Starting phenix.real_space_refine on Sun Jul 21 10:47:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r51_18890/07_2024/8r51_18890.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r51_18890/07_2024/8r51_18890.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r51_18890/07_2024/8r51_18890.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r51_18890/07_2024/8r51_18890.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r51_18890/07_2024/8r51_18890.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r51_18890/07_2024/8r51_18890.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 8898 2.51 5 N 2383 2.21 5 O 2649 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 1315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1620": "OE1" <-> "OE2" Residue "A PHE 1984": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 13978 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 13796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1793, 13796 Classifications: {'peptide': 1793} Incomplete info: {'truncation_to_alanine': 145} Link IDs: {'PTRANS': 64, 'TRANS': 1728} Unresolved chain links: 1 Chain breaks: 16 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 518 Unresolved non-hydrogen angles: 650 Unresolved non-hydrogen dihedrals: 403 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 17, 'HIS:plan': 1, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 21, 'PHE:plan': 3, 'GLU:plan': 26, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 347 Chain: "B" 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: "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: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 7.85, per 1000 atoms: 0.56 Number of scatterers: 13978 At special positions: 0 Unit cell: (127.072, 125.4, 110.352, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 2649 8.00 N 2383 7.00 C 8898 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A1169 " - pdb=" SG CYS A1172 " distance=2.03 Simple disulfide: pdb=" SG CYS A1466 " - pdb=" SG CYS A1474 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A2801 " - " ASN A1836 " " NAG A2802 " - " ASN A1543 " " NAG A2803 " - " ASN A2592 " " NAG A2804 " - " ASN A1656 " " NAG A2805 " - " ASN A1937 " " NAG B 1 " - " ASN A2280 " " NAG C 1 " - " ASN A1560 " " NAG D 1 " - " ASN A1751 " " NAG E 1 " - " ASN A2140 " Time building additional restraints: 5.35 Conformation dependent library (CDL) restraints added in 2.4 seconds 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3336 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 25 sheets defined 9.1% alpha, 37.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.91 Creating SS restraints... Processing helix chain 'A' and resid 845 through 850 Processing helix chain 'A' and resid 850 through 855 removed outlier: 4.106A pdb=" N ILE A 854 " --> pdb=" O ILE A 850 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLY A 855 " --> pdb=" O SER A 851 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 850 through 855' Processing helix chain 'A' and resid 1018 through 1020 No H-bonds generated for 'chain 'A' and resid 1018 through 1020' Processing helix chain 'A' and resid 1149 through 1151 No H-bonds generated for 'chain 'A' and resid 1149 through 1151' Processing helix chain 'A' and resid 1352 through 1356 Processing helix chain 'A' and resid 1481 through 1485 Processing helix chain 'A' and resid 1628 through 1631 removed outlier: 4.338A pdb=" N GLY A1631 " --> pdb=" O GLY A1628 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1628 through 1631' Processing helix chain 'A' and resid 2353 through 2357 Processing helix chain 'A' and resid 2386 through 2394 Processing helix chain 'A' and resid 2403 through 2407 Processing helix chain 'A' and resid 2416 through 2421 removed outlier: 3.659A pdb=" N THR A2420 " --> pdb=" O LYS A2416 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASP A2421 " --> pdb=" O ASP A2417 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2416 through 2421' Processing helix chain 'A' and resid 2422 through 2429 removed outlier: 3.927A pdb=" N THR A2428 " --> pdb=" O SER A2424 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE A2429 " --> pdb=" O TRP A2425 " (cutoff:3.500A) Processing helix chain 'A' and resid 2432 through 2437 removed outlier: 3.964A pdb=" N ALA A2436 " --> pdb=" O HIS A2432 " (cutoff:3.500A) Processing helix chain 'A' and resid 2451 through 2457 Processing helix chain 'A' and resid 2467 through 2481 removed outlier: 3.612A pdb=" N LEU A2481 " --> pdb=" O ALA A2477 " (cutoff:3.500A) Processing helix chain 'A' and resid 2534 through 2545 removed outlier: 4.105A pdb=" N LYS A2539 " --> pdb=" O GLU A2535 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL A2540 " --> pdb=" O ASP A2536 " (cutoff:3.500A) Processing helix chain 'A' and resid 2571 through 2579 Processing helix chain 'A' and resid 2628 through 2659 Processing helix chain 'A' and resid 2667 through 2678 Processing helix chain 'A' and resid 2694 through 2698 Processing sheet with id=AA1, first strand: chain 'A' and resid 873 through 875 Processing sheet with id=AA2, first strand: chain 'A' and resid 911 through 912 Processing sheet with id=AA3, first strand: chain 'A' and resid 903 through 905 Processing sheet with id=AA4, first strand: chain 'A' and resid 974 through 977 Processing sheet with id=AA5, first strand: chain 'A' and resid 993 through 994 Processing sheet with id=AA6, first strand: chain 'A' and resid 1054 through 1059 removed outlier: 3.505A pdb=" N LYS A1042 " --> pdb=" O GLU A1093 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1083 through 1086 Processing sheet with id=AA8, first strand: chain 'A' and resid 1130 through 1132 Processing sheet with id=AA9, first strand: chain 'A' and resid 1154 through 1159 removed outlier: 5.215A pdb=" N VAL A1155 " --> pdb=" O SER A1515 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N SER A1515 " --> pdb=" O VAL A1155 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N SER A1157 " --> pdb=" O ALA A1513 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ALA A1513 " --> pdb=" O SER A1157 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TYR A1502 " --> pdb=" O LEU A1493 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU A1493 " --> pdb=" O TYR A1502 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ALA A1504 " --> pdb=" O SER A1491 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1174 through 1175 Processing sheet with id=AB2, first strand: chain 'A' and resid 1187 through 1188 removed outlier: 3.501A pdb=" N TYR A1202 " --> pdb=" O ASP A1199 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ARG A1205 " --> pdb=" O SER A1214 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N SER A1214 " --> pdb=" O ARG A1205 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1234 through 1237 removed outlier: 5.544A pdb=" N LEU A1244 " --> pdb=" O PRO A1257 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG A1253 " --> pdb=" O ASP A1248 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA A1274 " --> pdb=" O ILE A1254 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ARG A1256 " --> pdb=" O VAL A1272 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N VAL A1272 " --> pdb=" O ARG A1256 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1294 through 1295 removed outlier: 3.762A pdb=" N ALA A1294 " --> pdb=" O ILE A1330 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE A1315 " --> pdb=" O ARG A1322 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N GLY A1304 " --> pdb=" O VAL A1316 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1361 through 1366 removed outlier: 3.736A pdb=" N ASP A1363 " --> pdb=" O LEU A1376 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL A1381 " --> pdb=" O ALA A1393 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1425 through 1426 removed outlier: 6.552A pdb=" N ILE A1445 " --> pdb=" O VAL A1457 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1520 through 1521 removed outlier: 4.277A pdb=" N LEU A1520 " --> pdb=" O GLU A1528 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N GLN A1547 " --> pdb=" O ASN A1560 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ASN A1560 " --> pdb=" O GLN A1547 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N THR A1549 " --> pdb=" O LEU A1558 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU A1558 " --> pdb=" O ASP A1574 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASP A1574 " --> pdb=" O LEU A1558 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ASN A1560 " --> pdb=" O VAL A1572 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N VAL A1572 " --> pdb=" O ASN A1560 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N SER A1562 " --> pdb=" O THR A1570 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N THR A1570 " --> pdb=" O ILE A1582 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP A1574 " --> pdb=" O ASN A1578 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ASN A1578 " --> pdb=" O ASP A1574 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG A1592 " --> pdb=" O ARG A1583 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N LYS A1612 " --> pdb=" O LEU A1623 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LEU A1623 " --> pdb=" O LYS A1612 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N MET A1614 " --> pdb=" O LEU A1621 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N LEU A1621 " --> pdb=" O ASP A1638 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ASP A1638 " --> pdb=" O LEU A1621 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU A1623 " --> pdb=" O LYS A1636 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LYS A1636 " --> pdb=" O LEU A1623 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR A1625 " --> pdb=" O ALA A1634 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASP A1638 " --> pdb=" O TRP A1642 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N TRP A1642 " --> pdb=" O ASP A1638 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1656 through 1658 Processing sheet with id=AB9, first strand: chain 'A' and resid 1698 through 1702 removed outlier: 6.881A pdb=" N GLU A1764 " --> pdb=" O LEU A1783 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LEU A1783 " --> pdb=" O GLU A1764 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ARG A1766 " --> pdb=" O ARG A1781 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ARG A1781 " --> pdb=" O ARG A1766 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ARG A1768 " --> pdb=" O PHE A1779 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N PHE A1779 " --> pdb=" O ARG A1768 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLU A1770 " --> pdb=" O ASN A1777 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL A1785 " --> pdb=" O ASN A1789 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ASN A1789 " --> pdb=" O VAL A1785 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A1825 " --> pdb=" O ALA A1816 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N THR A1824 " --> pdb=" O VAL A1837 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N ALA A1846 " --> pdb=" O VAL A1857 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER A1867 " --> pdb=" O ASP A1858 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N VAL A1866 " --> pdb=" O TYR A1878 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1734 through 1736 Processing sheet with id=AC2, first strand: chain 'A' and resid 1897 through 1899 removed outlier: 6.759A pdb=" N GLU A1898 " --> pdb=" O SER A1906 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N SER A1906 " --> pdb=" O MET A1918 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU A1951 " --> pdb=" O PHE A1964 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ARG A1961 " --> pdb=" O TYR A1977 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N TYR A1977 " --> pdb=" O ARG A1961 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU A1963 " --> pdb=" O ILE A1975 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ILE A1975 " --> pdb=" O LEU A1963 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LYS A1965 " --> pdb=" O SER A1973 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE A2004 " --> pdb=" O PHE A2023 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N PHE A2023 " --> pdb=" O ILE A2004 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N THR A2006 " --> pdb=" O PHE A2021 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N PHE A2021 " --> pdb=" O THR A2006 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ARG A2008 " --> pdb=" O GLN A2019 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLN A2019 " --> pdb=" O ARG A2008 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ARG A2010 " --> pdb=" O ASP A2017 " (cutoff:3.500A) removed outlier: 11.885A pdb=" N LEU A2015 " --> pdb=" O TYR A2037 " (cutoff:3.500A) removed outlier: 9.013A pdb=" N TYR A2037 " --> pdb=" O LEU A2015 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ASP A2017 " --> pdb=" O TYR A2035 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER A2045 " --> pdb=" O SER A2036 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1897 through 1899 removed outlier: 6.759A pdb=" N GLU A1898 " --> pdb=" O SER A1906 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N SER A1906 " --> pdb=" O MET A1918 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU A1951 " --> pdb=" O PHE A1964 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ARG A1961 " --> pdb=" O TYR A1977 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N TYR A1977 " --> pdb=" O ARG A1961 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU A1963 " --> pdb=" O ILE A1975 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ILE A1975 " --> pdb=" O LEU A1963 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LYS A1965 " --> pdb=" O SER A1973 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE A2004 " --> pdb=" O PHE A2023 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N PHE A2023 " --> pdb=" O ILE A2004 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N THR A2006 " --> pdb=" O PHE A2021 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N PHE A2021 " --> pdb=" O THR A2006 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ARG A2008 " --> pdb=" O GLN A2019 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLN A2019 " --> pdb=" O ARG A2008 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ARG A2010 " --> pdb=" O ASP A2017 " (cutoff:3.500A) removed outlier: 11.885A pdb=" N LEU A2015 " --> pdb=" O TYR A2037 " (cutoff:3.500A) removed outlier: 9.013A pdb=" N TYR A2037 " --> pdb=" O LEU A2015 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ASP A2017 " --> pdb=" O TYR A2035 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER A2045 " --> pdb=" O SER A2036 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N THR A2044 " --> pdb=" O TYR A2060 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N GLU A2070 " --> pdb=" O VAL A2077 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU A2109 " --> pdb=" O THR A2092 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N LYS A2104 " --> pdb=" O ILE A2120 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE A2110 " --> pdb=" O LEU A2114 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N LEU A2114 " --> pdb=" O ILE A2110 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N MET A2115 " --> pdb=" O ILE A2135 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ILE A2135 " --> pdb=" O MET A2115 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N TRP A2117 " --> pdb=" O ILE A2133 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ILE A2133 " --> pdb=" O TRP A2117 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N THR A2119 " --> pdb=" O ARG A2131 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ARG A2131 " --> pdb=" O THR A2119 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLN A2121 " --> pdb=" O THR A2129 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N THR A2129 " --> pdb=" O TYR A2146 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TRP A2165 " --> pdb=" O VAL A2157 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU A2159 " --> pdb=" O ILE A2163 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N ILE A2163 " --> pdb=" O LEU A2159 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 2168 through 2169 removed outlier: 5.629A pdb=" N HIS A2176 " --> pdb=" O LEU A2189 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU A2178 " --> pdb=" O THR A2187 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LEU A2200 " --> pdb=" O PRO A2188 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ARG A2190 " --> pdb=" O THR A2198 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N THR A2198 " --> pdb=" O TYR A2205 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ARG A2214 " --> pdb=" O PHE A2221 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG A2231 " --> pdb=" O GLU A2222 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N THR A2230 " --> pdb=" O TYR A2243 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N THR A2240 " --> pdb=" O THR A2256 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N THR A2256 " --> pdb=" O THR A2240 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ILE A2242 " --> pdb=" O SER A2254 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N SER A2254 " --> pdb=" O ILE A2242 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ARG A2244 " --> pdb=" O VAL A2252 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N VAL A2252 " --> pdb=" O PHE A2264 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE A2298 " --> pdb=" O ILE A2310 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE A2342 " --> pdb=" O GLN A2333 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 2358 through 2360 removed outlier: 3.856A pdb=" N LEU A2365 " --> pdb=" O ASP A2360 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG A2379 " --> pdb=" O ASP A2374 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 2516 through 2521 removed outlier: 3.515A pdb=" N ASN A2528 " --> pdb=" O MET A2517 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA A2547 " --> pdb=" O VAL A2525 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N TYR A2564 " --> pdb=" O LEU A2550 " (cutoff:3.500A) removed outlier: 9.169A pdb=" N ASN A2552 " --> pdb=" O THR A2562 " (cutoff:3.500A) removed outlier: 11.078A pdb=" N THR A2562 " --> pdb=" O ASN A2552 " (cutoff:3.500A) removed outlier: 9.432A pdb=" N HIS A2554 " --> pdb=" O LYS A2560 " (cutoff:3.500A) removed outlier: 10.391A pdb=" N LYS A2560 " --> pdb=" O HIS A2554 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A2619 " --> pdb=" O PHE A2616 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA A2610 " --> pdb=" O TYR A2625 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL A2595 " --> pdb=" O GLY A2583 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 2683 through 2687 530 hydrogen bonds defined for protein. 1359 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: 10.28 Time building geometry restraints manager: 5.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4526 1.34 - 1.46: 3237 1.46 - 1.58: 6428 1.58 - 1.69: 0 1.69 - 1.81: 85 Bond restraints: 14276 Sorted by residual: bond pdb=" N PHE A1315 " pdb=" CA PHE A1315 " ideal model delta sigma weight residual 1.455 1.483 -0.028 1.21e-02 6.83e+03 5.29e+00 bond pdb=" C1 NAG A2801 " pdb=" O5 NAG A2801 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.42e+00 bond pdb=" C1 NAG A2804 " pdb=" O5 NAG A2804 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.58e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.47e+00 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.91e+00 ... (remaining 14271 not shown) Histogram of bond angle deviations from ideal: 99.38 - 106.31: 315 106.31 - 113.25: 7777 113.25 - 120.18: 4758 120.18 - 127.12: 6410 127.12 - 134.05: 147 Bond angle restraints: 19407 Sorted by residual: angle pdb=" C ARG A1584 " pdb=" N ASP A1585 " pdb=" CA ASP A1585 " ideal model delta sigma weight residual 121.80 130.51 -8.71 2.44e+00 1.68e-01 1.27e+01 angle pdb=" N GLY A1759 " pdb=" CA GLY A1759 " pdb=" C GLY A1759 " ideal model delta sigma weight residual 110.66 117.29 -6.63 2.18e+00 2.10e-01 9.26e+00 angle pdb=" C ALA A1034 " pdb=" CA ALA A1034 " pdb=" CB ALA A1034 " ideal model delta sigma weight residual 110.42 115.88 -5.46 1.99e+00 2.53e-01 7.54e+00 angle pdb=" N ASN A1656 " pdb=" CA ASN A1656 " pdb=" C ASN A1656 " ideal model delta sigma weight residual 108.32 112.76 -4.44 1.64e+00 3.72e-01 7.34e+00 angle pdb=" C PHE A1200 " pdb=" N ASN A1201 " pdb=" CA ASN A1201 " ideal model delta sigma weight residual 125.66 130.22 -4.56 1.85e+00 2.92e-01 6.07e+00 ... (remaining 19402 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 7433 17.84 - 35.68: 849 35.68 - 53.52: 230 53.52 - 71.36: 47 71.36 - 89.20: 12 Dihedral angle restraints: 8571 sinusoidal: 3361 harmonic: 5210 Sorted by residual: dihedral pdb=" CB CYS A1466 " pdb=" SG CYS A1466 " pdb=" SG CYS A1474 " pdb=" CB CYS A1474 " ideal model delta sinusoidal sigma weight residual -86.00 -136.81 50.81 1 1.00e+01 1.00e-02 3.53e+01 dihedral pdb=" CA GLN A2011 " pdb=" C GLN A2011 " pdb=" N ILE A2012 " pdb=" CA ILE A2012 " ideal model delta harmonic sigma weight residual 180.00 161.55 18.45 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA ASP A1687 " pdb=" CB ASP A1687 " pdb=" CG ASP A1687 " pdb=" OD1 ASP A1687 " ideal model delta sinusoidal sigma weight residual -30.00 -89.86 59.86 1 2.00e+01 2.50e-03 1.20e+01 ... (remaining 8568 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 2148 0.106 - 0.212: 85 0.212 - 0.318: 0 0.318 - 0.424: 1 0.424 - 0.531: 1 Chirality restraints: 2235 Sorted by residual: chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A2140 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 7.04e+00 chirality pdb=" C1 NAG A2804 " pdb=" ND2 ASN A1656 " pdb=" C2 NAG A2804 " pdb=" O5 NAG A2804 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 3.95e+00 chirality pdb=" C1 NAG A2805 " pdb=" ND2 ASN A1937 " pdb=" C2 NAG A2805 " pdb=" O5 NAG A2805 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 9.02e-01 ... (remaining 2232 not shown) Planarity restraints: 2475 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A1656 " -0.022 2.00e-02 2.50e+03 2.07e-02 5.35e+00 pdb=" CG ASN A1656 " 0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN A1656 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN A1656 " 0.017 2.00e-02 2.50e+03 pdb=" C1 NAG A2804 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1716 " 0.015 2.00e-02 2.50e+03 1.30e-02 3.38e+00 pdb=" CG TYR A1716 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR A1716 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A1716 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A1716 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A1716 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A1716 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A1716 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A1656 " -0.007 2.00e-02 2.50e+03 1.47e-02 2.15e+00 pdb=" CG ASN A1656 " 0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN A1656 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN A1656 " -0.009 2.00e-02 2.50e+03 ... (remaining 2472 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 214 2.66 - 3.22: 12248 3.22 - 3.78: 20878 3.78 - 4.34: 30203 4.34 - 4.90: 52301 Nonbonded interactions: 115844 Sorted by model distance: nonbonded pdb=" OD1 ASP A1074 " pdb=" N ALA A1075 " model vdw 2.103 2.520 nonbonded pdb=" OE1 GLU A2558 " pdb=" O3 NAG A2805 " model vdw 2.120 2.440 nonbonded pdb=" OH TYR A2116 " pdb=" O SER A2312 " model vdw 2.211 2.440 nonbonded pdb=" OH TYR A2169 " pdb=" OH TYR A2337 " model vdw 2.217 2.440 nonbonded pdb=" OG SER A1637 " pdb=" OG1 THR A1643 " model vdw 2.225 2.440 ... (remaining 115839 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 45.880 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 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 : 0.004 0.039 14276 Z= 0.291 Angle : 0.524 8.709 19407 Z= 0.271 Chirality : 0.047 0.531 2235 Planarity : 0.003 0.030 2466 Dihedral : 16.460 89.203 5229 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.57 % Allowed : 28.76 % Favored : 70.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.21), residues: 1758 helix: 1.33 (0.50), residues: 114 sheet: 0.10 (0.22), residues: 632 loop : -0.65 (0.20), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A2388 HIS 0.004 0.001 HIS A2434 PHE 0.011 0.001 PHE A2368 TYR 0.032 0.001 TYR A1716 ARG 0.004 0.000 ARG A1584 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 153 time to evaluate : 1.532 Fit side-chains REVERT: A 1885 MET cc_start: 0.7801 (tmm) cc_final: 0.7600 (tmm) outliers start: 8 outliers final: 4 residues processed: 158 average time/residue: 0.2665 time to fit residues: 62.6750 Evaluate side-chains 156 residues out of total 1569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 152 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1382 LEU Chi-restraints excluded: chain A residue 1385 THR Chi-restraints excluded: chain A residue 1872 ASP Chi-restraints excluded: chain A residue 2156 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 151 optimal weight: 0.0980 chunk 135 optimal weight: 0.3980 chunk 75 optimal weight: 2.9990 chunk 46 optimal weight: 20.0000 chunk 91 optimal weight: 0.9990 chunk 72 optimal weight: 0.0870 chunk 140 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 85 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 162 optimal weight: 8.9990 overall best weight: 0.4760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.0751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14276 Z= 0.135 Angle : 0.480 5.679 19407 Z= 0.260 Chirality : 0.045 0.376 2235 Planarity : 0.003 0.030 2466 Dihedral : 4.690 57.264 2246 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.25 % Allowed : 27.00 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.21), residues: 1758 helix: 1.31 (0.50), residues: 117 sheet: 0.03 (0.21), residues: 633 loop : -0.58 (0.21), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A2117 HIS 0.007 0.001 HIS A2096 PHE 0.011 0.001 PHE A1723 TYR 0.019 0.001 TYR A1977 ARG 0.003 0.000 ARG A1396 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 172 time to evaluate : 1.447 Fit side-chains REVERT: A 1269 ASN cc_start: 0.6262 (t0) cc_final: 0.5994 (t0) REVERT: A 2011 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.7054 (mp10) outliers start: 46 outliers final: 27 residues processed: 206 average time/residue: 0.2580 time to fit residues: 79.9585 Evaluate side-chains 186 residues out of total 1569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 158 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 1006 ILE Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1362 THR Chi-restraints excluded: chain A residue 1371 ASN Chi-restraints excluded: chain A residue 1412 HIS Chi-restraints excluded: chain A residue 1585 ASP Chi-restraints excluded: chain A residue 1657 VAL Chi-restraints excluded: chain A residue 1664 VAL Chi-restraints excluded: chain A residue 1716 TYR Chi-restraints excluded: chain A residue 1791 LEU Chi-restraints excluded: chain A residue 1832 LEU Chi-restraints excluded: chain A residue 1872 ASP Chi-restraints excluded: chain A residue 1920 THR Chi-restraints excluded: chain A residue 1922 ARG Chi-restraints excluded: chain A residue 1952 GLN Chi-restraints excluded: chain A residue 1995 THR Chi-restraints excluded: chain A residue 2011 GLN Chi-restraints excluded: chain A residue 2210 ASP Chi-restraints excluded: chain A residue 2252 VAL Chi-restraints excluded: chain A residue 2253 SER Chi-restraints excluded: chain A residue 2262 LEU Chi-restraints excluded: chain A residue 2385 ILE Chi-restraints excluded: chain A residue 2410 SER Chi-restraints excluded: chain A residue 2426 LEU Chi-restraints excluded: chain A residue 2445 PHE Chi-restraints excluded: chain A residue 2466 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 135 optimal weight: 0.0870 chunk 110 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 162 optimal weight: 7.9990 chunk 175 optimal weight: 8.9990 chunk 145 optimal weight: 3.9990 chunk 161 optimal weight: 7.9990 chunk 55 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 overall best weight: 4.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 860 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1576 ASN A2107 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.0896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.081 14276 Z= 0.527 Angle : 0.641 7.469 19407 Z= 0.336 Chirality : 0.050 0.392 2235 Planarity : 0.004 0.042 2466 Dihedral : 5.013 42.706 2242 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 5.44 % Allowed : 25.37 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.20), residues: 1758 helix: 1.18 (0.50), residues: 116 sheet: -0.20 (0.20), residues: 646 loop : -0.82 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A2388 HIS 0.004 0.001 HIS A2434 PHE 0.016 0.002 PHE A1984 TYR 0.046 0.002 TYR A1716 ARG 0.005 0.001 ARG A1967 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 154 time to evaluate : 1.707 Fit side-chains revert: symmetry clash REVERT: A 903 TYR cc_start: 0.8221 (p90) cc_final: 0.7984 (p90) REVERT: A 2011 GLN cc_start: 0.9163 (OUTLIER) cc_final: 0.7408 (mp10) REVERT: A 2130 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8522 (mtmm) outliers start: 77 outliers final: 56 residues processed: 218 average time/residue: 0.2453 time to fit residues: 80.7680 Evaluate side-chains 210 residues out of total 1569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 152 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1010 ASP Chi-restraints excluded: chain A residue 1029 ILE Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1109 VAL Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1362 THR Chi-restraints excluded: chain A residue 1376 LEU Chi-restraints excluded: chain A residue 1390 VAL Chi-restraints excluded: chain A residue 1412 HIS Chi-restraints excluded: chain A residue 1500 THR Chi-restraints excluded: chain A residue 1523 SER Chi-restraints excluded: chain A residue 1549 THR Chi-restraints excluded: chain A residue 1585 ASP Chi-restraints excluded: chain A residue 1635 THR Chi-restraints excluded: chain A residue 1649 ASP Chi-restraints excluded: chain A residue 1657 VAL Chi-restraints excluded: chain A residue 1658 THR Chi-restraints excluded: chain A residue 1664 VAL Chi-restraints excluded: chain A residue 1671 MET Chi-restraints excluded: chain A residue 1672 ASP Chi-restraints excluded: chain A residue 1675 ILE Chi-restraints excluded: chain A residue 1716 TYR Chi-restraints excluded: chain A residue 1739 LEU Chi-restraints excluded: chain A residue 1790 LEU Chi-restraints excluded: chain A residue 1792 SER Chi-restraints excluded: chain A residue 1798 THR Chi-restraints excluded: chain A residue 1832 LEU Chi-restraints excluded: chain A residue 1848 ILE Chi-restraints excluded: chain A residue 1866 VAL Chi-restraints excluded: chain A residue 1872 ASP Chi-restraints excluded: chain A residue 1886 VAL Chi-restraints excluded: chain A residue 1917 THR Chi-restraints excluded: chain A residue 1920 THR Chi-restraints excluded: chain A residue 1922 ARG Chi-restraints excluded: chain A residue 1952 GLN Chi-restraints excluded: chain A residue 1995 THR Chi-restraints excluded: chain A residue 1996 VAL Chi-restraints excluded: chain A residue 2011 GLN Chi-restraints excluded: chain A residue 2066 SER Chi-restraints excluded: chain A residue 2083 ASN Chi-restraints excluded: chain A residue 2088 THR Chi-restraints excluded: chain A residue 2094 THR Chi-restraints excluded: chain A residue 2130 LYS Chi-restraints excluded: chain A residue 2241 VAL Chi-restraints excluded: chain A residue 2252 VAL Chi-restraints excluded: chain A residue 2253 SER Chi-restraints excluded: chain A residue 2262 LEU Chi-restraints excluded: chain A residue 2317 THR Chi-restraints excluded: chain A residue 2332 ILE Chi-restraints excluded: chain A residue 2385 ILE Chi-restraints excluded: chain A residue 2410 SER Chi-restraints excluded: chain A residue 2445 PHE Chi-restraints excluded: chain A residue 2538 ILE Chi-restraints excluded: chain A residue 2553 LEU Chi-restraints excluded: chain A residue 2569 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 160 optimal weight: 0.7980 chunk 122 optimal weight: 0.6980 chunk 84 optimal weight: 0.0020 chunk 18 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 109 optimal weight: 0.7980 chunk 163 optimal weight: 0.9990 chunk 173 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 154 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 860 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1576 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14276 Z= 0.141 Angle : 0.480 5.633 19407 Z= 0.256 Chirality : 0.044 0.363 2235 Planarity : 0.003 0.031 2466 Dihedral : 4.440 31.577 2242 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.53 % Allowed : 27.70 % Favored : 68.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.20), residues: 1758 helix: 1.34 (0.51), residues: 116 sheet: -0.29 (0.21), residues: 643 loop : -0.66 (0.20), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A2117 HIS 0.003 0.001 HIS A2096 PHE 0.010 0.001 PHE A2565 TYR 0.024 0.001 TYR A1716 ARG 0.004 0.000 ARG A1106 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 158 time to evaluate : 1.542 Fit side-chains REVERT: A 911 MET cc_start: 0.8316 (mmm) cc_final: 0.7590 (mmm) REVERT: A 1269 ASN cc_start: 0.6633 (t0) cc_final: 0.6306 (t0) REVERT: A 2011 GLN cc_start: 0.8988 (OUTLIER) cc_final: 0.7106 (mp10) outliers start: 50 outliers final: 35 residues processed: 197 average time/residue: 0.2482 time to fit residues: 73.5091 Evaluate side-chains 191 residues out of total 1569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 155 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 1029 ILE Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1101 THR Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1107 THR Chi-restraints excluded: chain A residue 1362 THR Chi-restraints excluded: chain A residue 1385 THR Chi-restraints excluded: chain A residue 1390 VAL Chi-restraints excluded: chain A residue 1469 ASP Chi-restraints excluded: chain A residue 1549 THR Chi-restraints excluded: chain A residue 1585 ASP Chi-restraints excluded: chain A residue 1657 VAL Chi-restraints excluded: chain A residue 1664 VAL Chi-restraints excluded: chain A residue 1692 SER Chi-restraints excluded: chain A residue 1716 TYR Chi-restraints excluded: chain A residue 1832 LEU Chi-restraints excluded: chain A residue 1872 ASP Chi-restraints excluded: chain A residue 1879 THR Chi-restraints excluded: chain A residue 1922 ARG Chi-restraints excluded: chain A residue 1952 GLN Chi-restraints excluded: chain A residue 1985 THR Chi-restraints excluded: chain A residue 1995 THR Chi-restraints excluded: chain A residue 1996 VAL Chi-restraints excluded: chain A residue 2011 GLN Chi-restraints excluded: chain A residue 2084 GLN Chi-restraints excluded: chain A residue 2124 ASN Chi-restraints excluded: chain A residue 2210 ASP Chi-restraints excluded: chain A residue 2252 VAL Chi-restraints excluded: chain A residue 2253 SER Chi-restraints excluded: chain A residue 2262 LEU Chi-restraints excluded: chain A residue 2351 VAL Chi-restraints excluded: chain A residue 2426 LEU Chi-restraints excluded: chain A residue 2445 PHE Chi-restraints excluded: chain A residue 2466 ILE Chi-restraints excluded: chain A residue 2538 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 144 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 128 optimal weight: 8.9990 chunk 71 optimal weight: 9.9990 chunk 147 optimal weight: 0.7980 chunk 119 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 155 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 860 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1576 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.076 14276 Z= 0.505 Angle : 0.620 7.180 19407 Z= 0.323 Chirality : 0.049 0.377 2235 Planarity : 0.004 0.040 2466 Dihedral : 4.884 34.826 2242 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 5.94 % Allowed : 26.01 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.20), residues: 1758 helix: 1.18 (0.50), residues: 116 sheet: -0.35 (0.20), residues: 651 loop : -0.86 (0.20), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A2388 HIS 0.004 0.001 HIS A2434 PHE 0.015 0.002 PHE A1984 TYR 0.045 0.002 TYR A1716 ARG 0.004 0.000 ARG A1584 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 154 time to evaluate : 1.608 Fit side-chains revert: symmetry clash REVERT: A 903 TYR cc_start: 0.8267 (p90) cc_final: 0.7993 (p90) REVERT: A 1205 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7381 (ttt180) REVERT: A 1269 ASN cc_start: 0.7010 (t0) cc_final: 0.6632 (t0) REVERT: A 1968 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.7483 (mtt180) REVERT: A 2011 GLN cc_start: 0.9138 (OUTLIER) cc_final: 0.7359 (mp10) REVERT: A 2130 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8549 (mtmm) outliers start: 84 outliers final: 64 residues processed: 228 average time/residue: 0.2534 time to fit residues: 87.0471 Evaluate side-chains 222 residues out of total 1569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 154 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 945 PHE Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1010 ASP Chi-restraints excluded: chain A residue 1029 ILE Chi-restraints excluded: chain A residue 1036 ILE Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1101 THR Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1109 VAL Chi-restraints excluded: chain A residue 1205 ARG Chi-restraints excluded: chain A residue 1362 THR Chi-restraints excluded: chain A residue 1385 THR Chi-restraints excluded: chain A residue 1390 VAL Chi-restraints excluded: chain A residue 1412 HIS Chi-restraints excluded: chain A residue 1420 SER Chi-restraints excluded: chain A residue 1434 ILE Chi-restraints excluded: chain A residue 1500 THR Chi-restraints excluded: chain A residue 1523 SER Chi-restraints excluded: chain A residue 1549 THR Chi-restraints excluded: chain A residue 1585 ASP Chi-restraints excluded: chain A residue 1635 THR Chi-restraints excluded: chain A residue 1649 ASP Chi-restraints excluded: chain A residue 1657 VAL Chi-restraints excluded: chain A residue 1658 THR Chi-restraints excluded: chain A residue 1664 VAL Chi-restraints excluded: chain A residue 1672 ASP Chi-restraints excluded: chain A residue 1675 ILE Chi-restraints excluded: chain A residue 1688 VAL Chi-restraints excluded: chain A residue 1692 SER Chi-restraints excluded: chain A residue 1716 TYR Chi-restraints excluded: chain A residue 1792 SER Chi-restraints excluded: chain A residue 1798 THR Chi-restraints excluded: chain A residue 1832 LEU Chi-restraints excluded: chain A residue 1847 SER Chi-restraints excluded: chain A residue 1848 ILE Chi-restraints excluded: chain A residue 1872 ASP Chi-restraints excluded: chain A residue 1879 THR Chi-restraints excluded: chain A residue 1885 MET Chi-restraints excluded: chain A residue 1886 VAL Chi-restraints excluded: chain A residue 1917 THR Chi-restraints excluded: chain A residue 1922 ARG Chi-restraints excluded: chain A residue 1952 GLN Chi-restraints excluded: chain A residue 1968 ARG Chi-restraints excluded: chain A residue 1985 THR Chi-restraints excluded: chain A residue 1995 THR Chi-restraints excluded: chain A residue 1996 VAL Chi-restraints excluded: chain A residue 2011 GLN Chi-restraints excluded: chain A residue 2044 THR Chi-restraints excluded: chain A residue 2083 ASN Chi-restraints excluded: chain A residue 2084 GLN Chi-restraints excluded: chain A residue 2124 ASN Chi-restraints excluded: chain A residue 2130 LYS Chi-restraints excluded: chain A residue 2183 SER Chi-restraints excluded: chain A residue 2252 VAL Chi-restraints excluded: chain A residue 2253 SER Chi-restraints excluded: chain A residue 2262 LEU Chi-restraints excluded: chain A residue 2288 SER Chi-restraints excluded: chain A residue 2317 THR Chi-restraints excluded: chain A residue 2332 ILE Chi-restraints excluded: chain A residue 2402 MET Chi-restraints excluded: chain A residue 2410 SER Chi-restraints excluded: chain A residue 2414 ASP Chi-restraints excluded: chain A residue 2445 PHE Chi-restraints excluded: chain A residue 2449 GLU Chi-restraints excluded: chain A residue 2538 ILE Chi-restraints excluded: chain A residue 2569 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 58 optimal weight: 0.9990 chunk 155 optimal weight: 0.8980 chunk 34 optimal weight: 7.9990 chunk 101 optimal weight: 0.9990 chunk 42 optimal weight: 10.0000 chunk 173 optimal weight: 2.9990 chunk 143 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 57 optimal weight: 10.0000 chunk 90 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 860 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1576 ASN A1999 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14276 Z= 0.174 Angle : 0.489 5.360 19407 Z= 0.260 Chirality : 0.044 0.354 2235 Planarity : 0.003 0.033 2466 Dihedral : 4.442 32.758 2242 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.10 % Allowed : 27.21 % Favored : 68.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.20), residues: 1758 helix: 1.32 (0.51), residues: 116 sheet: -0.36 (0.20), residues: 650 loop : -0.71 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A2117 HIS 0.003 0.001 HIS A2096 PHE 0.010 0.001 PHE A2565 TYR 0.027 0.001 TYR A1716 ARG 0.004 0.000 ARG A1106 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 162 time to evaluate : 1.678 Fit side-chains REVERT: A 903 TYR cc_start: 0.8184 (p90) cc_final: 0.7974 (p90) REVERT: A 911 MET cc_start: 0.8298 (mmm) cc_final: 0.7620 (mmm) REVERT: A 1269 ASN cc_start: 0.6775 (t0) cc_final: 0.6462 (t0) REVERT: A 1968 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.7429 (mtt180) REVERT: A 2011 GLN cc_start: 0.9006 (OUTLIER) cc_final: 0.7133 (mp10) REVERT: A 2130 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8447 (mtmm) outliers start: 58 outliers final: 47 residues processed: 212 average time/residue: 0.2413 time to fit residues: 77.3089 Evaluate side-chains 207 residues out of total 1569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 157 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 945 PHE Chi-restraints excluded: chain A residue 1006 ILE Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1101 THR Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1216 LEU Chi-restraints excluded: chain A residue 1362 THR Chi-restraints excluded: chain A residue 1385 THR Chi-restraints excluded: chain A residue 1390 VAL Chi-restraints excluded: chain A residue 1412 HIS Chi-restraints excluded: chain A residue 1426 VAL Chi-restraints excluded: chain A residue 1434 ILE Chi-restraints excluded: chain A residue 1549 THR Chi-restraints excluded: chain A residue 1576 ASN Chi-restraints excluded: chain A residue 1585 ASP Chi-restraints excluded: chain A residue 1657 VAL Chi-restraints excluded: chain A residue 1664 VAL Chi-restraints excluded: chain A residue 1672 ASP Chi-restraints excluded: chain A residue 1692 SER Chi-restraints excluded: chain A residue 1716 TYR Chi-restraints excluded: chain A residue 1832 LEU Chi-restraints excluded: chain A residue 1872 ASP Chi-restraints excluded: chain A residue 1879 THR Chi-restraints excluded: chain A residue 1886 VAL Chi-restraints excluded: chain A residue 1917 THR Chi-restraints excluded: chain A residue 1922 ARG Chi-restraints excluded: chain A residue 1952 GLN Chi-restraints excluded: chain A residue 1968 ARG Chi-restraints excluded: chain A residue 1985 THR Chi-restraints excluded: chain A residue 1995 THR Chi-restraints excluded: chain A residue 1996 VAL Chi-restraints excluded: chain A residue 2011 GLN Chi-restraints excluded: chain A residue 2084 GLN Chi-restraints excluded: chain A residue 2124 ASN Chi-restraints excluded: chain A residue 2130 LYS Chi-restraints excluded: chain A residue 2252 VAL Chi-restraints excluded: chain A residue 2253 SER Chi-restraints excluded: chain A residue 2262 LEU Chi-restraints excluded: chain A residue 2317 THR Chi-restraints excluded: chain A residue 2332 ILE Chi-restraints excluded: chain A residue 2351 VAL Chi-restraints excluded: chain A residue 2410 SER Chi-restraints excluded: chain A residue 2426 LEU Chi-restraints excluded: chain A residue 2445 PHE Chi-restraints excluded: chain A residue 2449 GLU Chi-restraints excluded: chain A residue 2466 ILE Chi-restraints excluded: chain A residue 2538 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 166 optimal weight: 0.9990 chunk 19 optimal weight: 0.3980 chunk 98 optimal weight: 2.9990 chunk 126 optimal weight: 6.9990 chunk 97 optimal weight: 0.7980 chunk 145 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 172 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 860 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1576 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14276 Z= 0.174 Angle : 0.486 6.111 19407 Z= 0.257 Chirality : 0.044 0.354 2235 Planarity : 0.003 0.034 2466 Dihedral : 4.295 31.638 2242 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 4.31 % Allowed : 27.77 % Favored : 67.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.20), residues: 1758 helix: 1.40 (0.51), residues: 116 sheet: -0.33 (0.20), residues: 651 loop : -0.67 (0.20), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A2117 HIS 0.002 0.001 HIS A2096 PHE 0.011 0.001 PHE A2565 TYR 0.026 0.001 TYR A1716 ARG 0.005 0.000 ARG A1391 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 160 time to evaluate : 1.600 Fit side-chains REVERT: A 911 MET cc_start: 0.8324 (mmm) cc_final: 0.7504 (mmm) REVERT: A 1269 ASN cc_start: 0.6631 (t0) cc_final: 0.6385 (t0) REVERT: A 1968 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.7362 (mtt180) REVERT: A 2011 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.7060 (mp10) outliers start: 61 outliers final: 50 residues processed: 210 average time/residue: 0.2576 time to fit residues: 80.6323 Evaluate side-chains 211 residues out of total 1569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 159 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 945 PHE Chi-restraints excluded: chain A residue 1006 ILE Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1010 ASP Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1101 THR Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1216 LEU Chi-restraints excluded: chain A residue 1362 THR Chi-restraints excluded: chain A residue 1385 THR Chi-restraints excluded: chain A residue 1390 VAL Chi-restraints excluded: chain A residue 1426 VAL Chi-restraints excluded: chain A residue 1434 ILE Chi-restraints excluded: chain A residue 1500 THR Chi-restraints excluded: chain A residue 1549 THR Chi-restraints excluded: chain A residue 1585 ASP Chi-restraints excluded: chain A residue 1657 VAL Chi-restraints excluded: chain A residue 1664 VAL Chi-restraints excluded: chain A residue 1672 ASP Chi-restraints excluded: chain A residue 1692 SER Chi-restraints excluded: chain A residue 1716 TYR Chi-restraints excluded: chain A residue 1798 THR Chi-restraints excluded: chain A residue 1832 LEU Chi-restraints excluded: chain A residue 1872 ASP Chi-restraints excluded: chain A residue 1879 THR Chi-restraints excluded: chain A residue 1885 MET Chi-restraints excluded: chain A residue 1886 VAL Chi-restraints excluded: chain A residue 1917 THR Chi-restraints excluded: chain A residue 1922 ARG Chi-restraints excluded: chain A residue 1952 GLN Chi-restraints excluded: chain A residue 1968 ARG Chi-restraints excluded: chain A residue 1985 THR Chi-restraints excluded: chain A residue 1995 THR Chi-restraints excluded: chain A residue 1996 VAL Chi-restraints excluded: chain A residue 2011 GLN Chi-restraints excluded: chain A residue 2084 GLN Chi-restraints excluded: chain A residue 2124 ASN Chi-restraints excluded: chain A residue 2252 VAL Chi-restraints excluded: chain A residue 2253 SER Chi-restraints excluded: chain A residue 2317 THR Chi-restraints excluded: chain A residue 2332 ILE Chi-restraints excluded: chain A residue 2351 VAL Chi-restraints excluded: chain A residue 2410 SER Chi-restraints excluded: chain A residue 2426 LEU Chi-restraints excluded: chain A residue 2445 PHE Chi-restraints excluded: chain A residue 2449 GLU Chi-restraints excluded: chain A residue 2454 LEU Chi-restraints excluded: chain A residue 2466 ILE Chi-restraints excluded: chain A residue 2538 ILE Chi-restraints excluded: chain A residue 2553 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 106 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 103 optimal weight: 0.0770 chunk 51 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 135 optimal weight: 7.9990 chunk 156 optimal weight: 0.0870 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 860 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14276 Z= 0.125 Angle : 0.456 6.011 19407 Z= 0.242 Chirality : 0.043 0.350 2235 Planarity : 0.003 0.034 2466 Dihedral : 3.906 26.595 2242 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.11 % Allowed : 28.83 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.20), residues: 1758 helix: 1.56 (0.51), residues: 117 sheet: -0.24 (0.20), residues: 646 loop : -0.60 (0.20), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A2117 HIS 0.002 0.000 HIS A1916 PHE 0.011 0.001 PHE A1897 TYR 0.017 0.001 TYR A1716 ARG 0.004 0.000 ARG A1106 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 169 time to evaluate : 1.639 Fit side-chains REVERT: A 911 MET cc_start: 0.8248 (mmm) cc_final: 0.7499 (mmm) REVERT: A 1269 ASN cc_start: 0.6309 (t0) cc_final: 0.6089 (t0) REVERT: A 1968 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.7294 (mtt180) REVERT: A 2011 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.7022 (mp10) REVERT: A 2130 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8427 (mtmm) outliers start: 44 outliers final: 35 residues processed: 207 average time/residue: 0.2546 time to fit residues: 79.0877 Evaluate side-chains 201 residues out of total 1569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 163 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 945 PHE Chi-restraints excluded: chain A residue 1010 ASP Chi-restraints excluded: chain A residue 1031 MET Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1101 THR Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1216 LEU Chi-restraints excluded: chain A residue 1390 VAL Chi-restraints excluded: chain A residue 1426 VAL Chi-restraints excluded: chain A residue 1469 ASP Chi-restraints excluded: chain A residue 1549 THR Chi-restraints excluded: chain A residue 1585 ASP Chi-restraints excluded: chain A residue 1657 VAL Chi-restraints excluded: chain A residue 1664 VAL Chi-restraints excluded: chain A residue 1716 TYR Chi-restraints excluded: chain A residue 1798 THR Chi-restraints excluded: chain A residue 1832 LEU Chi-restraints excluded: chain A residue 1847 SER Chi-restraints excluded: chain A residue 1886 VAL Chi-restraints excluded: chain A residue 1917 THR Chi-restraints excluded: chain A residue 1922 ARG Chi-restraints excluded: chain A residue 1968 ARG Chi-restraints excluded: chain A residue 1985 THR Chi-restraints excluded: chain A residue 1995 THR Chi-restraints excluded: chain A residue 1996 VAL Chi-restraints excluded: chain A residue 2011 GLN Chi-restraints excluded: chain A residue 2084 GLN Chi-restraints excluded: chain A residue 2124 ASN Chi-restraints excluded: chain A residue 2130 LYS Chi-restraints excluded: chain A residue 2252 VAL Chi-restraints excluded: chain A residue 2253 SER Chi-restraints excluded: chain A residue 2317 THR Chi-restraints excluded: chain A residue 2332 ILE Chi-restraints excluded: chain A residue 2351 VAL Chi-restraints excluded: chain A residue 2410 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 165 optimal weight: 5.9990 chunk 150 optimal weight: 0.7980 chunk 160 optimal weight: 0.1980 chunk 96 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 126 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 145 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 170 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 860 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14276 Z= 0.206 Angle : 0.490 7.852 19407 Z= 0.257 Chirality : 0.045 0.355 2235 Planarity : 0.003 0.036 2466 Dihedral : 3.941 26.793 2240 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.32 % Allowed : 28.69 % Favored : 67.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.20), residues: 1758 helix: 1.58 (0.51), residues: 117 sheet: -0.25 (0.20), residues: 651 loop : -0.60 (0.21), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A2117 HIS 0.003 0.001 HIS A2434 PHE 0.011 0.001 PHE A2565 TYR 0.023 0.001 TYR A1716 ARG 0.004 0.000 ARG A1106 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 162 time to evaluate : 1.760 Fit side-chains REVERT: A 1205 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.8045 (ttt180) REVERT: A 1968 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.7280 (mtt180) REVERT: A 2011 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.7083 (mp10) outliers start: 47 outliers final: 39 residues processed: 204 average time/residue: 0.2686 time to fit residues: 81.9787 Evaluate side-chains 200 residues out of total 1569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 158 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 945 PHE Chi-restraints excluded: chain A residue 1010 ASP Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1101 THR Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1205 ARG Chi-restraints excluded: chain A residue 1216 LEU Chi-restraints excluded: chain A residue 1362 THR Chi-restraints excluded: chain A residue 1385 THR Chi-restraints excluded: chain A residue 1390 VAL Chi-restraints excluded: chain A residue 1426 VAL Chi-restraints excluded: chain A residue 1576 ASN Chi-restraints excluded: chain A residue 1585 ASP Chi-restraints excluded: chain A residue 1657 VAL Chi-restraints excluded: chain A residue 1664 VAL Chi-restraints excluded: chain A residue 1716 TYR Chi-restraints excluded: chain A residue 1832 LEU Chi-restraints excluded: chain A residue 1847 SER Chi-restraints excluded: chain A residue 1886 VAL Chi-restraints excluded: chain A residue 1917 THR Chi-restraints excluded: chain A residue 1922 ARG Chi-restraints excluded: chain A residue 1968 ARG Chi-restraints excluded: chain A residue 1985 THR Chi-restraints excluded: chain A residue 1995 THR Chi-restraints excluded: chain A residue 1996 VAL Chi-restraints excluded: chain A residue 2011 GLN Chi-restraints excluded: chain A residue 2084 GLN Chi-restraints excluded: chain A residue 2124 ASN Chi-restraints excluded: chain A residue 2183 SER Chi-restraints excluded: chain A residue 2252 VAL Chi-restraints excluded: chain A residue 2253 SER Chi-restraints excluded: chain A residue 2317 THR Chi-restraints excluded: chain A residue 2332 ILE Chi-restraints excluded: chain A residue 2351 VAL Chi-restraints excluded: chain A residue 2410 SER Chi-restraints excluded: chain A residue 2445 PHE Chi-restraints excluded: chain A residue 2449 GLU Chi-restraints excluded: chain A residue 2454 LEU Chi-restraints excluded: chain A residue 2466 ILE Chi-restraints excluded: chain A residue 2569 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 103 optimal weight: 0.1980 chunk 80 optimal weight: 0.5980 chunk 118 optimal weight: 0.4980 chunk 178 optimal weight: 8.9990 chunk 164 optimal weight: 0.0970 chunk 142 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 112 optimal weight: 0.0000 chunk 151 optimal weight: 0.6980 overall best weight: 0.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 860 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14276 Z= 0.118 Angle : 0.466 8.034 19407 Z= 0.246 Chirality : 0.043 0.346 2235 Planarity : 0.003 0.034 2466 Dihedral : 3.712 22.848 2240 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.19 % Allowed : 29.89 % Favored : 67.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.21), residues: 1758 helix: 1.68 (0.51), residues: 117 sheet: -0.13 (0.20), residues: 644 loop : -0.54 (0.21), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1826 HIS 0.002 0.000 HIS A1546 PHE 0.012 0.001 PHE A1897 TYR 0.014 0.001 TYR A1716 ARG 0.003 0.000 ARG A1106 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 168 time to evaluate : 1.508 Fit side-chains REVERT: A 911 MET cc_start: 0.8142 (mmm) cc_final: 0.7388 (mmm) REVERT: A 1235 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8775 (mp) REVERT: A 1918 MET cc_start: 0.8666 (mpp) cc_final: 0.8400 (mpp) REVERT: A 1968 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.7232 (mtt180) outliers start: 31 outliers final: 27 residues processed: 195 average time/residue: 0.2702 time to fit residues: 78.6103 Evaluate side-chains 191 residues out of total 1569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 162 time to evaluate : 1.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 860 HIS Chi-restraints excluded: chain A residue 945 PHE Chi-restraints excluded: chain A residue 1010 ASP Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1101 THR Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1216 LEU Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1390 VAL Chi-restraints excluded: chain A residue 1426 VAL Chi-restraints excluded: chain A residue 1576 ASN Chi-restraints excluded: chain A residue 1585 ASP Chi-restraints excluded: chain A residue 1657 VAL Chi-restraints excluded: chain A residue 1664 VAL Chi-restraints excluded: chain A residue 1716 TYR Chi-restraints excluded: chain A residue 1798 THR Chi-restraints excluded: chain A residue 1832 LEU Chi-restraints excluded: chain A residue 1886 VAL Chi-restraints excluded: chain A residue 1917 THR Chi-restraints excluded: chain A residue 1922 ARG Chi-restraints excluded: chain A residue 1968 ARG Chi-restraints excluded: chain A residue 1996 VAL Chi-restraints excluded: chain A residue 2084 GLN Chi-restraints excluded: chain A residue 2124 ASN Chi-restraints excluded: chain A residue 2252 VAL Chi-restraints excluded: chain A residue 2253 SER Chi-restraints excluded: chain A residue 2317 THR Chi-restraints excluded: chain A residue 2332 ILE Chi-restraints excluded: chain A residue 2454 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 43 optimal weight: 7.9990 chunk 130 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 860 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.125799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.099695 restraints weight = 16607.313| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 1.58 r_work: 0.2900 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 14276 Z= 0.350 Angle : 0.557 6.891 19407 Z= 0.291 Chirality : 0.046 0.357 2235 Planarity : 0.003 0.037 2466 Dihedral : 4.179 28.344 2240 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 3.32 % Allowed : 28.76 % Favored : 67.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.20), residues: 1758 helix: 1.53 (0.51), residues: 117 sheet: -0.22 (0.20), residues: 647 loop : -0.67 (0.20), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 942 HIS 0.004 0.001 HIS A2434 PHE 0.013 0.001 PHE A1984 TYR 0.034 0.001 TYR A1716 ARG 0.004 0.000 ARG A1106 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3083.65 seconds wall clock time: 56 minutes 6.64 seconds (3366.64 seconds total)