processing sheet with id=AE9, first strand: chain 'B' and resid 2602 through 2603 removed outlier: 6.184A pdb=" N ASP B2615 " --> pdb=" O CYS B2674 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N ASN B2676 " --> pdb=" O ASP B2615 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N HIS B2617 " --> pdb=" O ASN B2676 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ARG B2678 " --> pdb=" O HIS B2617 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N PHE B2619 " --> pdb=" O ARG B2678 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 2737 through 2741 1126 hydrogen bonds defined for protein. 2868 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: 12.62 Time building geometry restraints manager: 3.73 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: 9961 1.34 - 1.46: 6893 1.46 - 1.58: 14178 1.58 - 1.70: 0 1.70 - 1.82: 238 Bond restraints: 31270 Sorted by residual: bond pdb=" C CYS B 869 " pdb=" N LEU B 870 " ideal model delta sigma weight residual 1.329 1.380 -0.050 1.36e-02 5.41e+03 1.36e+01 bond pdb=" C CYS A 869 " pdb=" N LEU A 870 " ideal model delta sigma weight residual 1.329 1.380 -0.050 1.36e-02 5.41e+03 1.36e+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 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 9.82e+00 bond pdb=" N LEU A 859 " pdb=" CA LEU A 859 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.35e-02 5.49e+03 6.02e+00 ... (remaining 31265 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 41083 2.03 - 4.06: 1148 4.06 - 6.09: 144 6.09 - 8.12: 15 8.12 - 10.15: 8 Bond angle restraints: 42398 Sorted by residual: angle pdb=" CA LEU A 870 " pdb=" C LEU A 870 " pdb=" N GLY A 871 " ideal model delta sigma weight residual 115.49 122.67 -7.18 1.24e+00 6.50e-01 3.35e+01 angle pdb=" CA LEU B 870 " pdb=" C LEU B 870 " pdb=" N GLY B 871 " ideal model delta sigma weight residual 115.49 122.64 -7.15 1.24e+00 6.50e-01 3.33e+01 angle pdb=" O LEU A 870 " pdb=" C LEU A 870 " pdb=" N GLY A 871 " ideal model delta sigma weight residual 122.96 116.86 6.10 1.13e+00 7.83e-01 2.91e+01 angle pdb=" O LEU B 870 " pdb=" C LEU B 870 " pdb=" N GLY B 871 " ideal model delta sigma weight residual 122.96 116.90 6.06 1.13e+00 7.83e-01 2.88e+01 angle pdb=" C LEU A 870 " pdb=" N GLY A 871 " pdb=" CA GLY A 871 " ideal model delta sigma weight residual 121.35 125.69 -4.34 1.03e+00 9.43e-01 1.77e+01 ... (remaining 42393 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 17489 17.70 - 35.41: 1283 35.41 - 53.11: 195 53.11 - 70.82: 46 70.82 - 88.52: 30 Dihedral angle restraints: 19043 sinusoidal: 8043 harmonic: 11000 Sorted by residual: 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 -148.05 -31.95 0 5.00e+00 4.00e-02 4.08e+01 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 -148.10 -31.90 0 5.00e+00 4.00e-02 4.07e+01 dihedral pdb=" CA ASN A1557 " pdb=" C ASN A1557 " pdb=" N ILE A1558 " pdb=" CA ILE A1558 " ideal model delta harmonic sigma weight residual -180.00 -150.65 -29.35 0 5.00e+00 4.00e-02 3.45e+01 ... (remaining 19040 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 3921 0.069 - 0.138: 765 0.138 - 0.207: 50 0.207 - 0.277: 8 0.277 - 0.346: 2 Chirality restraints: 4746 Sorted by residual: chirality pdb=" CB ILE B1989 " pdb=" CA ILE B1989 " pdb=" CG1 ILE B1989 " pdb=" CG2 ILE B1989 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CB ILE A1989 " pdb=" CA ILE A1989 " pdb=" CG1 ILE A1989 " pdb=" CG2 ILE A1989 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CB VAL A2534 " pdb=" CA VAL A2534 " pdb=" CG1 VAL A2534 " pdb=" CG2 VAL A2534 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 4743 not shown) Planarity restraints: 5496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A1753 " 0.016 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C GLN A1753 " -0.055 2.00e-02 2.50e+03 pdb=" O GLN A1753 " 0.021 2.00e-02 2.50e+03 pdb=" N ASP A1754 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B1753 " -0.016 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C GLN B1753 " 0.055 2.00e-02 2.50e+03 pdb=" O GLN B1753 " -0.021 2.00e-02 2.50e+03 pdb=" N ASP B1754 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 940 " -0.015 2.00e-02 2.50e+03 2.95e-02 8.71e+00 pdb=" C ASN A 940 " 0.051 2.00e-02 2.50e+03 pdb=" O ASN A 940 " -0.019 2.00e-02 2.50e+03 pdb=" N ILE A 941 " -0.017 2.00e-02 2.50e+03 ... (remaining 5493 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 909 2.70 - 3.25: 28162 3.25 - 3.80: 45225 3.80 - 4.35: 61746 4.35 - 4.90: 107074 Nonbonded interactions: 243116 Sorted by model distance: nonbonded pdb=" O ALA A1017 " pdb=" OH TYR A1142 " model vdw 2.150 3.040 nonbonded pdb=" O ALA B1017 " pdb=" OH TYR B1142 " model vdw 2.151 3.040 nonbonded pdb=" OG SER B2744 " pdb=" OE1 GLN B2747 " model vdw 2.169 3.040 nonbonded pdb=" OG SER A2744 " pdb=" OE1 GLN A2747 " model vdw 2.170 3.040 nonbonded pdb=" NH1 ARG A1300 " pdb=" OD1 ASN A1349 " model vdw 2.178 3.120 ... (remaining 243111 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: 0.04 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 37.610 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 31323 Z= 0.230 Angle : 0.810 10.151 42534 Z= 0.456 Chirality : 0.053 0.346 4746 Planarity : 0.006 0.070 5474 Dihedral : 12.931 88.520 11958 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.06 % Allowed : 0.72 % Favored : 99.22 % 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: -1.77 (0.13), residues: 3788 helix: -2.23 (0.29), residues: 218 sheet: -0.31 (0.14), residues: 1222 loop : -1.61 (0.12), residues: 2348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A2150 TYR 0.022 0.002 TYR B2085 PHE 0.021 0.002 PHE B 974 TRP 0.029 0.002 TRP A 990 HIS 0.010 0.001 HIS B 864 Details of bonding type rmsd covalent geometry : bond 0.00468 (31270) covalent geometry : angle 0.80291 (42398) SS BOND : bond 0.00619 ( 23) SS BOND : angle 1.86816 ( 46) hydrogen bonds : bond 0.15739 ( 980) hydrogen bonds : angle 7.87821 ( 2868) link_BETA1-4 : bond 0.00443 ( 8) link_BETA1-4 : angle 1.23664 ( 24) link_NAG-ASN : bond 0.00372 ( 22) link_NAG-ASN : angle 2.45739 ( 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 550 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 548 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 971 ILE cc_start: 0.8621 (tt) cc_final: 0.8171 (mp) REVERT: A 1549 GLU cc_start: 0.7601 (pt0) cc_final: 0.7027 (tt0) REVERT: A 1567 LYS cc_start: 0.8477 (mttp) cc_final: 0.8202 (mmtt) REVERT: A 2178 LYS cc_start: 0.7933 (ttmm) cc_final: 0.7718 (tttt) REVERT: A 2531 LYS cc_start: 0.8619 (tttm) cc_final: 0.8370 (ttpt) REVERT: A 2762 ARG cc_start: 0.7751 (ttm-80) cc_final: 0.7297 (mtt-85) REVERT: B 907 THR cc_start: 0.7804 (t) cc_final: 0.7533 (m) REVERT: B 971 ILE cc_start: 0.8617 (tt) cc_final: 0.8149 (mp) REVERT: B 1076 ARG cc_start: 0.7878 (tmt170) cc_final: 0.7511 (tmm160) REVERT: B 1304 LYS cc_start: 0.7930 (tmmt) cc_final: 0.7700 (tmtt) REVERT: B 1549 GLU cc_start: 0.7605 (pt0) cc_final: 0.6975 (tt0) REVERT: B 1567 LYS cc_start: 0.8465 (mttp) cc_final: 0.8196 (mmtt) REVERT: B 2531 LYS cc_start: 0.8611 (tttm) cc_final: 0.8348 (ttpt) REVERT: B 2662 ARG cc_start: 0.8210 (ttp80) cc_final: 0.7761 (ptt180) REVERT: B 2762 ARG cc_start: 0.7666 (ttm-80) cc_final: 0.7227 (mtt-85) outliers start: 2 outliers final: 2 residues processed: 548 average time/residue: 0.7650 time to fit residues: 486.2984 Evaluate side-chains 298 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 296 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1483 ILE Chi-restraints excluded: chain B residue 1483 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 30.0000 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 890 ASN A 946 ASN ** A1262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1419 ASN ** A1496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1571 ASN A1668 HIS A1725 HIS A1792 ASN A2087 ASN A2208 ASN A2309 HIS A2397 GLN A2462 GLN A2483 HIS A2600 HIS A2676 ASN A2701 GLN B 890 ASN B 946 ASN ** B1262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1419 ASN ** B1496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1571 ASN B1668 HIS B1792 ASN B2087 ASN B2208 ASN B2397 GLN B2462 GLN B2483 HIS B2600 HIS B2676 ASN B2701 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.168533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.108460 restraints weight = 38706.845| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.56 r_work: 0.3114 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 31323 Z= 0.174 Angle : 0.707 13.075 42534 Z= 0.368 Chirality : 0.049 0.230 4746 Planarity : 0.006 0.058 5474 Dihedral : 6.558 59.788 4846 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.29 % Allowed : 9.59 % Favored : 88.12 % 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: -0.99 (0.13), residues: 3788 helix: -0.28 (0.35), residues: 208 sheet: 0.22 (0.15), residues: 1228 loop : -1.22 (0.12), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A2150 TYR 0.020 0.002 TYR A2085 PHE 0.023 0.002 PHE A1562 TRP 0.015 0.001 TRP A 990 HIS 0.008 0.001 HIS B2000 Details of bonding type rmsd covalent geometry : bond 0.00406 (31270) covalent geometry : angle 0.70036 (42398) SS BOND : bond 0.01166 ( 23) SS BOND : angle 1.47139 ( 46) hydrogen bonds : bond 0.04845 ( 980) hydrogen bonds : angle 5.83641 ( 2868) link_BETA1-4 : bond 0.00305 ( 8) link_BETA1-4 : angle 1.17082 ( 24) link_NAG-ASN : bond 0.00275 ( 22) link_NAG-ASN : angle 2.27008 ( 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 390 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 314 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 899 LYS cc_start: 0.7938 (ptpp) cc_final: 0.7656 (ptpp) REVERT: A 907 THR cc_start: 0.7858 (t) cc_final: 0.7597 (m) REVERT: A 971 ILE cc_start: 0.8498 (tt) cc_final: 0.8240 (mp) REVERT: A 1076 ARG cc_start: 0.8541 (tmt170) cc_final: 0.7907 (tmm160) REVERT: A 1156 THR cc_start: 0.9116 (OUTLIER) cc_final: 0.8835 (p) REVERT: A 1304 LYS cc_start: 0.7563 (tmtt) cc_final: 0.7274 (tmtt) REVERT: A 1446 MET cc_start: 0.5765 (pp-130) cc_final: 0.5445 (mpp) REVERT: A 1549 GLU cc_start: 0.8031 (pt0) cc_final: 0.7324 (tt0) REVERT: A 1567 LYS cc_start: 0.8799 (mttp) cc_final: 0.8300 (mmtt) REVERT: A 1638 MET cc_start: 0.8642 (OUTLIER) cc_final: 0.8424 (ttp) REVERT: A 1654 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8038 (mpt) REVERT: A 1748 PHE cc_start: 0.8314 (t80) cc_final: 0.7949 (t80) REVERT: A 1792 ASN cc_start: 0.7886 (OUTLIER) cc_final: 0.7239 (t0) REVERT: A 1842 ASP cc_start: 0.8591 (m-30) cc_final: 0.8364 (m-30) REVERT: A 1901 MET cc_start: 0.8929 (OUTLIER) cc_final: 0.8694 (mtt) REVERT: A 2178 LYS cc_start: 0.8579 (ttmm) cc_final: 0.8135 (tttt) REVERT: A 2494 MET cc_start: 0.6041 (OUTLIER) cc_final: 0.5577 (mpp) REVERT: A 2525 GLU cc_start: 0.8633 (tp30) cc_final: 0.8397 (tm-30) REVERT: A 2531 LYS cc_start: 0.8995 (tttm) cc_final: 0.8528 (ttpt) REVERT: A 2762 ARG cc_start: 0.7734 (ttm-80) cc_final: 0.7373 (mtt-85) REVERT: B 1076 ARG cc_start: 0.8502 (tmt170) cc_final: 0.7888 (tmm160) REVERT: B 1399 MET cc_start: 0.5330 (OUTLIER) cc_final: 0.4913 (tmt) REVERT: B 1549 GLU cc_start: 0.8163 (pt0) cc_final: 0.7342 (tt0) REVERT: B 1567 LYS cc_start: 0.8769 (mttp) cc_final: 0.8256 (mmtt) REVERT: B 1748 PHE cc_start: 0.8289 (t80) cc_final: 0.7956 (t80) REVERT: B 1792 ASN cc_start: 0.7934 (OUTLIER) cc_final: 0.7244 (t0) REVERT: B 1901 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.8544 (mtm) REVERT: B 2178 LYS cc_start: 0.8568 (ttmm) cc_final: 0.8174 (tttt) REVERT: B 2531 LYS cc_start: 0.9008 (tttm) cc_final: 0.8530 (ttpt) REVERT: B 2762 ARG cc_start: 0.7698 (ttm-80) cc_final: 0.7328 (mtt-85) outliers start: 76 outliers final: 17 residues processed: 351 average time/residue: 0.7202 time to fit residues: 296.7030 Evaluate side-chains 299 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 273 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 957 ASP Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 1156 THR Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1353 ILE Chi-restraints excluded: chain A residue 1638 MET Chi-restraints excluded: chain A residue 1654 MET Chi-restraints excluded: chain A residue 1792 ASN Chi-restraints excluded: chain A residue 1801 THR Chi-restraints excluded: chain A residue 1901 MET Chi-restraints excluded: chain A residue 2138 VAL Chi-restraints excluded: chain A residue 2248 LEU Chi-restraints excluded: chain A residue 2318 THR Chi-restraints excluded: chain A residue 2395 ASN Chi-restraints excluded: chain A residue 2494 MET Chi-restraints excluded: chain B residue 1156 THR Chi-restraints excluded: chain B residue 1235 LEU Chi-restraints excluded: chain B residue 1353 ILE Chi-restraints excluded: chain B residue 1399 MET Chi-restraints excluded: chain B residue 1739 THR Chi-restraints excluded: chain B residue 1792 ASN Chi-restraints excluded: chain B residue 1801 THR Chi-restraints excluded: chain B residue 1901 MET Chi-restraints excluded: chain B residue 2138 VAL Chi-restraints excluded: chain B residue 2248 LEU Chi-restraints excluded: chain B residue 2318 THR 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: 5.9990 chunk 253 optimal weight: 10.0000 chunk 89 optimal weight: 0.3980 chunk 12 optimal weight: 10.0000 chunk 332 optimal weight: 2.9990 chunk 266 optimal weight: 3.9990 chunk 295 optimal weight: 0.0670 chunk 201 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 205 optimal weight: 5.9990 overall best weight: 1.0720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1262 ASN A1419 ASN A1496 GLN A1668 HIS A1725 HIS A1792 ASN A2342 GLN A2747 GLN B1262 ASN B1419 ASN ** B1496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1725 HIS B1792 ASN B2462 GLN B2651 GLN B2747 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.169533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.111483 restraints weight = 38668.747| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.52 r_work: 0.3127 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 31323 Z= 0.125 Angle : 0.622 9.620 42534 Z= 0.323 Chirality : 0.046 0.243 4746 Planarity : 0.005 0.062 5474 Dihedral : 5.951 59.827 4842 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.19 % Allowed : 12.15 % Favored : 85.66 % 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: -0.65 (0.13), residues: 3788 helix: 0.37 (0.36), residues: 208 sheet: 0.46 (0.15), residues: 1212 loop : -1.02 (0.12), residues: 2368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 955 TYR 0.016 0.001 TYR A1422 PHE 0.025 0.001 PHE B1562 TRP 0.014 0.001 TRP B 990 HIS 0.006 0.001 HIS B2224 Details of bonding type rmsd covalent geometry : bond 0.00283 (31270) covalent geometry : angle 0.61600 (42398) SS BOND : bond 0.00576 ( 23) SS BOND : angle 1.34249 ( 46) hydrogen bonds : bond 0.04098 ( 980) hydrogen bonds : angle 5.34530 ( 2868) link_BETA1-4 : bond 0.00501 ( 8) link_BETA1-4 : angle 1.16579 ( 24) link_NAG-ASN : bond 0.00251 ( 22) link_NAG-ASN : angle 2.03238 ( 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 361 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 288 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 899 LYS cc_start: 0.8026 (ptpp) cc_final: 0.7746 (ptpp) REVERT: A 1076 ARG cc_start: 0.8486 (tmt170) cc_final: 0.7873 (tmm160) REVERT: A 1156 THR cc_start: 0.9087 (OUTLIER) cc_final: 0.8824 (p) REVERT: A 1288 MET cc_start: 0.7726 (tpp) cc_final: 0.7506 (mtp) REVERT: A 1304 LYS cc_start: 0.7561 (tmtt) cc_final: 0.7198 (tmtt) REVERT: A 1446 MET cc_start: 0.5707 (pp-130) cc_final: 0.5471 (mpp) REVERT: A 1532 LYS cc_start: 0.8608 (ptpt) cc_final: 0.8355 (pttp) REVERT: A 1549 GLU cc_start: 0.7901 (pt0) cc_final: 0.6858 (tt0) REVERT: A 1564 ARG cc_start: 0.7913 (ttm170) cc_final: 0.7507 (ptp90) REVERT: A 1567 LYS cc_start: 0.8771 (mttp) cc_final: 0.8261 (mmtt) REVERT: A 1615 ASP cc_start: 0.7217 (t0) cc_final: 0.6685 (t0) REVERT: A 1654 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.8006 (mpt) REVERT: A 1725 HIS cc_start: 0.7993 (m-70) cc_final: 0.7785 (m170) REVERT: A 1748 PHE cc_start: 0.8363 (t80) cc_final: 0.8025 (t80) REVERT: A 1792 ASN cc_start: 0.7875 (OUTLIER) cc_final: 0.7073 (t0) REVERT: A 2157 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7789 (tm-30) REVERT: A 2178 LYS cc_start: 0.8596 (ttmm) cc_final: 0.8205 (tttt) REVERT: A 2494 MET cc_start: 0.6171 (OUTLIER) cc_final: 0.5465 (mpp) REVERT: A 2525 GLU cc_start: 0.8599 (tp30) cc_final: 0.8393 (tm-30) REVERT: A 2531 LYS cc_start: 0.9025 (tttm) cc_final: 0.8563 (ttpt) REVERT: A 2762 ARG cc_start: 0.7749 (ttm-80) cc_final: 0.7386 (mtt-85) REVERT: B 1076 ARG cc_start: 0.8473 (tmt170) cc_final: 0.7844 (tmm-80) REVERT: B 1089 MET cc_start: 0.6974 (mtm) cc_final: 0.6764 (mtt) REVERT: B 1399 MET cc_start: 0.4930 (OUTLIER) cc_final: 0.4616 (tmt) REVERT: B 1549 GLU cc_start: 0.7978 (pt0) cc_final: 0.7132 (tt0) REVERT: B 1567 LYS cc_start: 0.8753 (mttp) cc_final: 0.8254 (mmtt) REVERT: B 1725 HIS cc_start: 0.7956 (m-70) cc_final: 0.7724 (m170) REVERT: B 1748 PHE cc_start: 0.8332 (t80) cc_final: 0.7992 (t80) REVERT: B 2178 LYS cc_start: 0.8607 (ttmm) cc_final: 0.8192 (tttt) REVERT: B 2255 MET cc_start: 0.9296 (OUTLIER) cc_final: 0.7577 (mmt) REVERT: B 2531 LYS cc_start: 0.9037 (tttm) cc_final: 0.8566 (ttpt) REVERT: B 2762 ARG cc_start: 0.7723 (ttm-80) cc_final: 0.7357 (mtt-85) outliers start: 73 outliers final: 18 residues processed: 327 average time/residue: 0.7633 time to fit residues: 292.5507 Evaluate side-chains 291 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 266 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 957 ASP Chi-restraints excluded: chain A residue 1156 THR Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1353 ILE Chi-restraints excluded: chain A residue 1481 LEU Chi-restraints excluded: chain A residue 1654 MET Chi-restraints excluded: chain A residue 1792 ASN Chi-restraints excluded: chain A residue 2138 VAL Chi-restraints excluded: chain A residue 2157 GLU Chi-restraints excluded: chain A residue 2248 LEU Chi-restraints excluded: chain A residue 2252 GLN Chi-restraints excluded: chain A residue 2318 THR Chi-restraints excluded: chain A residue 2395 ASN Chi-restraints excluded: chain A residue 2494 MET Chi-restraints excluded: chain B residue 834 MET Chi-restraints excluded: chain B residue 1156 THR Chi-restraints excluded: chain B residue 1235 LEU Chi-restraints excluded: chain B residue 1353 ILE Chi-restraints excluded: chain B residue 1399 MET Chi-restraints excluded: chain B residue 1438 VAL Chi-restraints excluded: chain B residue 1801 THR Chi-restraints excluded: chain B residue 2138 VAL Chi-restraints excluded: chain B residue 2248 LEU Chi-restraints excluded: chain B residue 2255 MET Chi-restraints excluded: chain B residue 2318 THR 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: 10.0000 chunk 62 optimal weight: 1.9990 chunk 207 optimal weight: 50.0000 chunk 157 optimal weight: 0.9980 chunk 235 optimal weight: 9.9990 chunk 181 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 chunk 186 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1262 ASN A1419 ASN A1668 HIS A1792 ASN ** A2523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2651 GLN B1262 ASN B1419 ASN B1496 GLN B1668 HIS B1792 ASN B2651 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.165901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.107341 restraints weight = 38113.446| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.51 r_work: 0.3073 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 31323 Z= 0.241 Angle : 0.706 11.568 42534 Z= 0.364 Chirality : 0.050 0.225 4746 Planarity : 0.005 0.067 5474 Dihedral : 5.898 57.518 4842 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.95 % Allowed : 13.23 % Favored : 83.82 % 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: -0.62 (0.13), residues: 3788 helix: 0.38 (0.36), residues: 212 sheet: 0.53 (0.15), residues: 1198 loop : -1.03 (0.12), residues: 2378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1976 TYR 0.017 0.002 TYR A2085 PHE 0.023 0.002 PHE A 900 TRP 0.014 0.002 TRP B 990 HIS 0.007 0.001 HIS A2309 Details of bonding type rmsd covalent geometry : bond 0.00584 (31270) covalent geometry : angle 0.69980 (42398) SS BOND : bond 0.00499 ( 23) SS BOND : angle 1.22543 ( 46) hydrogen bonds : bond 0.04873 ( 980) hydrogen bonds : angle 5.40703 ( 2868) link_BETA1-4 : bond 0.00422 ( 8) link_BETA1-4 : angle 1.40363 ( 24) link_NAG-ASN : bond 0.00260 ( 22) link_NAG-ASN : angle 2.20216 ( 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 361 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 263 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1076 ARG cc_start: 0.8503 (tmt170) cc_final: 0.7794 (tmm-80) REVERT: A 1089 MET cc_start: 0.7125 (mtt) cc_final: 0.6909 (mtt) REVERT: A 1156 THR cc_start: 0.9116 (OUTLIER) cc_final: 0.8854 (p) REVERT: A 1207 MET cc_start: 0.8397 (ttp) cc_final: 0.7937 (mtp) REVERT: A 1304 LYS cc_start: 0.7607 (tmtt) cc_final: 0.7140 (tmtt) REVERT: A 1356 ASP cc_start: 0.7864 (t70) cc_final: 0.7367 (p0) REVERT: A 1446 MET cc_start: 0.5756 (pp-130) cc_final: 0.5540 (mpp) REVERT: A 1549 GLU cc_start: 0.7975 (pt0) cc_final: 0.7205 (tt0) REVERT: A 1567 LYS cc_start: 0.8773 (mttp) cc_final: 0.8293 (mmtm) REVERT: A 1654 MET cc_start: 0.9025 (OUTLIER) cc_final: 0.7925 (mpt) REVERT: A 1748 PHE cc_start: 0.8421 (t80) cc_final: 0.8051 (t80) REVERT: A 1792 ASN cc_start: 0.8305 (OUTLIER) cc_final: 0.7697 (m-40) REVERT: A 1901 MET cc_start: 0.8983 (OUTLIER) cc_final: 0.8765 (mtt) REVERT: A 2040 MET cc_start: 0.8343 (mmm) cc_final: 0.7988 (mtm) REVERT: A 2157 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7867 (tm-30) REVERT: A 2178 LYS cc_start: 0.8687 (ttmm) cc_final: 0.8269 (tttt) REVERT: A 2263 GLN cc_start: 0.9030 (tt0) cc_final: 0.8794 (tt0) REVERT: A 2531 LYS cc_start: 0.9063 (tttm) cc_final: 0.8585 (ttpt) REVERT: A 2701 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.8500 (mt0) REVERT: A 2762 ARG cc_start: 0.7854 (ttm-80) cc_final: 0.7544 (mtt-85) REVERT: B 968 ILE cc_start: 0.8532 (pt) cc_final: 0.8235 (pp) REVERT: B 1076 ARG cc_start: 0.8461 (tmt170) cc_final: 0.7771 (tmm-80) REVERT: B 1304 LYS cc_start: 0.7576 (tmtt) cc_final: 0.7151 (tmtt) REVERT: B 1356 ASP cc_start: 0.7836 (t70) cc_final: 0.7286 (p0) REVERT: B 1399 MET cc_start: 0.4818 (OUTLIER) cc_final: 0.4597 (tmt) REVERT: B 1446 MET cc_start: 0.6026 (pp-130) cc_final: 0.5562 (mpp) REVERT: B 1549 GLU cc_start: 0.8037 (pt0) cc_final: 0.7287 (tt0) REVERT: B 1567 LYS cc_start: 0.8730 (mttp) cc_final: 0.8239 (mmtt) REVERT: B 1748 PHE cc_start: 0.8434 (t80) cc_final: 0.8056 (t80) REVERT: B 1792 ASN cc_start: 0.8004 (OUTLIER) cc_final: 0.7450 (m-40) REVERT: B 1901 MET cc_start: 0.8994 (OUTLIER) cc_final: 0.8774 (mtt) REVERT: B 1961 VAL cc_start: 0.7696 (OUTLIER) cc_final: 0.7458 (p) REVERT: B 2255 MET cc_start: 0.9325 (OUTLIER) cc_final: 0.7602 (mmt) REVERT: B 2531 LYS cc_start: 0.9051 (tttm) cc_final: 0.8576 (ttpt) REVERT: B 2762 ARG cc_start: 0.7861 (ttm-80) cc_final: 0.7513 (mtt-85) outliers start: 98 outliers final: 38 residues processed: 331 average time/residue: 0.7068 time to fit residues: 276.9233 Evaluate side-chains 302 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 253 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 957 ASP Chi-restraints excluded: chain A residue 1068 THR Chi-restraints excluded: chain A residue 1156 THR Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1353 ILE Chi-restraints excluded: chain A residue 1481 LEU Chi-restraints excluded: chain A residue 1654 MET Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1792 ASN Chi-restraints excluded: chain A residue 1801 THR Chi-restraints excluded: chain A residue 1901 MET Chi-restraints excluded: chain A residue 2113 VAL Chi-restraints excluded: chain A residue 2138 VAL Chi-restraints excluded: chain A residue 2157 GLU Chi-restraints excluded: chain A residue 2248 LEU Chi-restraints excluded: chain A residue 2252 GLN Chi-restraints excluded: chain A residue 2318 THR Chi-restraints excluded: chain A residue 2395 ASN Chi-restraints excluded: chain A residue 2423 VAL Chi-restraints excluded: chain A residue 2445 MET Chi-restraints excluded: chain A residue 2534 VAL Chi-restraints excluded: chain A residue 2647 VAL Chi-restraints excluded: chain A residue 2701 GLN Chi-restraints excluded: chain B residue 957 ASP Chi-restraints excluded: chain B residue 964 THR Chi-restraints excluded: chain B residue 971 ILE Chi-restraints excluded: chain B residue 1068 THR Chi-restraints excluded: chain B residue 1156 THR Chi-restraints excluded: chain B residue 1235 LEU Chi-restraints excluded: chain B residue 1353 ILE Chi-restraints excluded: chain B residue 1399 MET Chi-restraints excluded: chain B residue 1438 VAL Chi-restraints excluded: chain B residue 1613 THR Chi-restraints excluded: chain B residue 1724 VAL Chi-restraints excluded: chain B residue 1770 LEU Chi-restraints excluded: chain B residue 1792 ASN Chi-restraints excluded: chain B residue 1901 MET Chi-restraints excluded: chain B residue 1961 VAL Chi-restraints excluded: chain B residue 2113 VAL Chi-restraints excluded: chain B residue 2138 VAL Chi-restraints excluded: chain B residue 2161 SER Chi-restraints excluded: chain B residue 2248 LEU Chi-restraints excluded: chain B residue 2255 MET Chi-restraints excluded: chain B residue 2318 THR Chi-restraints excluded: chain B residue 2423 VAL Chi-restraints excluded: chain B residue 2435 LEU Chi-restraints excluded: chain B residue 2445 MET Chi-restraints excluded: chain B residue 2534 VAL Chi-restraints excluded: chain B residue 2647 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 343 optimal weight: 0.7980 chunk 268 optimal weight: 0.7980 chunk 218 optimal weight: 5.9990 chunk 338 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 334 optimal weight: 0.9980 chunk 45 optimal weight: 10.0000 chunk 214 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 377 optimal weight: 8.9990 chunk 71 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1187 HIS A1419 ASN A1668 HIS A1725 HIS ** A1792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2403 HIS A2523 GLN A2651 GLN B1187 HIS B1419 ASN B1668 HIS B1725 HIS B2342 GLN B2403 HIS ** B2515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2523 GLN B2651 GLN B2701 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.168473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.109051 restraints weight = 38242.030| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.46 r_work: 0.3121 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 31323 Z= 0.115 Angle : 0.607 9.610 42534 Z= 0.313 Chirality : 0.046 0.240 4746 Planarity : 0.004 0.066 5474 Dihedral : 5.516 57.104 4842 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.50 % Allowed : 14.67 % Favored : 82.83 % 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: -0.38 (0.14), residues: 3788 helix: 0.77 (0.37), residues: 212 sheet: 0.68 (0.15), residues: 1232 loop : -0.89 (0.13), residues: 2344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2578 TYR 0.015 0.001 TYR B2025 PHE 0.025 0.001 PHE B1562 TRP 0.014 0.001 TRP B 990 HIS 0.007 0.001 HIS A2438 Details of bonding type rmsd covalent geometry : bond 0.00260 (31270) covalent geometry : angle 0.60032 (42398) SS BOND : bond 0.00256 ( 23) SS BOND : angle 1.13141 ( 46) hydrogen bonds : bond 0.03831 ( 980) hydrogen bonds : angle 5.08596 ( 2868) link_BETA1-4 : bond 0.00387 ( 8) link_BETA1-4 : angle 1.24691 ( 24) link_NAG-ASN : bond 0.00243 ( 22) link_NAG-ASN : angle 2.07434 ( 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 354 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 271 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1076 ARG cc_start: 0.8482 (tmt170) cc_final: 0.7863 (tmm160) REVERT: A 1156 THR cc_start: 0.9115 (OUTLIER) cc_final: 0.8851 (p) REVERT: A 1288 MET cc_start: 0.7908 (tpp) cc_final: 0.7662 (mtp) REVERT: A 1356 ASP cc_start: 0.7817 (t70) cc_final: 0.7290 (p0) REVERT: A 1567 LYS cc_start: 0.8743 (mttp) cc_final: 0.8283 (mmtm) REVERT: A 1615 ASP cc_start: 0.7381 (t0) cc_final: 0.6894 (t0) REVERT: A 1654 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.7902 (mpt) REVERT: A 1713 VAL cc_start: 0.8928 (OUTLIER) cc_final: 0.8713 (t) REVERT: A 1748 PHE cc_start: 0.8370 (t80) cc_final: 0.8005 (t80) REVERT: A 1792 ASN cc_start: 0.8280 (OUTLIER) cc_final: 0.7631 (m-40) REVERT: A 2178 LYS cc_start: 0.8622 (ttmm) cc_final: 0.8211 (tttt) REVERT: A 2263 GLN cc_start: 0.8963 (tt0) cc_final: 0.8731 (tt0) REVERT: A 2494 MET cc_start: 0.6346 (OUTLIER) cc_final: 0.6116 (mpt) REVERT: A 2531 LYS cc_start: 0.9021 (tttm) cc_final: 0.8541 (ttpt) REVERT: A 2701 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8451 (mt0) REVERT: A 2762 ARG cc_start: 0.7818 (ttm-80) cc_final: 0.7461 (mtt-85) REVERT: B 968 ILE cc_start: 0.8522 (pt) cc_final: 0.8213 (pp) REVERT: B 1076 ARG cc_start: 0.8449 (tmt170) cc_final: 0.7846 (tmm160) REVERT: B 1356 ASP cc_start: 0.7822 (t70) cc_final: 0.7268 (p0) REVERT: B 1399 MET cc_start: 0.4836 (OUTLIER) cc_final: 0.4617 (tmt) REVERT: B 1446 MET cc_start: 0.5973 (pp-130) cc_final: 0.5663 (mpp) REVERT: B 1564 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7889 (ptp90) REVERT: B 1567 LYS cc_start: 0.8721 (mttp) cc_final: 0.8261 (mmtm) REVERT: B 1713 VAL cc_start: 0.8931 (OUTLIER) cc_final: 0.8716 (t) REVERT: B 1725 HIS cc_start: 0.8020 (m-70) cc_final: 0.7789 (m170) REVERT: B 1748 PHE cc_start: 0.8345 (t80) cc_final: 0.7994 (t80) REVERT: B 1792 ASN cc_start: 0.8041 (OUTLIER) cc_final: 0.7113 (t0) REVERT: B 1961 VAL cc_start: 0.7383 (OUTLIER) cc_final: 0.7172 (p) REVERT: B 2178 LYS cc_start: 0.8605 (ttmm) cc_final: 0.8172 (tttt) REVERT: B 2263 GLN cc_start: 0.8945 (tt0) cc_final: 0.8708 (tt0) REVERT: B 2531 LYS cc_start: 0.9018 (tttm) cc_final: 0.8538 (ttpt) REVERT: B 2762 ARG cc_start: 0.7771 (ttm-80) cc_final: 0.7441 (mtt-85) outliers start: 83 outliers final: 38 residues processed: 327 average time/residue: 0.7173 time to fit residues: 277.2863 Evaluate side-chains 306 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 257 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 957 ASP Chi-restraints excluded: chain A residue 1068 THR Chi-restraints excluded: chain A residue 1156 THR Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1353 ILE Chi-restraints excluded: chain A residue 1498 THR Chi-restraints excluded: chain A residue 1613 THR Chi-restraints excluded: chain A residue 1654 MET Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain A residue 1792 ASN Chi-restraints excluded: chain A residue 1801 THR Chi-restraints excluded: chain A residue 2138 VAL Chi-restraints excluded: chain A residue 2248 LEU Chi-restraints excluded: chain A residue 2252 GLN Chi-restraints excluded: chain A residue 2318 THR Chi-restraints excluded: chain A residue 2395 ASN Chi-restraints excluded: chain A residue 2494 MET Chi-restraints excluded: chain A residue 2519 ILE Chi-restraints excluded: chain A residue 2534 VAL Chi-restraints excluded: chain A residue 2647 VAL Chi-restraints excluded: chain A residue 2701 GLN Chi-restraints excluded: chain B residue 957 ASP Chi-restraints excluded: chain B residue 971 ILE Chi-restraints excluded: chain B residue 1068 THR Chi-restraints excluded: chain B residue 1156 THR Chi-restraints excluded: chain B residue 1207 MET Chi-restraints excluded: chain B residue 1235 LEU Chi-restraints excluded: chain B residue 1353 ILE Chi-restraints excluded: chain B residue 1399 MET Chi-restraints excluded: chain B residue 1438 VAL Chi-restraints excluded: chain B residue 1498 THR Chi-restraints excluded: chain B residue 1564 ARG Chi-restraints excluded: chain B residue 1669 GLU Chi-restraints excluded: chain B residue 1713 VAL Chi-restraints excluded: chain B residue 1770 LEU Chi-restraints excluded: chain B residue 1792 ASN Chi-restraints excluded: chain B residue 1801 THR Chi-restraints excluded: chain B residue 1961 VAL Chi-restraints excluded: chain B residue 2113 VAL Chi-restraints excluded: chain B residue 2138 VAL Chi-restraints excluded: chain B residue 2161 SER Chi-restraints excluded: chain B residue 2248 LEU Chi-restraints excluded: chain B residue 2252 GLN Chi-restraints excluded: chain B residue 2318 THR Chi-restraints excluded: chain B residue 2395 ASN Chi-restraints excluded: chain B residue 2494 MET Chi-restraints excluded: chain B residue 2519 ILE Chi-restraints excluded: chain B residue 2534 VAL Chi-restraints excluded: chain B residue 2647 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 141 optimal weight: 4.9990 chunk 225 optimal weight: 2.9990 chunk 243 optimal weight: 9.9990 chunk 159 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 209 optimal weight: 5.9990 chunk 329 optimal weight: 3.9990 chunk 160 optimal weight: 0.9980 chunk 375 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 59 optimal weight: 0.5980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1668 HIS A1725 HIS A1792 ASN A2403 HIS A2651 GLN B1419 ASN B1668 HIS B1792 ASN B2403 HIS ** B2515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2527 GLN B2651 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.166640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.107567 restraints weight = 38116.915| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.61 r_work: 0.3078 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 31323 Z= 0.166 Angle : 0.637 10.966 42534 Z= 0.328 Chirality : 0.047 0.227 4746 Planarity : 0.005 0.065 5474 Dihedral : 5.480 57.724 4842 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.65 % Allowed : 14.85 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.38 (0.14), residues: 3788 helix: 0.76 (0.37), residues: 212 sheet: 0.65 (0.15), residues: 1244 loop : -0.88 (0.13), residues: 2332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1559 TYR 0.021 0.001 TYR A 895 PHE 0.028 0.002 PHE B 900 TRP 0.010 0.001 TRP B 990 HIS 0.006 0.001 HIS A2438 Details of bonding type rmsd covalent geometry : bond 0.00394 (31270) covalent geometry : angle 0.63018 (42398) SS BOND : bond 0.00345 ( 23) SS BOND : angle 1.29799 ( 46) hydrogen bonds : bond 0.04165 ( 980) hydrogen bonds : angle 5.08885 ( 2868) link_BETA1-4 : bond 0.00421 ( 8) link_BETA1-4 : angle 1.34505 ( 24) link_NAG-ASN : bond 0.00214 ( 22) link_NAG-ASN : angle 2.07685 ( 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 345 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 257 time to evaluate : 1.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 970 ILE cc_start: 0.8571 (pt) cc_final: 0.8287 (pp) REVERT: A 1076 ARG cc_start: 0.8516 (tmt170) cc_final: 0.7923 (tmm160) REVERT: A 1156 THR cc_start: 0.9122 (OUTLIER) cc_final: 0.8861 (p) REVERT: A 1207 MET cc_start: 0.8401 (ttp) cc_final: 0.7946 (mtp) REVERT: A 1288 MET cc_start: 0.7805 (tpp) cc_final: 0.7567 (mtp) REVERT: A 1356 ASP cc_start: 0.7832 (t70) cc_final: 0.7287 (p0) REVERT: A 1564 ARG cc_start: 0.8188 (ptp90) cc_final: 0.7862 (ptp90) REVERT: A 1567 LYS cc_start: 0.8769 (mttp) cc_final: 0.8280 (mmtm) REVERT: A 1615 ASP cc_start: 0.7462 (t0) cc_final: 0.7109 (t0) REVERT: A 1654 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.7892 (mpt) REVERT: A 1713 VAL cc_start: 0.8936 (OUTLIER) cc_final: 0.8704 (t) REVERT: A 1748 PHE cc_start: 0.8427 (t80) cc_final: 0.8062 (t80) REVERT: A 1792 ASN cc_start: 0.8345 (OUTLIER) cc_final: 0.7706 (m-40) REVERT: A 2040 MET cc_start: 0.8309 (mmm) cc_final: 0.7851 (mtm) REVERT: A 2157 GLU cc_start: 0.8152 (tt0) cc_final: 0.7943 (tm-30) REVERT: A 2178 LYS cc_start: 0.8670 (ttmm) cc_final: 0.8236 (tttt) REVERT: A 2263 GLN cc_start: 0.9013 (tt0) cc_final: 0.8790 (tt0) REVERT: A 2270 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8047 (mp0) REVERT: A 2525 GLU cc_start: 0.8632 (tp30) cc_final: 0.8418 (tm-30) REVERT: A 2531 LYS cc_start: 0.9075 (tttm) cc_final: 0.8586 (ttpt) REVERT: A 2701 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8480 (mt0) REVERT: A 2762 ARG cc_start: 0.7812 (ttm-80) cc_final: 0.7504 (mtt-85) REVERT: B 1076 ARG cc_start: 0.8468 (tmt170) cc_final: 0.7897 (tmm160) REVERT: B 1356 ASP cc_start: 0.7814 (t70) cc_final: 0.7234 (p0) REVERT: B 1446 MET cc_start: 0.5967 (pp-130) cc_final: 0.5617 (mpp) REVERT: B 1564 ARG cc_start: 0.8219 (ptp90) cc_final: 0.7790 (ptp90) REVERT: B 1567 LYS cc_start: 0.8719 (mttp) cc_final: 0.8228 (mmtm) REVERT: B 1713 VAL cc_start: 0.8934 (OUTLIER) cc_final: 0.8700 (t) REVERT: B 1748 PHE cc_start: 0.8390 (t80) cc_final: 0.8038 (t80) REVERT: B 1777 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8489 (mt-10) REVERT: B 1792 ASN cc_start: 0.8106 (OUTLIER) cc_final: 0.7476 (m-40) REVERT: B 1961 VAL cc_start: 0.7602 (OUTLIER) cc_final: 0.7399 (p) REVERT: B 2178 LYS cc_start: 0.8584 (ttmm) cc_final: 0.8132 (tttt) REVERT: B 2263 GLN cc_start: 0.8986 (tt0) cc_final: 0.8759 (tt0) REVERT: B 2531 LYS cc_start: 0.9072 (tttm) cc_final: 0.8585 (ttpt) REVERT: B 2762 ARG cc_start: 0.7799 (ttm-80) cc_final: 0.7464 (mtt-85) outliers start: 88 outliers final: 50 residues processed: 318 average time/residue: 0.6882 time to fit residues: 260.3526 Evaluate side-chains 307 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 248 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 957 ASP Chi-restraints excluded: chain A residue 1068 THR Chi-restraints excluded: chain A residue 1156 THR Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1353 ILE Chi-restraints excluded: chain A residue 1423 VAL Chi-restraints excluded: chain A residue 1481 LEU Chi-restraints excluded: chain A residue 1498 THR Chi-restraints excluded: chain A residue 1613 THR Chi-restraints excluded: chain A residue 1654 MET Chi-restraints excluded: chain A residue 1669 GLU Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain A residue 1792 ASN Chi-restraints excluded: chain A residue 1801 THR Chi-restraints excluded: chain A residue 2027 THR Chi-restraints excluded: chain A residue 2113 VAL Chi-restraints excluded: chain A residue 2138 VAL Chi-restraints excluded: chain A residue 2248 LEU Chi-restraints excluded: chain A residue 2252 GLN Chi-restraints excluded: chain A residue 2270 GLU Chi-restraints excluded: chain A residue 2318 THR Chi-restraints excluded: chain A residue 2395 ASN Chi-restraints excluded: chain A residue 2423 VAL Chi-restraints excluded: chain A residue 2445 MET Chi-restraints excluded: chain A residue 2519 ILE Chi-restraints excluded: chain A residue 2534 VAL Chi-restraints excluded: chain A residue 2647 VAL Chi-restraints excluded: chain A residue 2701 GLN Chi-restraints excluded: chain A residue 2758 ILE Chi-restraints excluded: chain B residue 957 ASP Chi-restraints excluded: chain B residue 971 ILE Chi-restraints excluded: chain B residue 1068 THR Chi-restraints excluded: chain B residue 1156 THR Chi-restraints excluded: chain B residue 1235 LEU Chi-restraints excluded: chain B residue 1353 ILE Chi-restraints excluded: chain B residue 1423 VAL Chi-restraints excluded: chain B residue 1438 VAL Chi-restraints excluded: chain B residue 1498 THR Chi-restraints excluded: chain B residue 1669 GLU Chi-restraints excluded: chain B residue 1713 VAL Chi-restraints excluded: chain B residue 1724 VAL Chi-restraints excluded: chain B residue 1770 LEU Chi-restraints excluded: chain B residue 1792 ASN Chi-restraints excluded: chain B residue 1801 THR Chi-restraints excluded: chain B residue 1961 VAL Chi-restraints excluded: chain B residue 2027 THR Chi-restraints excluded: chain B residue 2113 VAL Chi-restraints excluded: chain B residue 2138 VAL Chi-restraints excluded: chain B residue 2161 SER Chi-restraints excluded: chain B residue 2248 LEU Chi-restraints excluded: chain B residue 2252 GLN Chi-restraints excluded: chain B residue 2318 THR Chi-restraints excluded: chain B residue 2395 ASN Chi-restraints excluded: chain B residue 2423 VAL Chi-restraints excluded: chain B residue 2445 MET Chi-restraints excluded: chain B residue 2494 MET Chi-restraints excluded: chain B residue 2519 ILE Chi-restraints excluded: chain B residue 2534 VAL Chi-restraints excluded: chain B residue 2647 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 172 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 229 optimal weight: 30.0000 chunk 143 optimal weight: 0.6980 chunk 201 optimal weight: 5.9990 chunk 242 optimal weight: 8.9990 chunk 155 optimal weight: 0.9990 chunk 299 optimal weight: 6.9990 chunk 126 optimal weight: 2.9990 chunk 319 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1668 HIS A1725 HIS A1792 ASN A2527 GLN A2600 HIS A2651 GLN B1419 ASN B1668 HIS B1725 HIS ** B2515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2651 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.166905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.108148 restraints weight = 38015.001| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.59 r_work: 0.3081 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 31323 Z= 0.155 Angle : 0.628 9.636 42534 Z= 0.325 Chirality : 0.047 0.269 4746 Planarity : 0.004 0.070 5474 Dihedral : 5.410 57.502 4842 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.13 % Allowed : 14.67 % Favored : 82.20 % 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: -0.31 (0.14), residues: 3788 helix: 0.90 (0.37), residues: 210 sheet: 0.68 (0.15), residues: 1244 loop : -0.84 (0.13), residues: 2334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1559 TYR 0.013 0.001 TYR A1422 PHE 0.023 0.001 PHE A1562 TRP 0.009 0.001 TRP A1641 HIS 0.007 0.001 HIS A2438 Details of bonding type rmsd covalent geometry : bond 0.00365 (31270) covalent geometry : angle 0.62103 (42398) SS BOND : bond 0.00356 ( 23) SS BOND : angle 1.18919 ( 46) hydrogen bonds : bond 0.04040 ( 980) hydrogen bonds : angle 5.04163 ( 2868) link_BETA1-4 : bond 0.00382 ( 8) link_BETA1-4 : angle 1.34252 ( 24) link_NAG-ASN : bond 0.00811 ( 22) link_NAG-ASN : angle 2.15656 ( 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 353 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 249 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 970 ILE cc_start: 0.8586 (pt) cc_final: 0.8319 (pp) REVERT: A 1076 ARG cc_start: 0.8508 (tmt170) cc_final: 0.7927 (tmm160) REVERT: A 1156 THR cc_start: 0.9108 (OUTLIER) cc_final: 0.8840 (p) REVERT: A 1356 ASP cc_start: 0.7903 (t70) cc_final: 0.7351 (p0) REVERT: A 1446 MET cc_start: 0.6101 (pp-130) cc_final: 0.5647 (mpp) REVERT: A 1564 ARG cc_start: 0.8279 (ptp90) cc_final: 0.7910 (ptp90) REVERT: A 1567 LYS cc_start: 0.8786 (mttp) cc_final: 0.8299 (mmtm) REVERT: A 1615 ASP cc_start: 0.7493 (t0) cc_final: 0.7168 (t0) REVERT: A 1654 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.7910 (mpt) REVERT: A 1713 VAL cc_start: 0.8932 (OUTLIER) cc_final: 0.8702 (t) REVERT: A 1748 PHE cc_start: 0.8409 (t80) cc_final: 0.8050 (t80) REVERT: A 1792 ASN cc_start: 0.8307 (OUTLIER) cc_final: 0.7519 (t0) REVERT: A 2040 MET cc_start: 0.8279 (mmm) cc_final: 0.7805 (ptt) REVERT: A 2157 GLU cc_start: 0.8150 (tt0) cc_final: 0.7898 (tm-30) REVERT: A 2178 LYS cc_start: 0.8671 (ttmm) cc_final: 0.8228 (tttt) REVERT: A 2263 GLN cc_start: 0.9016 (tt0) cc_final: 0.8791 (tt0) REVERT: A 2270 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8053 (mp0) REVERT: A 2494 MET cc_start: 0.6083 (OUTLIER) cc_final: 0.5861 (mpt) REVERT: A 2531 LYS cc_start: 0.9077 (tttm) cc_final: 0.8580 (ttpt) REVERT: A 2538 ARG cc_start: 0.7693 (tpt170) cc_final: 0.7477 (mtp-110) REVERT: A 2701 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8487 (mt0) REVERT: A 2762 ARG cc_start: 0.7832 (ttm-80) cc_final: 0.7542 (mtt-85) REVERT: B 1076 ARG cc_start: 0.8476 (tmt170) cc_final: 0.7910 (tmm160) REVERT: B 1356 ASP cc_start: 0.7815 (t70) cc_final: 0.7235 (p0) REVERT: B 1399 MET cc_start: 0.4205 (tmt) cc_final: 0.3317 (tmt) REVERT: B 1446 MET cc_start: 0.6014 (pp-130) cc_final: 0.5627 (mpp) REVERT: B 1564 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7887 (ptp90) REVERT: B 1567 LYS cc_start: 0.8727 (mttp) cc_final: 0.8230 (mmtm) REVERT: B 1713 VAL cc_start: 0.8930 (OUTLIER) cc_final: 0.8697 (t) REVERT: B 1748 PHE cc_start: 0.8387 (t80) cc_final: 0.8033 (t80) REVERT: B 1755 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.8128 (mm-40) REVERT: B 1777 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8501 (mt-10) REVERT: B 1792 ASN cc_start: 0.8136 (OUTLIER) cc_final: 0.7316 (m-40) REVERT: B 1961 VAL cc_start: 0.7675 (OUTLIER) cc_final: 0.7472 (p) REVERT: B 2178 LYS cc_start: 0.8565 (ttmm) cc_final: 0.8112 (tttt) REVERT: B 2263 GLN cc_start: 0.8983 (tt0) cc_final: 0.8750 (tt0) REVERT: B 2531 LYS cc_start: 0.9070 (tttm) cc_final: 0.8578 (ttpt) REVERT: B 2762 ARG cc_start: 0.7807 (ttm-80) cc_final: 0.7520 (mtt-85) outliers start: 104 outliers final: 53 residues processed: 331 average time/residue: 0.6898 time to fit residues: 270.1784 Evaluate side-chains 305 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 240 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 957 ASP Chi-restraints excluded: chain A residue 1068 THR Chi-restraints excluded: chain A residue 1156 THR Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1353 ILE Chi-restraints excluded: chain A residue 1423 VAL Chi-restraints excluded: chain A residue 1481 LEU Chi-restraints excluded: chain A residue 1498 THR Chi-restraints excluded: chain A residue 1613 THR Chi-restraints excluded: chain A residue 1654 MET Chi-restraints excluded: chain A residue 1669 GLU Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1792 ASN Chi-restraints excluded: chain A residue 1801 THR Chi-restraints excluded: chain A residue 2027 THR Chi-restraints excluded: chain A residue 2113 VAL Chi-restraints excluded: chain A residue 2138 VAL Chi-restraints excluded: chain A residue 2248 LEU Chi-restraints excluded: chain A residue 2252 GLN Chi-restraints excluded: chain A residue 2270 GLU Chi-restraints excluded: chain A residue 2318 THR Chi-restraints excluded: chain A residue 2395 ASN Chi-restraints excluded: chain A residue 2423 VAL Chi-restraints excluded: chain A residue 2494 MET Chi-restraints excluded: chain A residue 2519 ILE Chi-restraints excluded: chain A residue 2534 VAL Chi-restraints excluded: chain A residue 2574 LEU Chi-restraints excluded: chain A residue 2647 VAL Chi-restraints excluded: chain A residue 2701 GLN Chi-restraints excluded: chain A residue 2758 ILE Chi-restraints excluded: chain B residue 853 MET Chi-restraints excluded: chain B residue 957 ASP Chi-restraints excluded: chain B residue 971 ILE Chi-restraints excluded: chain B residue 1068 THR Chi-restraints excluded: chain B residue 1156 THR Chi-restraints excluded: chain B residue 1235 LEU Chi-restraints excluded: chain B residue 1353 ILE Chi-restraints excluded: chain B residue 1423 VAL Chi-restraints excluded: chain B residue 1438 VAL Chi-restraints excluded: chain B residue 1498 THR Chi-restraints excluded: chain B residue 1564 ARG Chi-restraints excluded: chain B residue 1669 GLU Chi-restraints excluded: chain B residue 1713 VAL Chi-restraints excluded: chain B residue 1724 VAL Chi-restraints excluded: chain B residue 1755 GLN Chi-restraints excluded: chain B residue 1770 LEU Chi-restraints excluded: chain B residue 1790 THR Chi-restraints excluded: chain B residue 1792 ASN Chi-restraints excluded: chain B residue 1801 THR Chi-restraints excluded: chain B residue 1961 VAL Chi-restraints excluded: chain B residue 2027 THR Chi-restraints excluded: chain B residue 2113 VAL Chi-restraints excluded: chain B residue 2129 ASP Chi-restraints excluded: chain B residue 2138 VAL Chi-restraints excluded: chain B residue 2161 SER Chi-restraints excluded: chain B residue 2248 LEU Chi-restraints excluded: chain B residue 2252 GLN Chi-restraints excluded: chain B residue 2318 THR Chi-restraints excluded: chain B residue 2423 VAL Chi-restraints excluded: chain B residue 2519 ILE Chi-restraints excluded: chain B residue 2534 VAL Chi-restraints excluded: chain B residue 2574 LEU Chi-restraints excluded: chain B residue 2647 VAL Chi-restraints excluded: chain B residue 2758 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 186 optimal weight: 0.7980 chunk 326 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 121 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 212 optimal weight: 5.9990 chunk 225 optimal weight: 0.9990 chunk 294 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 67 optimal weight: 7.9990 chunk 286 optimal weight: 7.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1221 ASN A1668 HIS A1725 HIS ** A1792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2403 HIS ** A2541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2600 HIS A2651 GLN B1419 ASN B1668 HIS B1725 HIS B1792 ASN B2403 HIS ** B2515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2651 GLN B2701 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.167077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.107557 restraints weight = 38072.520| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.48 r_work: 0.3094 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 31323 Z= 0.145 Angle : 0.613 9.736 42534 Z= 0.317 Chirality : 0.046 0.278 4746 Planarity : 0.004 0.078 5474 Dihedral : 5.315 57.656 4842 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.68 % Allowed : 15.48 % Favored : 81.84 % 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: -0.25 (0.14), residues: 3788 helix: 0.97 (0.37), residues: 210 sheet: 0.82 (0.15), residues: 1202 loop : -0.83 (0.13), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2538 TYR 0.021 0.001 TYR A 895 PHE 0.030 0.001 PHE B 900 TRP 0.008 0.001 TRP A1641 HIS 0.006 0.001 HIS A2438 Details of bonding type rmsd covalent geometry : bond 0.00341 (31270) covalent geometry : angle 0.60654 (42398) SS BOND : bond 0.00315 ( 23) SS BOND : angle 1.14957 ( 46) hydrogen bonds : bond 0.03936 ( 980) hydrogen bonds : angle 4.98693 ( 2868) link_BETA1-4 : bond 0.00417 ( 8) link_BETA1-4 : angle 1.32851 ( 24) link_NAG-ASN : bond 0.00397 ( 22) link_NAG-ASN : angle 2.07676 ( 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 337 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 248 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 970 ILE cc_start: 0.8550 (pt) cc_final: 0.8251 (pp) REVERT: A 1076 ARG cc_start: 0.8506 (tmt170) cc_final: 0.7928 (tmm160) REVERT: A 1156 THR cc_start: 0.9090 (OUTLIER) cc_final: 0.8822 (p) REVERT: A 1356 ASP cc_start: 0.7849 (t70) cc_final: 0.7318 (p0) REVERT: A 1446 MET cc_start: 0.6136 (pp-130) cc_final: 0.5656 (mpp) REVERT: A 1564 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7831 (ptp90) REVERT: A 1567 LYS cc_start: 0.8765 (mttp) cc_final: 0.8286 (mmtm) REVERT: A 1615 ASP cc_start: 0.7478 (t0) cc_final: 0.7242 (t0) REVERT: A 1654 MET cc_start: 0.8940 (OUTLIER) cc_final: 0.7878 (mpt) REVERT: A 1713 VAL cc_start: 0.8930 (OUTLIER) cc_final: 0.8709 (t) REVERT: A 1748 PHE cc_start: 0.8389 (t80) cc_final: 0.8011 (t80) REVERT: A 1792 ASN cc_start: 0.8299 (OUTLIER) cc_final: 0.7758 (m-40) REVERT: A 2040 MET cc_start: 0.8232 (mmm) cc_final: 0.7783 (ptt) REVERT: A 2157 GLU cc_start: 0.8111 (tt0) cc_final: 0.7845 (tm-30) REVERT: A 2263 GLN cc_start: 0.9023 (tt0) cc_final: 0.8802 (tt0) REVERT: A 2270 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8037 (mp0) REVERT: A 2531 LYS cc_start: 0.9043 (tttm) cc_final: 0.8526 (ttpt) REVERT: A 2701 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.8469 (mt0) REVERT: A 2762 ARG cc_start: 0.7828 (ttm-80) cc_final: 0.7547 (mtt-85) REVERT: B 1076 ARG cc_start: 0.8463 (tmt170) cc_final: 0.7896 (tmm160) REVERT: B 1356 ASP cc_start: 0.7776 (t70) cc_final: 0.7196 (p0) REVERT: B 1399 MET cc_start: 0.4356 (tmt) cc_final: 0.3510 (tmt) REVERT: B 1446 MET cc_start: 0.6038 (pp-130) cc_final: 0.5645 (mpp) REVERT: B 1564 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7847 (ptp90) REVERT: B 1567 LYS cc_start: 0.8720 (mttp) cc_final: 0.8240 (mmtm) REVERT: B 1713 VAL cc_start: 0.8921 (OUTLIER) cc_final: 0.8694 (t) REVERT: B 1748 PHE cc_start: 0.8343 (t80) cc_final: 0.8002 (t80) REVERT: B 1755 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.8094 (mm110) REVERT: B 1792 ASN cc_start: 0.8298 (OUTLIER) cc_final: 0.7486 (m-40) REVERT: B 1961 VAL cc_start: 0.7635 (OUTLIER) cc_final: 0.7420 (p) REVERT: B 2178 LYS cc_start: 0.8552 (ttmm) cc_final: 0.8089 (tttt) REVERT: B 2263 GLN cc_start: 0.8968 (tt0) cc_final: 0.8737 (tt0) REVERT: B 2531 LYS cc_start: 0.9055 (tttm) cc_final: 0.8550 (ttpt) REVERT: B 2762 ARG cc_start: 0.7834 (ttm-80) cc_final: 0.7549 (mtt-85) outliers start: 89 outliers final: 53 residues processed: 316 average time/residue: 0.6819 time to fit residues: 255.6363 Evaluate side-chains 309 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 244 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 957 ASP Chi-restraints excluded: chain A residue 1068 THR Chi-restraints excluded: chain A residue 1156 THR Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1353 ILE Chi-restraints excluded: chain A residue 1423 VAL Chi-restraints excluded: chain A residue 1481 LEU Chi-restraints excluded: chain A residue 1498 THR Chi-restraints excluded: chain A residue 1564 ARG Chi-restraints excluded: chain A residue 1613 THR Chi-restraints excluded: chain A residue 1654 MET Chi-restraints excluded: chain A residue 1669 GLU Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1792 ASN Chi-restraints excluded: chain A residue 1801 THR Chi-restraints excluded: chain A residue 2027 THR Chi-restraints excluded: chain A residue 2113 VAL Chi-restraints excluded: chain A residue 2132 GLN Chi-restraints excluded: chain A residue 2138 VAL Chi-restraints excluded: chain A residue 2248 LEU Chi-restraints excluded: chain A residue 2270 GLU Chi-restraints excluded: chain A residue 2318 THR Chi-restraints excluded: chain A residue 2395 ASN Chi-restraints excluded: chain A residue 2423 VAL Chi-restraints excluded: chain A residue 2519 ILE Chi-restraints excluded: chain A residue 2534 VAL Chi-restraints excluded: chain A residue 2574 LEU Chi-restraints excluded: chain A residue 2647 VAL Chi-restraints excluded: chain A residue 2701 GLN Chi-restraints excluded: chain A residue 2758 ILE Chi-restraints excluded: chain B residue 957 ASP Chi-restraints excluded: chain B residue 971 ILE Chi-restraints excluded: chain B residue 1068 THR Chi-restraints excluded: chain B residue 1156 THR Chi-restraints excluded: chain B residue 1235 LEU Chi-restraints excluded: chain B residue 1353 ILE Chi-restraints excluded: chain B residue 1423 VAL Chi-restraints excluded: chain B residue 1438 VAL Chi-restraints excluded: chain B residue 1498 THR Chi-restraints excluded: chain B residue 1564 ARG Chi-restraints excluded: chain B residue 1669 GLU Chi-restraints excluded: chain B residue 1713 VAL Chi-restraints excluded: chain B residue 1755 GLN Chi-restraints excluded: chain B residue 1770 LEU Chi-restraints excluded: chain B residue 1790 THR Chi-restraints excluded: chain B residue 1792 ASN Chi-restraints excluded: chain B residue 1801 THR Chi-restraints excluded: chain B residue 1961 VAL Chi-restraints excluded: chain B residue 2027 THR Chi-restraints excluded: chain B residue 2113 VAL Chi-restraints excluded: chain B residue 2129 ASP Chi-restraints excluded: chain B residue 2132 GLN Chi-restraints excluded: chain B residue 2138 VAL Chi-restraints excluded: chain B residue 2161 SER Chi-restraints excluded: chain B residue 2248 LEU Chi-restraints excluded: chain B residue 2252 GLN Chi-restraints excluded: chain B residue 2318 THR Chi-restraints excluded: chain B residue 2395 ASN Chi-restraints excluded: chain B residue 2423 VAL Chi-restraints excluded: chain B residue 2519 ILE Chi-restraints excluded: chain B residue 2534 VAL Chi-restraints excluded: chain B residue 2574 LEU Chi-restraints excluded: chain B residue 2647 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 327 optimal weight: 6.9990 chunk 176 optimal weight: 0.2980 chunk 225 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 175 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 chunk 378 optimal weight: 0.6980 chunk 326 optimal weight: 0.6980 chunk 57 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1419 ASN A1668 HIS A1725 HIS A2600 HIS A2651 GLN B1221 ASN B1419 ASN B1668 HIS B1725 HIS ** B2515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2651 GLN B2701 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.168512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.108737 restraints weight = 38154.547| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.27 r_work: 0.3143 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 31323 Z= 0.101 Angle : 0.576 11.595 42534 Z= 0.297 Chirality : 0.045 0.246 4746 Planarity : 0.004 0.080 5474 Dihedral : 5.078 57.763 4842 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.22 % Allowed : 16.24 % Favored : 81.54 % 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: -0.09 (0.14), residues: 3788 helix: 1.24 (0.37), residues: 208 sheet: 0.97 (0.15), residues: 1198 loop : -0.76 (0.13), residues: 2382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1559 TYR 0.014 0.001 TYR A2025 PHE 0.025 0.001 PHE A1562 TRP 0.009 0.001 TRP A 990 HIS 0.006 0.001 HIS A2438 Details of bonding type rmsd covalent geometry : bond 0.00227 (31270) covalent geometry : angle 0.57033 (42398) SS BOND : bond 0.00223 ( 23) SS BOND : angle 0.93762 ( 46) hydrogen bonds : bond 0.03394 ( 980) hydrogen bonds : angle 4.81081 ( 2868) link_BETA1-4 : bond 0.00416 ( 8) link_BETA1-4 : angle 1.24023 ( 24) link_NAG-ASN : bond 0.00416 ( 22) link_NAG-ASN : angle 1.97545 ( 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 336 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 262 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 970 ILE cc_start: 0.8613 (pt) cc_final: 0.8347 (pp) REVERT: A 1076 ARG cc_start: 0.8483 (tmt170) cc_final: 0.7916 (tmm160) REVERT: A 1156 THR cc_start: 0.9067 (OUTLIER) cc_final: 0.8801 (p) REVERT: A 1356 ASP cc_start: 0.7845 (t70) cc_final: 0.7272 (p0) REVERT: A 1446 MET cc_start: 0.6175 (pp-130) cc_final: 0.5727 (mpp) REVERT: A 1564 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7797 (ptp90) REVERT: A 1567 LYS cc_start: 0.8754 (mttp) cc_final: 0.8275 (mmtm) REVERT: A 1654 MET cc_start: 0.8852 (OUTLIER) cc_final: 0.7892 (mpt) REVERT: A 1748 PHE cc_start: 0.8353 (t80) cc_final: 0.8012 (t80) REVERT: A 1792 ASN cc_start: 0.8291 (OUTLIER) cc_final: 0.7666 (m-40) REVERT: A 1867 GLN cc_start: 0.8669 (mm-40) cc_final: 0.8469 (mm-40) REVERT: A 2040 MET cc_start: 0.8176 (mmm) cc_final: 0.7748 (ptt) REVERT: A 2157 GLU cc_start: 0.8032 (tt0) cc_final: 0.7761 (tm-30) REVERT: A 2178 LYS cc_start: 0.8604 (ttmm) cc_final: 0.8165 (tttt) REVERT: A 2263 GLN cc_start: 0.8979 (tt0) cc_final: 0.8747 (tt0) REVERT: A 2531 LYS cc_start: 0.9016 (tttm) cc_final: 0.8482 (ttpt) REVERT: A 2701 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.8468 (mt0) REVERT: A 2762 ARG cc_start: 0.7802 (ttm-80) cc_final: 0.7520 (mtt-85) REVERT: B 1076 ARG cc_start: 0.8448 (tmt170) cc_final: 0.7890 (tmm160) REVERT: B 1156 THR cc_start: 0.9057 (OUTLIER) cc_final: 0.8768 (p) REVERT: B 1164 ASP cc_start: 0.8388 (t0) cc_final: 0.8175 (t0) REVERT: B 1356 ASP cc_start: 0.7767 (t70) cc_final: 0.7173 (p0) REVERT: B 1399 MET cc_start: 0.4411 (tmt) cc_final: 0.3600 (tmt) REVERT: B 1446 MET cc_start: 0.6120 (pp-130) cc_final: 0.5669 (mpp) REVERT: B 1549 GLU cc_start: 0.7822 (pt0) cc_final: 0.7301 (mt-10) REVERT: B 1564 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7675 (ptp90) REVERT: B 1567 LYS cc_start: 0.8710 (mttp) cc_final: 0.8231 (mmtm) REVERT: B 1748 PHE cc_start: 0.8289 (t80) cc_final: 0.7925 (t80) REVERT: B 1792 ASN cc_start: 0.8011 (OUTLIER) cc_final: 0.7171 (m-40) REVERT: B 1961 VAL cc_start: 0.7384 (OUTLIER) cc_final: 0.7184 (p) REVERT: B 2178 LYS cc_start: 0.8487 (ttmm) cc_final: 0.8030 (tttt) REVERT: B 2263 GLN cc_start: 0.8939 (tt0) cc_final: 0.8698 (tt0) REVERT: B 2531 LYS cc_start: 0.9003 (tttm) cc_final: 0.8476 (ttpt) REVERT: B 2762 ARG cc_start: 0.7773 (ttm-80) cc_final: 0.7492 (mtt-85) outliers start: 74 outliers final: 46 residues processed: 317 average time/residue: 0.6894 time to fit residues: 259.4916 Evaluate side-chains 307 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 252 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 957 ASP Chi-restraints excluded: chain A residue 1068 THR Chi-restraints excluded: chain A residue 1156 THR Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1353 ILE Chi-restraints excluded: chain A residue 1423 VAL Chi-restraints excluded: chain A residue 1481 LEU Chi-restraints excluded: chain A residue 1498 THR Chi-restraints excluded: chain A residue 1564 ARG Chi-restraints excluded: chain A residue 1613 THR Chi-restraints excluded: chain A residue 1654 MET Chi-restraints excluded: chain A residue 1669 GLU Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1792 ASN Chi-restraints excluded: chain A residue 1801 THR Chi-restraints excluded: chain A residue 2113 VAL Chi-restraints excluded: chain A residue 2138 VAL Chi-restraints excluded: chain A residue 2248 LEU Chi-restraints excluded: chain A residue 2252 GLN Chi-restraints excluded: chain A residue 2318 THR Chi-restraints excluded: chain A residue 2395 ASN Chi-restraints excluded: chain A residue 2423 VAL Chi-restraints excluded: chain A residue 2519 ILE Chi-restraints excluded: chain A residue 2534 VAL Chi-restraints excluded: chain A residue 2574 LEU Chi-restraints excluded: chain A residue 2647 VAL Chi-restraints excluded: chain A residue 2701 GLN Chi-restraints excluded: chain B residue 957 ASP Chi-restraints excluded: chain B residue 971 ILE Chi-restraints excluded: chain B residue 1068 THR Chi-restraints excluded: chain B residue 1156 THR Chi-restraints excluded: chain B residue 1235 LEU Chi-restraints excluded: chain B residue 1353 ILE Chi-restraints excluded: chain B residue 1423 VAL Chi-restraints excluded: chain B residue 1438 VAL Chi-restraints excluded: chain B residue 1498 THR Chi-restraints excluded: chain B residue 1564 ARG Chi-restraints excluded: chain B residue 1669 GLU Chi-restraints excluded: chain B residue 1724 VAL Chi-restraints excluded: chain B residue 1770 LEU Chi-restraints excluded: chain B residue 1790 THR Chi-restraints excluded: chain B residue 1792 ASN Chi-restraints excluded: chain B residue 1801 THR Chi-restraints excluded: chain B residue 1961 VAL Chi-restraints excluded: chain B residue 2138 VAL Chi-restraints excluded: chain B residue 2161 SER Chi-restraints excluded: chain B residue 2248 LEU Chi-restraints excluded: chain B residue 2252 GLN Chi-restraints excluded: chain B residue 2318 THR Chi-restraints excluded: chain B residue 2423 VAL Chi-restraints excluded: chain B residue 2519 ILE Chi-restraints excluded: chain B residue 2534 VAL Chi-restraints excluded: chain B residue 2574 LEU Chi-restraints excluded: chain B residue 2647 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 167 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 201 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 163 optimal weight: 0.0070 chunk 365 optimal weight: 0.8980 chunk 368 optimal weight: 4.9990 chunk 151 optimal weight: 0.7980 chunk 189 optimal weight: 5.9990 chunk 48 optimal weight: 30.0000 chunk 119 optimal weight: 1.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1419 ASN A1668 HIS A1725 HIS A1792 ASN A2600 HIS A2651 GLN B1419 ASN B1668 HIS B1725 HIS B1792 ASN ** B2515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2651 GLN B2701 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.168743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.109095 restraints weight = 38098.152| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.26 r_work: 0.3148 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 31323 Z= 0.101 Angle : 0.572 11.166 42534 Z= 0.295 Chirality : 0.045 0.238 4746 Planarity : 0.004 0.074 5474 Dihedral : 4.930 58.267 4842 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.16 % Allowed : 16.51 % Favored : 81.33 % 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: -0.01 (0.14), residues: 3788 helix: 1.36 (0.37), residues: 208 sheet: 0.99 (0.15), residues: 1208 loop : -0.70 (0.13), residues: 2372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1559 TYR 0.023 0.001 TYR B 895 PHE 0.031 0.001 PHE B 900 TRP 0.007 0.001 TRP A1813 HIS 0.007 0.001 HIS A2438 Details of bonding type rmsd covalent geometry : bond 0.00226 (31270) covalent geometry : angle 0.56631 (42398) SS BOND : bond 0.00214 ( 23) SS BOND : angle 0.85192 ( 46) hydrogen bonds : bond 0.03310 ( 980) hydrogen bonds : angle 4.70892 ( 2868) link_BETA1-4 : bond 0.00378 ( 8) link_BETA1-4 : angle 1.20677 ( 24) link_NAG-ASN : bond 0.00382 ( 22) link_NAG-ASN : angle 1.90774 ( 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 343 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 271 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 970 ILE cc_start: 0.8640 (pt) cc_final: 0.8386 (pp) REVERT: A 1076 ARG cc_start: 0.8494 (tmt170) cc_final: 0.7935 (tmm160) REVERT: A 1156 THR cc_start: 0.9053 (OUTLIER) cc_final: 0.8785 (p) REVERT: A 1356 ASP cc_start: 0.7832 (t70) cc_final: 0.7245 (p0) REVERT: A 1446 MET cc_start: 0.6202 (pp-130) cc_final: 0.5627 (mpp) REVERT: A 1564 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7783 (ptp90) REVERT: A 1567 LYS cc_start: 0.8725 (mttp) cc_final: 0.8244 (mmtm) REVERT: A 1654 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.7868 (mpt) REVERT: A 1748 PHE cc_start: 0.8350 (t80) cc_final: 0.7984 (t80) REVERT: A 1792 ASN cc_start: 0.8178 (OUTLIER) cc_final: 0.7587 (m-40) REVERT: A 2040 MET cc_start: 0.8138 (mmm) cc_final: 0.7767 (ptt) REVERT: A 2157 GLU cc_start: 0.8069 (tt0) cc_final: 0.7734 (tm-30) REVERT: A 2263 GLN cc_start: 0.8968 (tt0) cc_final: 0.8736 (tt0) REVERT: A 2531 LYS cc_start: 0.9009 (tttm) cc_final: 0.8469 (ttpt) REVERT: A 2762 ARG cc_start: 0.7808 (ttm-80) cc_final: 0.7515 (mtt-85) REVERT: B 1076 ARG cc_start: 0.8444 (tmt170) cc_final: 0.7896 (tmm160) REVERT: B 1156 THR cc_start: 0.9046 (OUTLIER) cc_final: 0.8760 (p) REVERT: B 1164 ASP cc_start: 0.8363 (t0) cc_final: 0.8131 (t0) REVERT: B 1399 MET cc_start: 0.4539 (tmt) cc_final: 0.3720 (tmt) REVERT: B 1446 MET cc_start: 0.6119 (pp-130) cc_final: 0.5641 (mpp) REVERT: B 1549 GLU cc_start: 0.7799 (pt0) cc_final: 0.7240 (mt-10) REVERT: B 1564 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7658 (ptp90) REVERT: B 1567 LYS cc_start: 0.8675 (mttp) cc_final: 0.8203 (mmtm) REVERT: B 1748 PHE cc_start: 0.8283 (t80) cc_final: 0.7933 (t80) REVERT: B 1792 ASN cc_start: 0.8174 (OUTLIER) cc_final: 0.7376 (m-40) REVERT: B 2178 LYS cc_start: 0.8499 (ttmm) cc_final: 0.8051 (tttt) REVERT: B 2263 GLN cc_start: 0.8949 (tt0) cc_final: 0.8713 (tt0) REVERT: B 2531 LYS cc_start: 0.9004 (tttm) cc_final: 0.8475 (ttpt) REVERT: B 2762 ARG cc_start: 0.7768 (ttm-80) cc_final: 0.7475 (mtt-85) outliers start: 72 outliers final: 46 residues processed: 322 average time/residue: 0.6811 time to fit residues: 261.0991 Evaluate side-chains 315 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 262 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 957 ASP Chi-restraints excluded: chain A residue 1068 THR Chi-restraints excluded: chain A residue 1156 THR Chi-restraints excluded: chain A residue 1353 ILE Chi-restraints excluded: chain A residue 1423 VAL Chi-restraints excluded: chain A residue 1481 LEU Chi-restraints excluded: chain A residue 1498 THR Chi-restraints excluded: chain A residue 1564 ARG Chi-restraints excluded: chain A residue 1654 MET Chi-restraints excluded: chain A residue 1669 GLU Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1792 ASN Chi-restraints excluded: chain A residue 1801 THR Chi-restraints excluded: chain A residue 2027 THR Chi-restraints excluded: chain A residue 2113 VAL Chi-restraints excluded: chain A residue 2138 VAL Chi-restraints excluded: chain A residue 2248 LEU Chi-restraints excluded: chain A residue 2252 GLN Chi-restraints excluded: chain A residue 2318 THR Chi-restraints excluded: chain A residue 2423 VAL Chi-restraints excluded: chain A residue 2519 ILE Chi-restraints excluded: chain A residue 2534 VAL Chi-restraints excluded: chain A residue 2574 LEU Chi-restraints excluded: chain A residue 2647 VAL Chi-restraints excluded: chain B residue 853 MET Chi-restraints excluded: chain B residue 957 ASP Chi-restraints excluded: chain B residue 971 ILE Chi-restraints excluded: chain B residue 1068 THR Chi-restraints excluded: chain B residue 1156 THR Chi-restraints excluded: chain B residue 1235 LEU Chi-restraints excluded: chain B residue 1353 ILE Chi-restraints excluded: chain B residue 1423 VAL Chi-restraints excluded: chain B residue 1438 VAL Chi-restraints excluded: chain B residue 1498 THR Chi-restraints excluded: chain B residue 1564 ARG Chi-restraints excluded: chain B residue 1669 GLU Chi-restraints excluded: chain B residue 1724 VAL Chi-restraints excluded: chain B residue 1770 LEU Chi-restraints excluded: chain B residue 1790 THR Chi-restraints excluded: chain B residue 1792 ASN Chi-restraints excluded: chain B residue 1801 THR Chi-restraints excluded: chain B residue 2027 THR Chi-restraints excluded: chain B residue 2113 VAL Chi-restraints excluded: chain B residue 2138 VAL Chi-restraints excluded: chain B residue 2248 LEU Chi-restraints excluded: chain B residue 2252 GLN Chi-restraints excluded: chain B residue 2318 THR Chi-restraints excluded: chain B residue 2423 VAL Chi-restraints excluded: chain B residue 2519 ILE Chi-restraints excluded: chain B residue 2534 VAL Chi-restraints excluded: chain B residue 2574 LEU Chi-restraints excluded: chain B residue 2647 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 210 optimal weight: 0.0770 chunk 26 optimal weight: 0.6980 chunk 366 optimal weight: 2.9990 chunk 311 optimal weight: 0.8980 chunk 193 optimal weight: 30.0000 chunk 324 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 155 optimal weight: 0.9980 chunk 44 optimal weight: 10.0000 chunk 48 optimal weight: 30.0000 chunk 169 optimal weight: 4.9990 overall best weight: 1.1340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1419 ASN A1668 HIS A1725 HIS A1792 ASN A2600 HIS A2651 GLN B1419 ASN B1668 HIS B1725 HIS B1792 ASN ** B2515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2651 GLN B2701 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.168081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.108012 restraints weight = 38178.570| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.27 r_work: 0.3127 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 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 : 0.003 0.036 31323 Z= 0.120 Angle : 0.592 10.657 42534 Z= 0.304 Chirality : 0.045 0.233 4746 Planarity : 0.004 0.061 5474 Dihedral : 4.943 58.391 4842 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.98 % Allowed : 17.02 % Favored : 81.00 % 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: -0.04 (0.14), residues: 3788 helix: 1.16 (0.37), residues: 214 sheet: 0.90 (0.15), residues: 1266 loop : -0.69 (0.13), residues: 2308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1559 TYR 0.014 0.001 TYR A1422 PHE 0.023 0.001 PHE A1562 TRP 0.007 0.001 TRP B 987 HIS 0.007 0.001 HIS A2438 Details of bonding type rmsd covalent geometry : bond 0.00277 (31270) covalent geometry : angle 0.58640 (42398) SS BOND : bond 0.00257 ( 23) SS BOND : angle 0.86930 ( 46) hydrogen bonds : bond 0.03514 ( 980) hydrogen bonds : angle 4.73954 ( 2868) link_BETA1-4 : bond 0.00401 ( 8) link_BETA1-4 : angle 1.24255 ( 24) link_NAG-ASN : bond 0.00363 ( 22) link_NAG-ASN : angle 1.91116 ( 66) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14487.37 seconds wall clock time: 246 minutes 26.23 seconds (14786.23 seconds total)