Starting phenix.real_space_refine on Sat Jun 14 06:35:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tbw_25800/06_2025/7tbw_25800.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tbw_25800/06_2025/7tbw_25800.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tbw_25800/06_2025/7tbw_25800.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tbw_25800/06_2025/7tbw_25800.map" model { file = "/net/cci-nas-00/data/ceres_data/7tbw_25800/06_2025/7tbw_25800.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tbw_25800/06_2025/7tbw_25800.cif" } resolution = 3.1 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= 0.002 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 90 5.16 5 C 9895 2.51 5 N 2563 2.21 5 O 2782 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 69 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15338 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 15129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1928, 15129 Classifications: {'peptide': 1928} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PCIS': 2, 'PTRANS': 91, 'TRANS': 1834} Chain breaks: 14 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 252 Unresolved non-hydrogen dihedrals: 166 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 87 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} 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 Chain: "A" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 120 Unusual residues: {' MG': 2, 'ATP': 2, 'CLR': 1, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 8.76, per 1000 atoms: 0.57 Number of scatterers: 15338 At special positions: 0 Unit cell: (105.5, 91.152, 207.624, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 90 16.00 P 6 15.00 Mg 2 11.99 O 2782 8.00 N 2563 7.00 C 9895 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 81 " distance=2.03 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 309 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 504 " distance=2.03 Simple disulfide: pdb=" SG CYS A 626 " - pdb=" SG CYS A1465 " distance=2.03 Simple disulfide: pdb=" SG CYS A1418 " - pdb=" SG CYS A1429 " distance=2.03 Simple disulfide: pdb=" SG CYS A1463 " - pdb=" SG CYS A1477 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-3 " BMA C 3 " - " BMA C 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " BETA1-6 " BMA C 3 " - " BMA C 5 " NAG-ASN " NAG A2506 " - " ASN A 98 " " NAG A2507 " - " ASN A1637 " " NAG B 1 " - " ASN A 400 " " NAG C 1 " - " ASN A1504 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.93 Conformation dependent library (CDL) restraints added in 1.9 seconds 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3606 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 10 sheets defined 58.2% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.12 Creating SS restraints... Processing helix chain 'A' and resid 3 through 21 Processing helix chain 'A' and resid 21 through 45 removed outlier: 3.715A pdb=" N LEU A 25 " --> pdb=" O GLN A 21 " (cutoff:3.500A) Proline residue: A 32 - end of helix removed outlier: 4.163A pdb=" N ILE A 35 " --> pdb=" O TRP A 31 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER A 45 " --> pdb=" O SER A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 65 through 76 removed outlier: 3.533A pdb=" N ASN A 76 " --> pdb=" O GLY A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 90 Processing helix chain 'A' and resid 100 through 118 removed outlier: 3.516A pdb=" N ARG A 104 " --> pdb=" O SER A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 136 Processing helix chain 'A' and resid 200 through 210 removed outlier: 3.571A pdb=" N LEU A 206 " --> pdb=" O GLU A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 227 removed outlier: 3.973A pdb=" N GLU A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 234 removed outlier: 3.815A pdb=" N MET A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ASP A 234 " --> pdb=" O ARG A 230 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 229 through 234' Processing helix chain 'A' and resid 235 through 240 removed outlier: 3.959A pdb=" N LEU A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 275 removed outlier: 3.673A pdb=" N GLU A 256 " --> pdb=" O LYS A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 289 removed outlier: 3.537A pdb=" N THR A 289 " --> pdb=" O VAL A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 309 removed outlier: 3.730A pdb=" N GLN A 302 " --> pdb=" O THR A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 364 Processing helix chain 'A' and resid 368 through 380 removed outlier: 3.696A pdb=" N TRP A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) Proline residue: A 377 - end of helix Processing helix chain 'A' and resid 389 through 405 Processing helix chain 'A' and resid 406 through 410 removed outlier: 4.380A pdb=" N PHE A 409 " --> pdb=" O LEU A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 417 Processing helix chain 'A' and resid 418 through 427 removed outlier: 4.513A pdb=" N LYS A 422 " --> pdb=" O GLU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 441 Processing helix chain 'A' and resid 444 through 454 removed outlier: 3.509A pdb=" N ASP A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 468 Processing helix chain 'A' and resid 483 through 502 removed outlier: 3.581A pdb=" N ALA A 487 " --> pdb=" O THR A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 529 Processing helix chain 'A' and resid 586 through 591 removed outlier: 3.781A pdb=" N TRP A 590 " --> pdb=" O MET A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 609 Processing helix chain 'A' and resid 630 through 644 removed outlier: 3.578A pdb=" N ARG A 634 " --> pdb=" O ASP A 630 " (cutoff:3.500A) Proline residue: A 641 - end of helix Processing helix chain 'A' and resid 645 through 665 removed outlier: 3.747A pdb=" N SER A 651 " --> pdb=" O ALA A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 675 Processing helix chain 'A' and resid 677 through 707 removed outlier: 3.913A pdb=" N LEU A 681 " --> pdb=" O ASP A 677 " (cutoff:3.500A) Proline residue: A 692 - end of helix Processing helix chain 'A' and resid 714 through 738 Processing helix chain 'A' and resid 742 through 757 removed outlier: 3.934A pdb=" N ALA A 748 " --> pdb=" O ASN A 744 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N GLY A 751 " --> pdb=" O ALA A 747 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE A 752 " --> pdb=" O ALA A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 768 removed outlier: 3.691A pdb=" N VAL A 762 " --> pdb=" O TYR A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 780 Processing helix chain 'A' and resid 784 through 800 removed outlier: 3.506A pdb=" N GLY A 788 " --> pdb=" O PRO A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 846 Processing helix chain 'A' and resid 939 through 947 Processing helix chain 'A' and resid 967 through 973 removed outlier: 3.582A pdb=" N ILE A 971 " --> pdb=" O GLU A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1000 Processing helix chain 'A' and resid 1004 through 1020 removed outlier: 3.809A pdb=" N GLY A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1033 Processing helix chain 'A' and resid 1034 through 1046 Processing helix chain 'A' and resid 1064 through 1078 removed outlier: 3.553A pdb=" N ARG A1069 " --> pdb=" O PRO A1065 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY A1070 " --> pdb=" O TYR A1066 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1097 Processing helix chain 'A' and resid 1114 through 1122 removed outlier: 3.552A pdb=" N LEU A1122 " --> pdb=" O LEU A1118 " (cutoff:3.500A) Processing helix chain 'A' and resid 1182 through 1191 removed outlier: 3.636A pdb=" N HIS A1190 " --> pdb=" O LEU A1186 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A1191 " --> pdb=" O ILE A1187 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1228 removed outlier: 3.520A pdb=" N ARG A1228 " --> pdb=" O GLU A1224 " (cutoff:3.500A) Processing helix chain 'A' and resid 1243 through 1254 Processing helix chain 'A' and resid 1321 through 1342 Processing helix chain 'A' and resid 1343 through 1351 removed outlier: 3.554A pdb=" N PHE A1347 " --> pdb=" O SER A1343 " (cutoff:3.500A) Processing helix chain 'A' and resid 1351 through 1365 removed outlier: 4.113A pdb=" N ALA A1355 " --> pdb=" O ILE A1351 " (cutoff:3.500A) Processing helix chain 'A' and resid 1400 through 1409 removed outlier: 4.275A pdb=" N LEU A1404 " --> pdb=" O GLY A1400 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR A1409 " --> pdb=" O LEU A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1445 through 1450 Processing helix chain 'A' and resid 1504 through 1523 removed outlier: 3.701A pdb=" N ASN A1523 " --> pdb=" O LYS A1519 " (cutoff:3.500A) Processing helix chain 'A' and resid 1548 through 1561 Processing helix chain 'A' and resid 1570 through 1583 Processing helix chain 'A' and resid 1600 through 1618 removed outlier: 3.500A pdb=" N SER A1604 " --> pdb=" O HIS A1600 " (cutoff:3.500A) Processing helix chain 'A' and resid 1643 through 1668 removed outlier: 3.968A pdb=" N THR A1651 " --> pdb=" O ALA A1647 " (cutoff:3.500A) Processing helix chain 'A' and resid 1671 through 1681 removed outlier: 3.924A pdb=" N PHE A1675 " --> pdb=" O SER A1671 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU A1676 " --> pdb=" O PHE A1672 " (cutoff:3.500A) Processing helix chain 'A' and resid 1683 through 1691 Processing helix chain 'A' and resid 1694 through 1724 Proline residue: A1713 - end of helix Processing helix chain 'A' and resid 1734 through 1754 Proline residue: A1751 - end of helix Processing helix chain 'A' and resid 1762 through 1790 Processing helix chain 'A' and resid 1795 through 1808 removed outlier: 3.910A pdb=" N ILE A1799 " --> pdb=" O LYS A1795 " (cutoff:3.500A) Processing helix chain 'A' and resid 1810 through 1834 Processing helix chain 'A' and resid 1848 through 1872 removed outlier: 4.213A pdb=" N ASN A1852 " --> pdb=" O LEU A1848 " (cutoff:3.500A) Processing helix chain 'A' and resid 1892 through 1905 Processing helix chain 'A' and resid 1951 through 1961 Processing helix chain 'A' and resid 1980 through 1986 removed outlier: 3.993A pdb=" N VAL A1984 " --> pdb=" O ASN A1980 " (cutoff:3.500A) Processing helix chain 'A' and resid 2002 through 2015 Processing helix chain 'A' and resid 2017 through 2019 No H-bonds generated for 'chain 'A' and resid 2017 through 2019' Processing helix chain 'A' and resid 2020 through 2031 Processing helix chain 'A' and resid 2041 through 2045 Processing helix chain 'A' and resid 2046 through 2059 removed outlier: 4.171A pdb=" N ARG A2051 " --> pdb=" O GLY A2047 " (cutoff:3.500A) Processing helix chain 'A' and resid 2076 through 2093 Processing helix chain 'A' and resid 2103 through 2110 removed outlier: 3.755A pdb=" N CYS A2107 " --> pdb=" O SER A2103 " (cutoff:3.500A) Processing helix chain 'A' and resid 2128 through 2135 Processing helix chain 'A' and resid 2152 through 2163 Processing helix chain 'A' and resid 2186 through 2197 removed outlier: 3.723A pdb=" N ILE A2190 " --> pdb=" O SER A2186 " (cutoff:3.500A) Processing helix chain 'A' and resid 2212 through 2224 removed outlier: 3.743A pdb=" N VAL A2216 " --> pdb=" O THR A2212 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN A2224 " --> pdb=" O PHE A2220 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 50 Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 60 removed outlier: 6.507A pdb=" N GLY A 616 " --> pdb=" O VAL A1590 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N VAL A1592 " --> pdb=" O GLY A 616 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TYR A 618 " --> pdb=" O VAL A1592 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N PHE A1594 " --> pdb=" O TYR A 618 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N GLN A 620 " --> pdb=" O PHE A1594 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N TYR A1388 " --> pdb=" O GLY A1533 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N PHE A1535 " --> pdb=" O TYR A1388 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N PHE A1390 " --> pdb=" O PHE A1535 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LEU A1537 " --> pdb=" O PHE A1390 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N SER A1392 " --> pdb=" O LEU A1537 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N VAL A1539 " --> pdb=" O SER A1392 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP A1499 " --> pdb=" O PRO A1487 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR A1437 " --> pdb=" O GLN A1488 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 535 through 537 removed outlier: 6.198A pdb=" N VAL A 552 " --> pdb=" O THR A1630 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N PHE A1632 " --> pdb=" O VAL A 552 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N TYR A 554 " --> pdb=" O PHE A1632 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 922 through 923 removed outlier: 4.434A pdb=" N LEU A 904 " --> pdb=" O SER A 954 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N SER A 954 " --> pdb=" O LEU A 904 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 975 through 978 removed outlier: 5.909A pdb=" N SER A 930 " --> pdb=" O ALA A1102 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ILE A1104 " --> pdb=" O SER A 930 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU A 932 " --> pdb=" O ILE A1104 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N SER A1105 " --> pdb=" O LEU A1109 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N LEU A1109 " --> pdb=" O SER A1105 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1195 through 1198 removed outlier: 5.951A pdb=" N LEU A1196 " --> pdb=" O VAL A1207 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL A1207 " --> pdb=" O LEU A1196 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU A1198 " --> pdb=" O THR A1205 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1934 through 1936 removed outlier: 3.655A pdb=" N LEU A1912 " --> pdb=" O ILE A1936 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU A1917 " --> pdb=" O ARG A1967 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ARG A1967 " --> pdb=" O LEU A1917 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1989 through 1991 removed outlier: 6.282A pdb=" N GLY A1989 " --> pdb=" O PHE A2067 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ASP A2069 " --> pdb=" O GLY A1989 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N CYS A1991 " --> pdb=" O ASP A2069 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N PHE A1942 " --> pdb=" O LEU A2099 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N CYS A1941 " --> pdb=" O ARG A2113 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ALA A2115 " --> pdb=" O CYS A1941 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLY A1943 " --> pdb=" O ALA A2115 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N MET A2117 " --> pdb=" O GLY A1943 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU A1945 " --> pdb=" O MET A2117 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1989 through 1991 removed outlier: 6.282A pdb=" N GLY A1989 " --> pdb=" O PHE A2067 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ASP A2069 " --> pdb=" O GLY A1989 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N CYS A1991 " --> pdb=" O ASP A2069 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N PHE A1942 " --> pdb=" O LEU A2099 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N CYS A1941 " --> pdb=" O ARG A2113 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ALA A2115 " --> pdb=" O CYS A1941 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLY A1943 " --> pdb=" O ALA A2115 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N MET A2117 " --> pdb=" O GLY A1943 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU A1945 " --> pdb=" O MET A2117 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 2168 through 2169 removed outlier: 3.994A pdb=" N GLN A2177 " --> pdb=" O LYS A2169 " (cutoff:3.500A) 815 hydrogen bonds defined for protein. 2382 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.99 Time building geometry restraints manager: 4.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4830 1.34 - 1.46: 3558 1.46 - 1.58: 7146 1.58 - 1.70: 10 1.70 - 1.81: 146 Bond restraints: 15690 Sorted by residual: bond pdb=" C4 ATP A2503 " pdb=" C5 ATP A2503 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.93e+01 bond pdb=" C4 ATP A2502 " pdb=" C5 ATP A2502 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.71e+01 bond pdb=" C5 ATP A2502 " pdb=" C6 ATP A2502 " ideal model delta sigma weight residual 1.409 1.483 -0.074 1.00e-02 1.00e+04 5.42e+01 bond pdb=" C5 ATP A2503 " pdb=" C6 ATP A2503 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.32e+01 bond pdb=" C8 ATP A2502 " pdb=" N7 ATP A2502 " ideal model delta sigma weight residual 1.310 1.358 -0.048 1.00e-02 1.00e+04 2.34e+01 ... (remaining 15685 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.88: 21202 3.88 - 7.76: 89 7.76 - 11.63: 6 11.63 - 15.51: 2 15.51 - 19.39: 2 Bond angle restraints: 21301 Sorted by residual: angle pdb=" PB ATP A2503 " pdb=" O3B ATP A2503 " pdb=" PG ATP A2503 " ideal model delta sigma weight residual 139.87 120.48 19.39 1.00e+00 1.00e+00 3.76e+02 angle pdb=" PB ATP A2502 " pdb=" O3B ATP A2502 " pdb=" PG ATP A2502 " ideal model delta sigma weight residual 139.87 121.15 18.72 1.00e+00 1.00e+00 3.50e+02 angle pdb=" PA ATP A2502 " pdb=" O3A ATP A2502 " pdb=" PB ATP A2502 " ideal model delta sigma weight residual 136.83 121.34 15.49 1.00e+00 1.00e+00 2.40e+02 angle pdb=" PA ATP A2503 " pdb=" O3A ATP A2503 " pdb=" PB ATP A2503 " ideal model delta sigma weight residual 136.83 122.51 14.32 1.00e+00 1.00e+00 2.05e+02 angle pdb=" C5 ATP A2503 " pdb=" C4 ATP A2503 " pdb=" N3 ATP A2503 " ideal model delta sigma weight residual 126.80 118.68 8.12 1.00e+00 1.00e+00 6.60e+01 ... (remaining 21296 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.46: 9038 23.46 - 46.93: 402 46.93 - 70.39: 51 70.39 - 93.85: 33 93.85 - 117.32: 18 Dihedral angle restraints: 9542 sinusoidal: 3963 harmonic: 5579 Sorted by residual: dihedral pdb=" CB CYS A1463 " pdb=" SG CYS A1463 " pdb=" SG CYS A1477 " pdb=" CB CYS A1477 " ideal model delta sinusoidal sigma weight residual -86.00 -150.28 64.28 1 1.00e+01 1.00e-02 5.43e+01 dihedral pdb=" CA SER A 783 " pdb=" C SER A 783 " pdb=" N PRO A 784 " pdb=" CA PRO A 784 " ideal model delta harmonic sigma weight residual 180.00 147.82 32.18 0 5.00e+00 4.00e-02 4.14e+01 dihedral pdb=" CA LEU A2180 " pdb=" C LEU A2180 " pdb=" N PRO A2181 " pdb=" CA PRO A2181 " ideal model delta harmonic sigma weight residual -180.00 -157.26 -22.74 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 9539 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2244 0.071 - 0.142: 190 0.142 - 0.212: 1 0.212 - 0.283: 4 0.283 - 0.354: 2 Chirality restraints: 2441 Sorted by residual: chirality pdb=" C14 CLR A2501 " pdb=" C13 CLR A2501 " pdb=" C15 CLR A2501 " pdb=" C8 CLR A2501 " both_signs ideal model delta sigma weight residual False -2.32 -2.67 0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" C5 BMA C 4 " pdb=" C4 BMA C 4 " pdb=" C6 BMA C 4 " pdb=" O5 BMA C 4 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.88e+00 ... (remaining 2438 not shown) Planarity restraints: 2663 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 783 " 0.044 5.00e-02 4.00e+02 6.59e-02 6.95e+00 pdb=" N PRO A 784 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 784 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 784 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 386 " 0.034 5.00e-02 4.00e+02 5.11e-02 4.19e+00 pdb=" N PRO A 387 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 387 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 387 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 759 " -0.027 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO A 760 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 760 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 760 " -0.023 5.00e-02 4.00e+02 ... (remaining 2660 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 188 2.66 - 3.22: 14627 3.22 - 3.78: 24311 3.78 - 4.34: 32517 4.34 - 4.90: 52827 Nonbonded interactions: 124470 Sorted by model distance: nonbonded pdb=" O2B ATP A2503 " pdb="MG MG A2504 " model vdw 2.101 2.170 nonbonded pdb=" OG SER A1953 " pdb="MG MG A2504 " model vdw 2.149 2.170 nonbonded pdb=" O2G ATP A2503 " pdb="MG MG A2504 " model vdw 2.204 2.170 nonbonded pdb=" OE1 GLN A1993 " pdb="MG MG A2504 " model vdw 2.209 2.170 nonbonded pdb=" OD1 ASN A 820 " pdb=" OG1 THR A 822 " model vdw 2.254 3.040 ... (remaining 124465 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.640 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: 0.620 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 37.630 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 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 : 0.003 0.083 15706 Z= 0.209 Angle : 0.626 19.392 21340 Z= 0.393 Chirality : 0.041 0.354 2441 Planarity : 0.003 0.066 2659 Dihedral : 14.879 117.319 5918 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.23 % Allowed : 7.24 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 1.09 % 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: -2.02 (0.18), residues: 1898 helix: -0.18 (0.15), residues: 1070 sheet: -1.14 (0.40), residues: 154 loop : -3.31 (0.20), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1334 HIS 0.002 0.000 HIS A1626 PHE 0.009 0.001 PHE A1663 TYR 0.006 0.001 TYR A1698 ARG 0.002 0.000 ARG A 437 Details of bonding type rmsd link_NAG-ASN : bond 0.00197 ( 4) link_NAG-ASN : angle 1.35544 ( 12) link_BETA1-4 : bond 0.00441 ( 3) link_BETA1-4 : angle 1.12809 ( 9) hydrogen bonds : bond 0.12869 ( 811) hydrogen bonds : angle 4.98277 ( 2382) link_BETA1-6 : bond 0.00399 ( 1) link_BETA1-6 : angle 1.31467 ( 3) SS BOND : bond 0.00220 ( 6) SS BOND : angle 0.95366 ( 12) link_BETA1-3 : bond 0.00263 ( 1) link_BETA1-3 : angle 1.29950 ( 3) covalent geometry : bond 0.00303 (15690) covalent geometry : angle 0.62490 (21301) Misc. bond : bond 0.00050 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 334 time to evaluate : 1.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 575 ASP cc_start: 0.7278 (p0) cc_final: 0.6916 (p0) REVERT: A 601 GLU cc_start: 0.6987 (mm-30) cc_final: 0.6701 (mm-30) REVERT: A 815 GLU cc_start: 0.5963 (mm-30) cc_final: 0.5509 (mm-30) REVERT: A 827 MET cc_start: 0.7791 (tpp) cc_final: 0.7489 (tpt) REVERT: A 831 ASP cc_start: 0.6880 (m-30) cc_final: 0.6565 (m-30) REVERT: A 984 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7622 (pp) REVERT: A 1430 GLN cc_start: 0.6846 (mp10) cc_final: 0.6071 (tm-30) REVERT: A 1720 ILE cc_start: 0.7638 (mt) cc_final: 0.7131 (mt) REVERT: A 1799 ILE cc_start: 0.5837 (mp) cc_final: 0.5529 (mt) REVERT: A 1802 ILE cc_start: 0.7494 (mp) cc_final: 0.7245 (mt) REVERT: A 1861 VAL cc_start: 0.8118 (t) cc_final: 0.7869 (t) REVERT: A 2180 LEU cc_start: 0.6528 (OUTLIER) cc_final: 0.5640 (mm) outliers start: 20 outliers final: 11 residues processed: 351 average time/residue: 0.3155 time to fit residues: 158.0850 Evaluate side-chains 216 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 203 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 858 PHE Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1441 VAL Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1602 ILE Chi-restraints excluded: chain A residue 1812 HIS Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 2110 LEU Chi-restraints excluded: chain A residue 2180 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 7.9990 chunk 145 optimal weight: 0.5980 chunk 80 optimal weight: 0.0870 chunk 49 optimal weight: 0.0470 chunk 98 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 91 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN A 302 GLN A 356 ASN A 508 ASN A 551 HIS A 621 GLN A 732 GLN A 744 ASN A 935 ASN A 973 GLN A1038 GLN A1185 ASN A1326 GLN A1393 ASN A1600 HIS A1610 ASN A1678 GLN A1702 ASN A1800 ASN A1871 GLN A1948 ASN A2172 HIS A2177 GLN A2179 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.154535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.118245 restraints weight = 24400.168| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.84 r_work: 0.3385 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15706 Z= 0.119 Angle : 0.596 9.970 21340 Z= 0.282 Chirality : 0.041 0.202 2441 Planarity : 0.004 0.086 2659 Dihedral : 10.795 91.473 2398 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.46 % Allowed : 11.72 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 1.09 % 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: -0.79 (0.19), residues: 1898 helix: 0.82 (0.16), residues: 1095 sheet: -0.97 (0.40), residues: 152 loop : -2.81 (0.22), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 278 HIS 0.006 0.001 HIS A 551 PHE 0.016 0.001 PHE A1786 TYR 0.014 0.001 TYR A 115 ARG 0.007 0.000 ARG A2030 Details of bonding type rmsd link_NAG-ASN : bond 0.00256 ( 4) link_NAG-ASN : angle 1.44356 ( 12) link_BETA1-4 : bond 0.00422 ( 3) link_BETA1-4 : angle 2.96790 ( 9) hydrogen bonds : bond 0.03648 ( 811) hydrogen bonds : angle 3.96463 ( 2382) link_BETA1-6 : bond 0.01034 ( 1) link_BETA1-6 : angle 2.60319 ( 3) SS BOND : bond 0.00520 ( 6) SS BOND : angle 0.98412 ( 12) link_BETA1-3 : bond 0.01091 ( 1) link_BETA1-3 : angle 1.95455 ( 3) covalent geometry : bond 0.00257 (15690) covalent geometry : angle 0.59053 (21301) Misc. bond : bond 0.00052 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 212 time to evaluate : 1.638 Fit side-chains revert: symmetry clash REVERT: A 8 ARG cc_start: 0.7561 (mtt180) cc_final: 0.6773 (tpt170) REVERT: A 415 MET cc_start: 0.8388 (tmm) cc_final: 0.7748 (tmm) REVERT: A 575 ASP cc_start: 0.7647 (p0) cc_final: 0.7374 (p0) REVERT: A 622 MET cc_start: 0.7599 (mtt) cc_final: 0.7368 (mtt) REVERT: A 640 MET cc_start: 0.8431 (tpp) cc_final: 0.8039 (tpp) REVERT: A 815 GLU cc_start: 0.6380 (mm-30) cc_final: 0.6079 (mm-30) REVERT: A 984 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7832 (pp) REVERT: A 1078 TYR cc_start: 0.8760 (m-10) cc_final: 0.8434 (m-10) REVERT: A 1126 TYR cc_start: 0.6913 (m-80) cc_final: 0.6497 (m-80) REVERT: A 1127 TYR cc_start: 0.8119 (m-80) cc_final: 0.7823 (m-80) REVERT: A 1190 HIS cc_start: 0.5391 (m-70) cc_final: 0.4365 (m170) REVERT: A 1430 GLN cc_start: 0.6770 (mp10) cc_final: 0.5936 (tm-30) REVERT: A 1572 ARG cc_start: 0.7771 (mtm180) cc_final: 0.7205 (mmt90) REVERT: A 1802 ILE cc_start: 0.7614 (OUTLIER) cc_final: 0.7379 (mt) REVERT: A 1813 PHE cc_start: 0.8215 (t80) cc_final: 0.7892 (t80) REVERT: A 2000 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8318 (mt) outliers start: 40 outliers final: 21 residues processed: 241 average time/residue: 0.2783 time to fit residues: 101.0613 Evaluate side-chains 213 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 189 time to evaluate : 1.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1441 VAL Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1496 ILE Chi-restraints excluded: chain A residue 1602 ILE Chi-restraints excluded: chain A residue 1630 THR Chi-restraints excluded: chain A residue 1802 ILE Chi-restraints excluded: chain A residue 1812 HIS Chi-restraints excluded: chain A residue 1833 GLU Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 2000 LEU Chi-restraints excluded: chain A residue 2046 SER Chi-restraints excluded: chain A residue 2110 LEU Chi-restraints excluded: chain A residue 2167 VAL Chi-restraints excluded: chain A residue 2176 LEU Chi-restraints excluded: chain A residue 2180 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 105 optimal weight: 0.1980 chunk 6 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 183 optimal weight: 6.9990 chunk 167 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 171 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN ** A1089 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1610 ASN A1688 GLN A1800 ASN A1826 GLN A2179 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.144124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.102464 restraints weight = 23970.074| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.31 r_work: 0.3188 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 15706 Z= 0.154 Angle : 0.629 11.539 21340 Z= 0.303 Chirality : 0.043 0.208 2441 Planarity : 0.004 0.092 2659 Dihedral : 8.584 74.197 2394 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.19 % Allowed : 12.03 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 1.09 % 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: -0.18 (0.20), residues: 1898 helix: 1.23 (0.16), residues: 1098 sheet: -0.77 (0.39), residues: 160 loop : -2.42 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 484 HIS 0.005 0.001 HIS A2006 PHE 0.021 0.001 PHE A1535 TYR 0.017 0.001 TYR A 793 ARG 0.014 0.001 ARG A 500 Details of bonding type rmsd link_NAG-ASN : bond 0.00328 ( 4) link_NAG-ASN : angle 1.56962 ( 12) link_BETA1-4 : bond 0.00666 ( 3) link_BETA1-4 : angle 3.68236 ( 9) hydrogen bonds : bond 0.03890 ( 811) hydrogen bonds : angle 3.92596 ( 2382) link_BETA1-6 : bond 0.02982 ( 1) link_BETA1-6 : angle 3.44313 ( 3) SS BOND : bond 0.00260 ( 6) SS BOND : angle 1.20886 ( 12) link_BETA1-3 : bond 0.01249 ( 1) link_BETA1-3 : angle 2.06651 ( 3) covalent geometry : bond 0.00347 (15690) covalent geometry : angle 0.62177 (21301) Misc. bond : bond 0.00076 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 197 time to evaluate : 1.698 Fit side-chains revert: symmetry clash REVERT: A 8 ARG cc_start: 0.7778 (mtt180) cc_final: 0.7290 (mpt-90) REVERT: A 302 GLN cc_start: 0.7139 (tp40) cc_final: 0.6671 (mp10) REVERT: A 518 TRP cc_start: 0.7444 (m100) cc_final: 0.6742 (m-10) REVERT: A 622 MET cc_start: 0.8640 (mtt) cc_final: 0.8408 (mtt) REVERT: A 640 MET cc_start: 0.8780 (tpt) cc_final: 0.8360 (tpp) REVERT: A 643 PHE cc_start: 0.8173 (m-10) cc_final: 0.7900 (m-10) REVERT: A 984 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8161 (pp) REVERT: A 1078 TYR cc_start: 0.8927 (m-10) cc_final: 0.8574 (m-10) REVERT: A 1126 TYR cc_start: 0.7119 (m-80) cc_final: 0.6679 (m-80) REVERT: A 1344 ARG cc_start: 0.8463 (mtt180) cc_final: 0.8060 (mtt-85) REVERT: A 1427 THR cc_start: 0.7396 (OUTLIER) cc_final: 0.7150 (m) REVERT: A 1572 ARG cc_start: 0.7879 (mtm180) cc_final: 0.7263 (mmt90) REVERT: A 1800 ASN cc_start: 0.7258 (t0) cc_final: 0.7026 (t0) REVERT: A 1813 PHE cc_start: 0.8508 (t80) cc_final: 0.8239 (t80) REVERT: A 2179 GLN cc_start: 0.7416 (OUTLIER) cc_final: 0.6306 (mt0) outliers start: 52 outliers final: 33 residues processed: 233 average time/residue: 0.2768 time to fit residues: 98.1644 Evaluate side-chains 216 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 180 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 856 TRP Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1402 LEU Chi-restraints excluded: chain A residue 1427 THR Chi-restraints excluded: chain A residue 1441 VAL Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1497 LEU Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1602 ILE Chi-restraints excluded: chain A residue 1648 LEU Chi-restraints excluded: chain A residue 1812 HIS Chi-restraints excluded: chain A residue 1833 GLU Chi-restraints excluded: chain A residue 1847 ASP Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 2046 SER Chi-restraints excluded: chain A residue 2110 LEU Chi-restraints excluded: chain A residue 2118 VAL Chi-restraints excluded: chain A residue 2125 LEU Chi-restraints excluded: chain A residue 2139 TYR Chi-restraints excluded: chain A residue 2140 THR Chi-restraints excluded: chain A residue 2179 GLN Chi-restraints excluded: chain A residue 2180 LEU Chi-restraints excluded: chain A residue 2203 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 190 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 185 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 184 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 179 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 744 ASN A1393 ASN ** A1634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1986 GLN A2179 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.138013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.096761 restraints weight = 23736.873| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.47 r_work: 0.3040 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 15706 Z= 0.191 Angle : 0.649 8.961 21340 Z= 0.317 Chirality : 0.044 0.198 2441 Planarity : 0.005 0.106 2659 Dihedral : 8.304 80.050 2394 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 3.38 % Allowed : 12.95 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.05 % 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: -0.07 (0.20), residues: 1898 helix: 1.26 (0.16), residues: 1098 sheet: -0.75 (0.38), residues: 165 loop : -2.24 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 278 HIS 0.006 0.001 HIS A 551 PHE 0.026 0.002 PHE A 82 TYR 0.015 0.001 TYR A 115 ARG 0.006 0.001 ARG A 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00274 ( 4) link_NAG-ASN : angle 1.96161 ( 12) link_BETA1-4 : bond 0.00391 ( 3) link_BETA1-4 : angle 3.19090 ( 9) hydrogen bonds : bond 0.04140 ( 811) hydrogen bonds : angle 4.01082 ( 2382) link_BETA1-6 : bond 0.00901 ( 1) link_BETA1-6 : angle 1.51740 ( 3) SS BOND : bond 0.00601 ( 6) SS BOND : angle 1.67961 ( 12) link_BETA1-3 : bond 0.00320 ( 1) link_BETA1-3 : angle 1.78960 ( 3) covalent geometry : bond 0.00445 (15690) covalent geometry : angle 0.64300 (21301) Misc. bond : bond 0.00093 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 175 time to evaluate : 1.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.7751 (mtt180) cc_final: 0.7143 (tpt170) REVERT: A 83 ARG cc_start: 0.8206 (tpt90) cc_final: 0.7825 (ttm-80) REVERT: A 302 GLN cc_start: 0.7140 (tp40) cc_final: 0.6690 (mp10) REVERT: A 415 MET cc_start: 0.8464 (tmm) cc_final: 0.7814 (tmm) REVERT: A 518 TRP cc_start: 0.7489 (m100) cc_final: 0.6899 (m-10) REVERT: A 640 MET cc_start: 0.8688 (tpt) cc_final: 0.8465 (tpp) REVERT: A 909 ARG cc_start: 0.7271 (mtt180) cc_final: 0.7021 (mtp-110) REVERT: A 984 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8224 (pp) REVERT: A 1078 TYR cc_start: 0.8817 (m-10) cc_final: 0.8506 (m-10) REVERT: A 1190 HIS cc_start: 0.5430 (m-70) cc_final: 0.4433 (m170) REVERT: A 1344 ARG cc_start: 0.8410 (mtt180) cc_final: 0.8045 (mtt-85) REVERT: A 1388 TYR cc_start: 0.8779 (m-80) cc_final: 0.8411 (m-80) REVERT: A 1402 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8552 (tt) REVERT: A 1446 MET cc_start: 0.6765 (mpp) cc_final: 0.6547 (pmm) outliers start: 55 outliers final: 31 residues processed: 215 average time/residue: 0.2636 time to fit residues: 87.1719 Evaluate side-chains 195 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 162 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 856 TRP Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1402 LEU Chi-restraints excluded: chain A residue 1441 VAL Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1496 ILE Chi-restraints excluded: chain A residue 1497 LEU Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1630 THR Chi-restraints excluded: chain A residue 1638 LEU Chi-restraints excluded: chain A residue 1798 ASN Chi-restraints excluded: chain A residue 1812 HIS Chi-restraints excluded: chain A residue 1833 GLU Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 2021 VAL Chi-restraints excluded: chain A residue 2046 SER Chi-restraints excluded: chain A residue 2118 VAL Chi-restraints excluded: chain A residue 2152 LEU Chi-restraints excluded: chain A residue 2167 VAL Chi-restraints excluded: chain A residue 2176 LEU Chi-restraints excluded: chain A residue 2180 LEU Chi-restraints excluded: chain A residue 2203 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 146 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 11 optimal weight: 0.2980 chunk 176 optimal weight: 0.9990 chunk 101 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1498 GLN ** A1634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1780 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.137675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.097795 restraints weight = 23815.829| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.65 r_work: 0.3035 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 15706 Z= 0.143 Angle : 0.607 9.053 21340 Z= 0.296 Chirality : 0.042 0.181 2441 Planarity : 0.005 0.096 2659 Dihedral : 8.082 80.711 2388 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.19 % Allowed : 14.24 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 2.17 % 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: 0.14 (0.20), residues: 1898 helix: 1.43 (0.16), residues: 1094 sheet: -0.58 (0.38), residues: 165 loop : -2.14 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 278 HIS 0.003 0.001 HIS A 551 PHE 0.019 0.001 PHE A 36 TYR 0.014 0.001 TYR A1388 ARG 0.003 0.000 ARG A2014 Details of bonding type rmsd link_NAG-ASN : bond 0.00204 ( 4) link_NAG-ASN : angle 1.68973 ( 12) link_BETA1-4 : bond 0.00481 ( 3) link_BETA1-4 : angle 2.98691 ( 9) hydrogen bonds : bond 0.03912 ( 811) hydrogen bonds : angle 3.94096 ( 2382) link_BETA1-6 : bond 0.01065 ( 1) link_BETA1-6 : angle 1.54185 ( 3) SS BOND : bond 0.00415 ( 6) SS BOND : angle 1.26064 ( 12) link_BETA1-3 : bond 0.00494 ( 1) link_BETA1-3 : angle 1.85580 ( 3) covalent geometry : bond 0.00330 (15690) covalent geometry : angle 0.60208 (21301) Misc. bond : bond 0.00059 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 172 time to evaluate : 1.621 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.7749 (mtt180) cc_final: 0.7201 (tpt170) REVERT: A 83 ARG cc_start: 0.8234 (tpt90) cc_final: 0.7775 (ttm-80) REVERT: A 302 GLN cc_start: 0.7122 (tp40) cc_final: 0.6673 (mp10) REVERT: A 438 MET cc_start: 0.7731 (ttm) cc_final: 0.6845 (tmm) REVERT: A 511 GLU cc_start: 0.7788 (mp0) cc_final: 0.7446 (mp0) REVERT: A 518 TRP cc_start: 0.7660 (m100) cc_final: 0.6948 (m-10) REVERT: A 640 MET cc_start: 0.8713 (tpt) cc_final: 0.8463 (tpp) REVERT: A 984 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8207 (pp) REVERT: A 1078 TYR cc_start: 0.8805 (m-10) cc_final: 0.8498 (m-10) REVERT: A 1190 HIS cc_start: 0.5435 (m-70) cc_final: 0.4533 (m-70) REVERT: A 1344 ARG cc_start: 0.8407 (mtt180) cc_final: 0.8041 (mtt-85) REVERT: A 1388 TYR cc_start: 0.8770 (m-80) cc_final: 0.8470 (m-80) REVERT: A 1446 MET cc_start: 0.6855 (mpp) cc_final: 0.6647 (pmm) outliers start: 52 outliers final: 36 residues processed: 211 average time/residue: 0.2587 time to fit residues: 83.9616 Evaluate side-chains 199 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 162 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 856 TRP Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1219 VAL Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1496 ILE Chi-restraints excluded: chain A residue 1497 LEU Chi-restraints excluded: chain A residue 1498 GLN Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1638 LEU Chi-restraints excluded: chain A residue 1812 HIS Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 1869 LEU Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 1965 VAL Chi-restraints excluded: chain A residue 2046 SER Chi-restraints excluded: chain A residue 2114 MET Chi-restraints excluded: chain A residue 2118 VAL Chi-restraints excluded: chain A residue 2139 TYR Chi-restraints excluded: chain A residue 2140 THR Chi-restraints excluded: chain A residue 2152 LEU Chi-restraints excluded: chain A residue 2167 VAL Chi-restraints excluded: chain A residue 2180 LEU Chi-restraints excluded: chain A residue 2203 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 55 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 119 optimal weight: 0.0670 chunk 141 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 171 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 175 optimal weight: 0.6980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1498 GLN A1617 ASN ** A1634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1900 GLN A1986 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.139326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.099879 restraints weight = 23846.053| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.32 r_work: 0.3084 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15706 Z= 0.121 Angle : 0.603 10.118 21340 Z= 0.291 Chirality : 0.042 0.174 2441 Planarity : 0.004 0.092 2659 Dihedral : 7.999 80.246 2387 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.64 % Allowed : 15.35 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.05 % 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: 0.24 (0.20), residues: 1898 helix: 1.52 (0.16), residues: 1095 sheet: -0.59 (0.39), residues: 161 loop : -2.10 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 278 HIS 0.003 0.000 HIS A1634 PHE 0.015 0.001 PHE A 36 TYR 0.018 0.001 TYR A1388 ARG 0.003 0.000 ARG A2014 Details of bonding type rmsd link_NAG-ASN : bond 0.00147 ( 4) link_NAG-ASN : angle 1.74799 ( 12) link_BETA1-4 : bond 0.00300 ( 3) link_BETA1-4 : angle 2.64949 ( 9) hydrogen bonds : bond 0.03748 ( 811) hydrogen bonds : angle 3.89960 ( 2382) link_BETA1-6 : bond 0.00895 ( 1) link_BETA1-6 : angle 1.35088 ( 3) SS BOND : bond 0.00394 ( 6) SS BOND : angle 1.17010 ( 12) link_BETA1-3 : bond 0.00495 ( 1) link_BETA1-3 : angle 1.73275 ( 3) covalent geometry : bond 0.00272 (15690) covalent geometry : angle 0.59797 (21301) Misc. bond : bond 0.00055 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 169 time to evaluate : 1.899 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.7826 (mtt180) cc_final: 0.7133 (tpt170) REVERT: A 37 LEU cc_start: 0.8395 (mt) cc_final: 0.7889 (mt) REVERT: A 83 ARG cc_start: 0.8320 (tpt90) cc_final: 0.7835 (ttm-80) REVERT: A 302 GLN cc_start: 0.7171 (tp40) cc_final: 0.6673 (mp10) REVERT: A 415 MET cc_start: 0.8480 (tmm) cc_final: 0.7821 (tmm) REVERT: A 438 MET cc_start: 0.7711 (ttm) cc_final: 0.6663 (tmm) REVERT: A 442 SER cc_start: 0.5605 (OUTLIER) cc_final: 0.5106 (m) REVERT: A 511 GLU cc_start: 0.7883 (mp0) cc_final: 0.7523 (mp0) REVERT: A 518 TRP cc_start: 0.7738 (m100) cc_final: 0.7021 (m-10) REVERT: A 640 MET cc_start: 0.8814 (tpt) cc_final: 0.8549 (tpp) REVERT: A 984 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8151 (pp) REVERT: A 1078 TYR cc_start: 0.8880 (m-10) cc_final: 0.8572 (m-10) REVERT: A 1190 HIS cc_start: 0.5428 (m-70) cc_final: 0.4531 (m-70) REVERT: A 1344 ARG cc_start: 0.8509 (mtt180) cc_final: 0.8087 (mtt-85) REVERT: A 1388 TYR cc_start: 0.8890 (m-80) cc_final: 0.8578 (m-80) REVERT: A 1446 MET cc_start: 0.7137 (mpp) cc_final: 0.6757 (pmm) REVERT: A 1799 ILE cc_start: 0.6209 (mp) cc_final: 0.5827 (mt) outliers start: 43 outliers final: 34 residues processed: 202 average time/residue: 0.2621 time to fit residues: 81.8255 Evaluate side-chains 199 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 163 time to evaluate : 1.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 856 TRP Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1496 ILE Chi-restraints excluded: chain A residue 1497 LEU Chi-restraints excluded: chain A residue 1498 GLN Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1617 ASN Chi-restraints excluded: chain A residue 1638 LEU Chi-restraints excluded: chain A residue 1812 HIS Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 1869 LEU Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 1965 VAL Chi-restraints excluded: chain A residue 2021 VAL Chi-restraints excluded: chain A residue 2125 LEU Chi-restraints excluded: chain A residue 2152 LEU Chi-restraints excluded: chain A residue 2167 VAL Chi-restraints excluded: chain A residue 2180 LEU Chi-restraints excluded: chain A residue 2203 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 70 optimal weight: 0.5980 chunk 129 optimal weight: 10.0000 chunk 51 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 160 optimal weight: 1.9990 chunk 177 optimal weight: 0.0030 chunk 48 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 147 optimal weight: 0.8980 chunk 45 optimal weight: 0.2980 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1986 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.139166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.098060 restraints weight = 23822.939| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.23 r_work: 0.3107 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15706 Z= 0.114 Angle : 0.594 11.250 21340 Z= 0.286 Chirality : 0.041 0.169 2441 Planarity : 0.004 0.089 2659 Dihedral : 7.843 79.825 2387 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.01 % Allowed : 15.29 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 2.17 % 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: 0.34 (0.20), residues: 1898 helix: 1.59 (0.16), residues: 1095 sheet: -0.48 (0.39), residues: 161 loop : -2.06 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 278 HIS 0.002 0.000 HIS A 551 PHE 0.013 0.001 PHE A 36 TYR 0.018 0.001 TYR A1388 ARG 0.002 0.000 ARG A1531 Details of bonding type rmsd link_NAG-ASN : bond 0.00161 ( 4) link_NAG-ASN : angle 1.77650 ( 12) link_BETA1-4 : bond 0.00276 ( 3) link_BETA1-4 : angle 2.54082 ( 9) hydrogen bonds : bond 0.03616 ( 811) hydrogen bonds : angle 3.86520 ( 2382) link_BETA1-6 : bond 0.00905 ( 1) link_BETA1-6 : angle 1.33989 ( 3) SS BOND : bond 0.00376 ( 6) SS BOND : angle 1.05769 ( 12) link_BETA1-3 : bond 0.00568 ( 1) link_BETA1-3 : angle 1.70029 ( 3) covalent geometry : bond 0.00253 (15690) covalent geometry : angle 0.58976 (21301) Misc. bond : bond 0.00050 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 169 time to evaluate : 1.728 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.7852 (mtt180) cc_final: 0.7165 (tpt170) REVERT: A 83 ARG cc_start: 0.8309 (tpt90) cc_final: 0.7829 (ttm-80) REVERT: A 302 GLN cc_start: 0.7168 (tp40) cc_final: 0.6696 (mp10) REVERT: A 386 THR cc_start: 0.5814 (OUTLIER) cc_final: 0.5591 (t) REVERT: A 415 MET cc_start: 0.8488 (tmm) cc_final: 0.7818 (tmm) REVERT: A 438 MET cc_start: 0.7735 (ttm) cc_final: 0.6685 (tmm) REVERT: A 442 SER cc_start: 0.5560 (OUTLIER) cc_final: 0.5064 (m) REVERT: A 518 TRP cc_start: 0.7707 (m100) cc_final: 0.7009 (m-10) REVERT: A 640 MET cc_start: 0.8793 (tpt) cc_final: 0.8519 (tpp) REVERT: A 984 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8153 (pp) REVERT: A 1078 TYR cc_start: 0.8837 (m-10) cc_final: 0.8539 (m-10) REVERT: A 1190 HIS cc_start: 0.5387 (m-70) cc_final: 0.4504 (m-70) REVERT: A 1344 ARG cc_start: 0.8504 (mtt180) cc_final: 0.8088 (mtt-85) REVERT: A 1388 TYR cc_start: 0.8829 (m-80) cc_final: 0.8575 (m-80) REVERT: A 1402 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8591 (tt) REVERT: A 1446 MET cc_start: 0.7067 (mpp) cc_final: 0.6753 (pmm) REVERT: A 1799 ILE cc_start: 0.6235 (mp) cc_final: 0.5848 (mt) REVERT: A 1865 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8742 (mt) outliers start: 49 outliers final: 34 residues processed: 206 average time/residue: 0.2658 time to fit residues: 84.6203 Evaluate side-chains 205 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 166 time to evaluate : 1.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 856 TRP Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1219 VAL Chi-restraints excluded: chain A residue 1402 LEU Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1496 ILE Chi-restraints excluded: chain A residue 1497 LEU Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1638 LEU Chi-restraints excluded: chain A residue 1812 HIS Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 1869 LEU Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 1965 VAL Chi-restraints excluded: chain A residue 2125 LEU Chi-restraints excluded: chain A residue 2140 THR Chi-restraints excluded: chain A residue 2152 LEU Chi-restraints excluded: chain A residue 2167 VAL Chi-restraints excluded: chain A residue 2180 LEU Chi-restraints excluded: chain A residue 2203 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 135 optimal weight: 5.9990 chunk 154 optimal weight: 5.9990 chunk 35 optimal weight: 0.0470 chunk 149 optimal weight: 0.2980 chunk 145 optimal weight: 0.8980 chunk 93 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 31 optimal weight: 9.9990 chunk 62 optimal weight: 0.0570 chunk 8 optimal weight: 0.3980 chunk 151 optimal weight: 1.9990 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 732 GLN ** A1634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.140186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.099526 restraints weight = 23589.298| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.20 r_work: 0.3134 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15706 Z= 0.109 Angle : 0.584 9.572 21340 Z= 0.280 Chirality : 0.041 0.166 2441 Planarity : 0.004 0.086 2659 Dihedral : 7.639 78.224 2387 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.52 % Allowed : 15.65 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 2.17 % 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: 0.43 (0.20), residues: 1898 helix: 1.67 (0.16), residues: 1090 sheet: -0.36 (0.39), residues: 156 loop : -2.04 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 278 HIS 0.002 0.000 HIS A 551 PHE 0.009 0.001 PHE A2135 TYR 0.014 0.001 TYR A1388 ARG 0.002 0.000 ARG A2014 Details of bonding type rmsd link_NAG-ASN : bond 0.00202 ( 4) link_NAG-ASN : angle 1.67976 ( 12) link_BETA1-4 : bond 0.00262 ( 3) link_BETA1-4 : angle 2.40816 ( 9) hydrogen bonds : bond 0.03450 ( 811) hydrogen bonds : angle 3.81402 ( 2382) link_BETA1-6 : bond 0.00925 ( 1) link_BETA1-6 : angle 1.31024 ( 3) SS BOND : bond 0.00362 ( 6) SS BOND : angle 0.98448 ( 12) link_BETA1-3 : bond 0.00509 ( 1) link_BETA1-3 : angle 1.53847 ( 3) covalent geometry : bond 0.00237 (15690) covalent geometry : angle 0.57972 (21301) Misc. bond : bond 0.00045 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 170 time to evaluate : 1.789 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.7842 (mtt180) cc_final: 0.7163 (tpt170) REVERT: A 83 ARG cc_start: 0.8289 (tpt90) cc_final: 0.7778 (ttm-80) REVERT: A 302 GLN cc_start: 0.7136 (tp40) cc_final: 0.6663 (mp10) REVERT: A 386 THR cc_start: 0.5852 (OUTLIER) cc_final: 0.5592 (t) REVERT: A 415 MET cc_start: 0.8476 (tmm) cc_final: 0.7852 (tmm) REVERT: A 418 GLU cc_start: 0.7776 (tt0) cc_final: 0.7343 (pt0) REVERT: A 438 MET cc_start: 0.7732 (ttm) cc_final: 0.6695 (tmm) REVERT: A 442 SER cc_start: 0.5556 (OUTLIER) cc_final: 0.5067 (m) REVERT: A 518 TRP cc_start: 0.7691 (m100) cc_final: 0.6988 (m-10) REVERT: A 640 MET cc_start: 0.8774 (tpt) cc_final: 0.8490 (tpp) REVERT: A 984 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8125 (pp) REVERT: A 1078 TYR cc_start: 0.8813 (m-10) cc_final: 0.8529 (m-10) REVERT: A 1190 HIS cc_start: 0.5391 (m-70) cc_final: 0.4511 (m-70) REVERT: A 1344 ARG cc_start: 0.8490 (mtt180) cc_final: 0.8085 (mtt-85) REVERT: A 1430 GLN cc_start: 0.7325 (mp10) cc_final: 0.5546 (tm-30) REVERT: A 1446 MET cc_start: 0.7085 (mpp) cc_final: 0.6694 (pmm) REVERT: A 1477 CYS cc_start: 0.3237 (OUTLIER) cc_final: 0.2405 (t) REVERT: A 1799 ILE cc_start: 0.6234 (mp) cc_final: 0.5871 (mt) REVERT: A 1865 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8675 (mt) REVERT: A 2130 HIS cc_start: 0.8185 (t70) cc_final: 0.7735 (t70) outliers start: 41 outliers final: 30 residues processed: 199 average time/residue: 0.2684 time to fit residues: 82.4879 Evaluate side-chains 197 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 162 time to evaluate : 1.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 856 TRP Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1219 VAL Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1477 CYS Chi-restraints excluded: chain A residue 1496 ILE Chi-restraints excluded: chain A residue 1497 LEU Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1638 LEU Chi-restraints excluded: chain A residue 1812 HIS Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 1965 VAL Chi-restraints excluded: chain A residue 2021 VAL Chi-restraints excluded: chain A residue 2125 LEU Chi-restraints excluded: chain A residue 2140 THR Chi-restraints excluded: chain A residue 2152 LEU Chi-restraints excluded: chain A residue 2167 VAL Chi-restraints excluded: chain A residue 2180 LEU Chi-restraints excluded: chain A residue 2203 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 112 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 124 optimal weight: 0.7980 chunk 191 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 chunk 88 optimal weight: 0.2980 chunk 142 optimal weight: 0.1980 chunk 134 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1318 GLN ** A1634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.140104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.100555 restraints weight = 23697.118| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.48 r_work: 0.3105 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15706 Z= 0.116 Angle : 0.597 10.838 21340 Z= 0.285 Chirality : 0.041 0.168 2441 Planarity : 0.004 0.087 2659 Dihedral : 7.534 78.573 2385 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.82 % Allowed : 15.84 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 2.17 % 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: 0.46 (0.20), residues: 1898 helix: 1.68 (0.16), residues: 1089 sheet: -0.12 (0.40), residues: 148 loop : -2.04 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 278 HIS 0.002 0.000 HIS A 551 PHE 0.015 0.001 PHE A 36 TYR 0.031 0.001 TYR A1388 ARG 0.002 0.000 ARG A 742 Details of bonding type rmsd link_NAG-ASN : bond 0.00203 ( 4) link_NAG-ASN : angle 1.53091 ( 12) link_BETA1-4 : bond 0.00319 ( 3) link_BETA1-4 : angle 2.41319 ( 9) hydrogen bonds : bond 0.03513 ( 811) hydrogen bonds : angle 3.79472 ( 2382) link_BETA1-6 : bond 0.00928 ( 1) link_BETA1-6 : angle 1.32044 ( 3) SS BOND : bond 0.00335 ( 6) SS BOND : angle 1.04986 ( 12) link_BETA1-3 : bond 0.00470 ( 1) link_BETA1-3 : angle 1.48439 ( 3) covalent geometry : bond 0.00260 (15690) covalent geometry : angle 0.59359 (21301) Misc. bond : bond 0.00050 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 163 time to evaluate : 1.651 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.7919 (mtt180) cc_final: 0.7263 (tpt170) REVERT: A 83 ARG cc_start: 0.8342 (tpt90) cc_final: 0.7831 (ttm-80) REVERT: A 302 GLN cc_start: 0.7127 (tp40) cc_final: 0.6671 (mp10) REVERT: A 386 THR cc_start: 0.6075 (OUTLIER) cc_final: 0.5805 (t) REVERT: A 415 MET cc_start: 0.8492 (tmm) cc_final: 0.7886 (tmm) REVERT: A 418 GLU cc_start: 0.7814 (tt0) cc_final: 0.7438 (pt0) REVERT: A 438 MET cc_start: 0.7731 (ttm) cc_final: 0.6691 (tmm) REVERT: A 442 SER cc_start: 0.5582 (OUTLIER) cc_final: 0.5086 (m) REVERT: A 518 TRP cc_start: 0.7725 (m100) cc_final: 0.7026 (m-10) REVERT: A 640 MET cc_start: 0.8804 (tpt) cc_final: 0.8525 (tpp) REVERT: A 984 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8168 (pp) REVERT: A 1078 TYR cc_start: 0.8829 (m-10) cc_final: 0.8552 (m-10) REVERT: A 1190 HIS cc_start: 0.5420 (m-70) cc_final: 0.4536 (m-70) REVERT: A 1344 ARG cc_start: 0.8560 (mtt180) cc_final: 0.8174 (mtt-85) REVERT: A 1383 MET cc_start: 0.8788 (ptm) cc_final: 0.8582 (ptp) REVERT: A 1430 GLN cc_start: 0.7348 (mp10) cc_final: 0.5595 (tm-30) REVERT: A 1446 MET cc_start: 0.7127 (mpp) cc_final: 0.6721 (pmm) REVERT: A 1477 CYS cc_start: 0.3320 (OUTLIER) cc_final: 0.2500 (t) REVERT: A 1799 ILE cc_start: 0.6310 (mp) cc_final: 0.5894 (mt) REVERT: A 1865 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8705 (mt) REVERT: A 2130 HIS cc_start: 0.8210 (t70) cc_final: 0.7769 (t70) outliers start: 46 outliers final: 35 residues processed: 198 average time/residue: 0.2603 time to fit residues: 79.6331 Evaluate side-chains 202 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 162 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 683 PHE Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 856 TRP Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1219 VAL Chi-restraints excluded: chain A residue 1402 LEU Chi-restraints excluded: chain A residue 1427 THR Chi-restraints excluded: chain A residue 1441 VAL Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1477 CYS Chi-restraints excluded: chain A residue 1496 ILE Chi-restraints excluded: chain A residue 1497 LEU Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1638 LEU Chi-restraints excluded: chain A residue 1812 HIS Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 1965 VAL Chi-restraints excluded: chain A residue 2021 VAL Chi-restraints excluded: chain A residue 2125 LEU Chi-restraints excluded: chain A residue 2140 THR Chi-restraints excluded: chain A residue 2152 LEU Chi-restraints excluded: chain A residue 2167 VAL Chi-restraints excluded: chain A residue 2180 LEU Chi-restraints excluded: chain A residue 2203 ILE Chi-restraints excluded: chain A residue 2211 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 124 optimal weight: 3.9990 chunk 18 optimal weight: 50.0000 chunk 5 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 149 optimal weight: 0.9980 chunk 76 optimal weight: 0.4980 chunk 156 optimal weight: 3.9990 chunk 187 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 153 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1498 GLN ** A1634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.137802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.096795 restraints weight = 23943.548| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.58 r_work: 0.3039 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 15706 Z= 0.147 Angle : 0.624 10.501 21340 Z= 0.300 Chirality : 0.042 0.208 2441 Planarity : 0.004 0.090 2659 Dihedral : 7.757 80.876 2385 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.76 % Allowed : 16.08 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.05 % 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: 0.45 (0.20), residues: 1898 helix: 1.65 (0.16), residues: 1092 sheet: -0.30 (0.39), residues: 158 loop : -1.99 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 278 HIS 0.004 0.001 HIS A2006 PHE 0.020 0.001 PHE A 36 TYR 0.031 0.001 TYR A1388 ARG 0.003 0.000 ARG A 742 Details of bonding type rmsd link_NAG-ASN : bond 0.00213 ( 4) link_NAG-ASN : angle 1.54022 ( 12) link_BETA1-4 : bond 0.00365 ( 3) link_BETA1-4 : angle 2.49664 ( 9) hydrogen bonds : bond 0.03813 ( 811) hydrogen bonds : angle 3.87194 ( 2382) link_BETA1-6 : bond 0.00871 ( 1) link_BETA1-6 : angle 1.32575 ( 3) SS BOND : bond 0.00386 ( 6) SS BOND : angle 1.37894 ( 12) link_BETA1-3 : bond 0.00443 ( 1) link_BETA1-3 : angle 1.46769 ( 3) covalent geometry : bond 0.00342 (15690) covalent geometry : angle 0.62045 (21301) Misc. bond : bond 0.00061 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 163 time to evaluate : 2.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.7896 (mtt180) cc_final: 0.7152 (tpt170) REVERT: A 83 ARG cc_start: 0.8410 (tpt90) cc_final: 0.7824 (ttm-80) REVERT: A 302 GLN cc_start: 0.7128 (tp40) cc_final: 0.6609 (mp10) REVERT: A 386 THR cc_start: 0.5971 (OUTLIER) cc_final: 0.5722 (t) REVERT: A 415 MET cc_start: 0.8532 (tmm) cc_final: 0.7914 (tmm) REVERT: A 418 GLU cc_start: 0.7929 (tt0) cc_final: 0.7547 (pt0) REVERT: A 438 MET cc_start: 0.7740 (ttm) cc_final: 0.6700 (tmm) REVERT: A 442 SER cc_start: 0.5582 (OUTLIER) cc_final: 0.5084 (m) REVERT: A 486 GLU cc_start: 0.8307 (mp0) cc_final: 0.8101 (pm20) REVERT: A 518 TRP cc_start: 0.7850 (m100) cc_final: 0.7104 (m-10) REVERT: A 640 MET cc_start: 0.8787 (tpt) cc_final: 0.8484 (tpp) REVERT: A 742 ARG cc_start: 0.6595 (mtt90) cc_final: 0.6108 (mtt90) REVERT: A 984 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8148 (pp) REVERT: A 1078 TYR cc_start: 0.8863 (m-10) cc_final: 0.8544 (m-10) REVERT: A 1190 HIS cc_start: 0.5431 (m-70) cc_final: 0.4535 (m-70) REVERT: A 1344 ARG cc_start: 0.8537 (mtt180) cc_final: 0.8090 (mtt-85) REVERT: A 1477 CYS cc_start: 0.3608 (OUTLIER) cc_final: 0.2753 (t) REVERT: A 1799 ILE cc_start: 0.6371 (mp) cc_final: 0.5928 (mt) REVERT: A 1865 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8773 (mt) outliers start: 45 outliers final: 36 residues processed: 197 average time/residue: 0.2836 time to fit residues: 86.5767 Evaluate side-chains 200 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 159 time to evaluate : 1.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 683 PHE Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 856 TRP Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1219 VAL Chi-restraints excluded: chain A residue 1402 LEU Chi-restraints excluded: chain A residue 1427 THR Chi-restraints excluded: chain A residue 1441 VAL Chi-restraints excluded: chain A residue 1463 CYS Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1477 CYS Chi-restraints excluded: chain A residue 1497 LEU Chi-restraints excluded: chain A residue 1498 GLN Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1638 LEU Chi-restraints excluded: chain A residue 1812 HIS Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 1965 VAL Chi-restraints excluded: chain A residue 2021 VAL Chi-restraints excluded: chain A residue 2125 LEU Chi-restraints excluded: chain A residue 2140 THR Chi-restraints excluded: chain A residue 2152 LEU Chi-restraints excluded: chain A residue 2167 VAL Chi-restraints excluded: chain A residue 2180 LEU Chi-restraints excluded: chain A residue 2203 ILE Chi-restraints excluded: chain A residue 2211 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 6 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 165 optimal weight: 5.9990 chunk 132 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 82 optimal weight: 0.0270 chunk 59 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 overall best weight: 0.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1498 GLN ** A1634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.137324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.098234 restraints weight = 23670.282| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.32 r_work: 0.3062 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15706 Z= 0.138 Angle : 0.793 52.941 21340 Z= 0.424 Chirality : 0.042 0.239 2441 Planarity : 0.004 0.090 2659 Dihedral : 7.758 81.054 2385 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.95 % Allowed : 16.08 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.05 % 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: 0.45 (0.20), residues: 1898 helix: 1.66 (0.16), residues: 1091 sheet: -0.30 (0.40), residues: 158 loop : -2.00 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 278 HIS 0.003 0.001 HIS A 551 PHE 0.020 0.001 PHE A 36 TYR 0.036 0.001 TYR A1388 ARG 0.002 0.000 ARG A 742 Details of bonding type rmsd link_NAG-ASN : bond 0.00200 ( 4) link_NAG-ASN : angle 1.52481 ( 12) link_BETA1-4 : bond 0.00334 ( 3) link_BETA1-4 : angle 2.47584 ( 9) hydrogen bonds : bond 0.03792 ( 811) hydrogen bonds : angle 3.87295 ( 2382) link_BETA1-6 : bond 0.00780 ( 1) link_BETA1-6 : angle 1.27435 ( 3) SS BOND : bond 0.00367 ( 6) SS BOND : angle 1.35733 ( 12) link_BETA1-3 : bond 0.00442 ( 1) link_BETA1-3 : angle 1.48295 ( 3) covalent geometry : bond 0.00317 (15690) covalent geometry : angle 0.79038 (21301) Misc. bond : bond 0.00061 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9226.60 seconds wall clock time: 158 minutes 58.25 seconds (9538.25 seconds total)