Starting phenix.real_space_refine on Thu May 15 22:13:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eop_28451/05_2025/8eop_28451.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eop_28451/05_2025/8eop_28451.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8eop_28451/05_2025/8eop_28451.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eop_28451/05_2025/8eop_28451.map" model { file = "/net/cci-nas-00/data/ceres_data/8eop_28451/05_2025/8eop_28451.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eop_28451/05_2025/8eop_28451.cif" } resolution = 3.7 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 63 5.16 5 C 8504 2.51 5 N 2320 2.21 5 O 2370 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 13265 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 13050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1687, 13050 Classifications: {'peptide': 1687} Link IDs: {'PTRANS': 105, 'TRANS': 1581} Chain breaks: 9 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 148 Unusual residues: {' MG': 2, 'ATP': 2, 'NAG': 6} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 8.53, per 1000 atoms: 0.64 Number of scatterers: 13265 At special positions: 0 Unit cell: (159.131, 147.574, 105.791, 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 63 16.00 P 6 15.00 Mg 2 11.99 O 2370 8.00 N 2320 7.00 C 8504 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, 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 225 " distance=2.03 Simple disulfide: pdb=" SG CYS A 267 " - pdb=" SG CYS A 406 " distance=2.03 Simple disulfide: pdb=" SG CYS A1347 " - pdb=" SG CYS A1359 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A2201 " - " ASN A 78 " " NAG A2202 " - " ASN A 98 " " NAG A2203 " - " ASN A 312 " " NAG A2204 " - " ASN A 340 " " NAG A2205 " - " ASN A1518 " " NAG A2206 " - " ASN A1457 " " NAG B 1 " - " ASN A1386 " " NAG C 1 " - " ASN A1381 " Time building additional restraints: 3.67 Conformation dependent library (CDL) restraints added in 1.9 seconds 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3094 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 10 sheets defined 60.2% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.78 Creating SS restraints... Processing helix chain 'A' and resid 2 through 21 removed outlier: 3.533A pdb=" N GLN A 21 " --> pdb=" O TYR A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 31 removed outlier: 4.238A pdb=" N LEU A 25 " --> pdb=" O GLN A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 45 removed outlier: 3.695A pdb=" N SER A 45 " --> pdb=" O ALA A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 65 Processing helix chain 'A' and resid 66 through 76 removed outlier: 3.606A 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 116 removed outlier: 3.954A pdb=" N ALA A 116 " --> pdb=" O VAL A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 126 Processing helix chain 'A' and resid 183 through 194 Processing helix chain 'A' and resid 198 through 208 Processing helix chain 'A' and resid 215 through 225 removed outlier: 3.803A pdb=" N LEU A 219 " --> pdb=" O GLY A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 275 Processing helix chain 'A' and resid 277 through 292 removed outlier: 4.777A pdb=" N LEU A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N TRP A 284 " --> pdb=" O SER A 280 " (cutoff:3.500A) Proline residue: A 289 - end of helix removed outlier: 3.532A pdb=" N LEU A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 312 Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 319 through 340 removed outlier: 3.829A pdb=" N ASP A 323 " --> pdb=" O THR A 319 " (cutoff:3.500A) Proline residue: A 333 - end of helix Processing helix chain 'A' and resid 342 through 354 removed outlier: 3.611A pdb=" N MET A 354 " --> pdb=" O ARG A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 378 Processing helix chain 'A' and resid 387 through 407 removed outlier: 3.928A pdb=" N LEU A 407 " --> pdb=" O VAL A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 429 Processing helix chain 'A' and resid 430 through 432 No H-bonds generated for 'chain 'A' and resid 430 through 432' Processing helix chain 'A' and resid 496 through 502 removed outlier: 3.741A pdb=" N TRP A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY A 502 " --> pdb=" O TYR A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 520 Processing helix chain 'A' and resid 540 through 558 removed outlier: 3.870A pdb=" N ARG A 544 " --> pdb=" O ASP A 540 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG A 548 " --> pdb=" O ARG A 544 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER A 549 " --> pdb=" O VAL A 545 " (cutoff:3.500A) Proline residue: A 551 - end of helix removed outlier: 4.052A pdb=" N TRP A 558 " --> pdb=" O LEU A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 575 removed outlier: 3.550A pdb=" N THR A 563 " --> pdb=" O ILE A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 584 removed outlier: 3.738A pdb=" N MET A 584 " --> pdb=" O THR A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 617 Proline residue: A 602 - end of helix Processing helix chain 'A' and resid 624 through 647 removed outlier: 3.788A pdb=" N VAL A 628 " --> pdb=" O HIS A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 659 Processing helix chain 'A' and resid 661 through 666 Processing helix chain 'A' and resid 668 through 677 removed outlier: 3.723A pdb=" N VAL A 672 " --> pdb=" O TYR A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 690 Processing helix chain 'A' and resid 692 through 710 Processing helix chain 'A' and resid 732 through 755 Processing helix chain 'A' and resid 846 through 855 Processing helix chain 'A' and resid 879 through 881 No H-bonds generated for 'chain 'A' and resid 879 through 881' Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 916 through 928 Processing helix chain 'A' and resid 936 through 940 removed outlier: 3.540A pdb=" N LEU A 940 " --> pdb=" O THR A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 955 Processing helix chain 'A' and resid 971 through 985 removed outlier: 3.823A pdb=" N GLY A 977 " --> pdb=" O ALA A 973 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR A 985 " --> pdb=" O LEU A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1005 Processing helix chain 'A' and resid 1021 through 1027 Processing helix chain 'A' and resid 1140 through 1151 Processing helix chain 'A' and resid 1213 through 1235 removed outlier: 3.712A pdb=" N THR A1217 " --> pdb=" O GLY A1213 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A1221 " --> pdb=" O THR A1217 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU A1226 " --> pdb=" O GLN A1222 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N SER A1235 " --> pdb=" O LEU A1231 " (cutoff:3.500A) Processing helix chain 'A' and resid 1235 through 1244 removed outlier: 3.969A pdb=" N LEU A1239 " --> pdb=" O SER A1235 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL A1244 " --> pdb=" O PHE A1240 " (cutoff:3.500A) Processing helix chain 'A' and resid 1244 through 1259 removed outlier: 3.579A pdb=" N VAL A1250 " --> pdb=" O PRO A1246 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY A1251 " --> pdb=" O ALA A1247 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE A1259 " --> pdb=" O VAL A1255 " (cutoff:3.500A) Processing helix chain 'A' and resid 1272 through 1276 Processing helix chain 'A' and resid 1290 through 1305 removed outlier: 3.523A pdb=" N ALA A1294 " --> pdb=" O ASP A1290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1310 through 1314 Processing helix chain 'A' and resid 1324 through 1334 Processing helix chain 'A' and resid 1388 through 1402 removed outlier: 3.788A pdb=" N VAL A1392 " --> pdb=" O SER A1388 " (cutoff:3.500A) Proline residue: A1396 - end of helix Processing helix chain 'A' and resid 1428 through 1441 removed outlier: 3.507A pdb=" N LEU A1432 " --> pdb=" O SER A1428 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY A1433 " --> pdb=" O GLY A1429 " (cutoff:3.500A) Processing helix chain 'A' and resid 1449 through 1466 removed outlier: 4.099A pdb=" N ASP A1466 " --> pdb=" O ALA A1462 " (cutoff:3.500A) Processing helix chain 'A' and resid 1482 through 1499 Processing helix chain 'A' and resid 1533 through 1549 removed outlier: 3.704A pdb=" N PHE A1548 " --> pdb=" O PHE A1544 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL A1549 " --> pdb=" O ALA A1545 " (cutoff:3.500A) Processing helix chain 'A' and resid 1550 through 1552 No H-bonds generated for 'chain 'A' and resid 1550 through 1552' Processing helix chain 'A' and resid 1553 through 1563 removed outlier: 4.363A pdb=" N LEU A1557 " --> pdb=" O PHE A1553 " (cutoff:3.500A) Processing helix chain 'A' and resid 1565 through 1573 removed outlier: 3.546A pdb=" N GLN A1569 " --> pdb=" O ALA A1565 " (cutoff:3.500A) Processing helix chain 'A' and resid 1575 through 1605 removed outlier: 3.766A pdb=" N LEU A1592 " --> pdb=" O MET A1588 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N VAL A1593 " --> pdb=" O CYS A1589 " (cutoff:3.500A) Proline residue: A1594 - end of helix Processing helix chain 'A' and resid 1615 through 1631 removed outlier: 3.818A pdb=" N THR A1631 " --> pdb=" O GLY A1627 " (cutoff:3.500A) Processing helix chain 'A' and resid 1632 through 1634 No H-bonds generated for 'chain 'A' and resid 1632 through 1634' Processing helix chain 'A' and resid 1635 through 1639 removed outlier: 3.627A pdb=" N PHE A1639 " --> pdb=" O PRO A1636 " (cutoff:3.500A) Processing helix chain 'A' and resid 1643 through 1671 removed outlier: 3.566A pdb=" N ALA A1647 " --> pdb=" O VAL A1643 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY A1662 " --> pdb=" O ILE A1658 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ALA A1665 " --> pdb=" O ASN A1661 " (cutoff:3.500A) Processing helix chain 'A' and resid 1676 through 1688 removed outlier: 3.856A pdb=" N GLN A1686 " --> pdb=" O ARG A1682 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL A1687 " --> pdb=" O ILE A1683 " (cutoff:3.500A) Processing helix chain 'A' and resid 1693 through 1698 removed outlier: 3.525A pdb=" N GLY A1697 " --> pdb=" O HIS A1693 " (cutoff:3.500A) Processing helix chain 'A' and resid 1698 through 1717 removed outlier: 3.624A pdb=" N MET A1703 " --> pdb=" O GLY A1699 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL A1704 " --> pdb=" O LEU A1700 " (cutoff:3.500A) Processing helix chain 'A' and resid 1730 through 1753 Proline residue: A1742 - end of helix removed outlier: 4.295A pdb=" N LEU A1745 " --> pdb=" O GLY A1741 " (cutoff:3.500A) Processing helix chain 'A' and resid 1774 through 1786 Processing helix chain 'A' and resid 1832 through 1842 removed outlier: 3.831A pdb=" N GLY A1842 " --> pdb=" O ARG A1838 " (cutoff:3.500A) Processing helix chain 'A' and resid 1861 through 1868 removed outlier: 4.388A pdb=" N SER A1868 " --> pdb=" O ALA A1864 " (cutoff:3.500A) Processing helix chain 'A' and resid 1883 through 1896 Processing helix chain 'A' and resid 1898 through 1900 No H-bonds generated for 'chain 'A' and resid 1898 through 1900' Processing helix chain 'A' and resid 1901 through 1913 removed outlier: 3.828A pdb=" N LEU A1913 " --> pdb=" O GLY A1909 " (cutoff:3.500A) Processing helix chain 'A' and resid 1922 through 1926 removed outlier: 3.611A pdb=" N TYR A1926 " --> pdb=" O ALA A1923 " (cutoff:3.500A) Processing helix chain 'A' and resid 1927 through 1941 removed outlier: 3.741A pdb=" N ALA A1939 " --> pdb=" O ALA A1935 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU A1940 " --> pdb=" O THR A1936 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL A1941 " --> pdb=" O ALA A1937 " (cutoff:3.500A) Processing helix chain 'A' and resid 1957 through 1975 Processing helix chain 'A' and resid 2008 through 2016 Processing helix chain 'A' and resid 2094 through 2104 removed outlier: 3.773A pdb=" N GLN A2104 " --> pdb=" O PHE A2100 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 51 removed outlier: 3.641A pdb=" N LEU A 49 " --> pdb=" O ASP A 539 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR A 537 " --> pdb=" O HIS A 51 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 removed outlier: 3.730A pdb=" N ILE A1473 " --> pdb=" O TYR A 528 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N SER A1284 " --> pdb=" O LEU A1419 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 439 through 441 removed outlier: 3.787A pdb=" N ARG A 463 " --> pdb=" O LEU A 441 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 807 through 813 removed outlier: 3.511A pdb=" N ARG A 810 " --> pdb=" O SER A 864 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER A 864 " --> pdb=" O ARG A 810 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N LEU A 812 " --> pdb=" O GLY A 862 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N GLY A 862 " --> pdb=" O LEU A 812 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 883 through 884 removed outlier: 6.614A pdb=" N GLY A 884 " --> pdb=" O ILE A 962 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N VAL A 961 " --> pdb=" O ILE A 992 " (cutoff:3.500A) removed outlier: 9.072A pdb=" N SER A 994 " --> pdb=" O VAL A 961 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N THR A 837 " --> pdb=" O LEU A 993 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ALA A 838 " --> pdb=" O ALA A1009 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N VAL A1011 " --> pdb=" O ALA A 838 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N LEU A 840 " --> pdb=" O VAL A1011 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS A1018 " --> pdb=" O VAL A1010 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ALA A1012 " --> pdb=" O LEU A1016 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N LEU A1016 " --> pdb=" O ALA A1012 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1372 through 1373 Processing sheet with id=AA7, first strand: chain 'A' and resid 1814 through 1817 removed outlier: 3.953A pdb=" N LEU A1815 " --> pdb=" O LEU A1795 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU A1793 " --> pdb=" O ILE A1817 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LEU A1798 " --> pdb=" O ARG A1848 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ARG A1848 " --> pdb=" O LEU A1798 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS A1856 " --> pdb=" O LEU A1853 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1822 through 1823 Processing sheet with id=AA9, first strand: chain 'A' and resid 1870 through 1872 removed outlier: 7.171A pdb=" N GLY A1870 " --> pdb=" O PHE A1948 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 1998 through 1999 659 hydrogen bonds defined for protein. 1929 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: 4.73 Time building geometry restraints manager: 4.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4312 1.34 - 1.46: 2808 1.46 - 1.58: 6355 1.58 - 1.70: 8 1.70 - 1.82: 95 Bond restraints: 13578 Sorted by residual: bond pdb=" CA ALA A1919 " pdb=" CB ALA A1919 " ideal model delta sigma weight residual 1.530 1.489 0.041 1.54e-02 4.22e+03 7.25e+00 bond pdb=" N ASP A1920 " pdb=" CA ASP A1920 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.56e+00 bond pdb=" CA SER A1916 " pdb=" CB SER A1916 " ideal model delta sigma weight residual 1.530 1.490 0.040 1.69e-02 3.50e+03 5.69e+00 bond pdb=" N SER A1916 " pdb=" CA SER A1916 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.29e-02 6.01e+03 5.45e+00 bond pdb=" C ARG A 880 " pdb=" N PRO A 881 " ideal model delta sigma weight residual 1.334 1.352 -0.018 8.40e-03 1.42e+04 4.74e+00 ... (remaining 13573 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 17940 1.66 - 3.32: 442 3.32 - 4.98: 77 4.98 - 6.64: 13 6.64 - 8.30: 2 Bond angle restraints: 18474 Sorted by residual: angle pdb=" N ILE A 559 " pdb=" CA ILE A 559 " pdb=" C ILE A 559 " ideal model delta sigma weight residual 113.71 109.79 3.92 9.50e-01 1.11e+00 1.70e+01 angle pdb=" N ILE A 879 " pdb=" CA ILE A 879 " pdb=" C ILE A 879 " ideal model delta sigma weight residual 112.96 109.37 3.59 1.00e+00 1.00e+00 1.29e+01 angle pdb=" CB ARG A 350 " pdb=" CG ARG A 350 " pdb=" CD ARG A 350 " ideal model delta sigma weight residual 111.30 119.24 -7.94 2.30e+00 1.89e-01 1.19e+01 angle pdb=" N VAL A 915 " pdb=" CA VAL A 915 " pdb=" C VAL A 915 " ideal model delta sigma weight residual 106.21 109.07 -2.86 1.07e+00 8.73e-01 7.13e+00 angle pdb=" C ASN A 98 " pdb=" N ASP A 99 " pdb=" CA ASP A 99 " ideal model delta sigma weight residual 121.54 126.60 -5.06 1.91e+00 2.74e-01 7.01e+00 ... (remaining 18469 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.78: 7603 21.78 - 43.56: 556 43.56 - 65.34: 67 65.34 - 87.12: 26 87.12 - 108.89: 10 Dihedral angle restraints: 8262 sinusoidal: 3457 harmonic: 4805 Sorted by residual: dihedral pdb=" CB CYS A1347 " pdb=" SG CYS A1347 " pdb=" SG CYS A1359 " pdb=" CB CYS A1359 " ideal model delta sinusoidal sigma weight residual 93.00 165.23 -72.23 1 1.00e+01 1.00e-02 6.67e+01 dihedral pdb=" O4 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C5 BMA B 3 " pdb=" O5 BMA B 3 " ideal model delta sinusoidal sigma weight residual 288.71 179.82 108.89 1 3.00e+01 1.11e-03 1.41e+01 dihedral pdb=" C3 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C5 BMA B 3 " pdb=" O5 BMA B 3 " ideal model delta sinusoidal sigma weight residual 47.62 -59.41 107.03 1 3.00e+01 1.11e-03 1.38e+01 ... (remaining 8259 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 2016 0.089 - 0.178: 107 0.178 - 0.266: 2 0.266 - 0.355: 1 0.355 - 0.444: 2 Chirality restraints: 2128 Sorted by residual: chirality pdb=" C1 NAG A2202 " pdb=" ND2 ASN A 98 " pdb=" C2 NAG A2202 " pdb=" O5 NAG A2202 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.93e+00 chirality pdb=" C1 NAG A2206 " pdb=" ND2 ASN A1457 " pdb=" C2 NAG A2206 " pdb=" O5 NAG A2206 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 2125 not shown) Planarity restraints: 2352 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A1915 " -0.017 2.00e-02 2.50e+03 3.37e-02 1.13e+01 pdb=" C LEU A1915 " 0.058 2.00e-02 2.50e+03 pdb=" O LEU A1915 " -0.022 2.00e-02 2.50e+03 pdb=" N SER A1916 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A1366 " 0.049 5.00e-02 4.00e+02 7.27e-02 8.46e+00 pdb=" N PRO A1367 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO A1367 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A1367 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 979 " 0.016 2.00e-02 2.50e+03 1.32e-02 4.34e+00 pdb=" CG TRP A 979 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP A 979 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP A 979 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 979 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 979 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 979 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 979 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 979 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 979 " 0.003 2.00e-02 2.50e+03 ... (remaining 2349 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 95 2.58 - 3.16: 10744 3.16 - 3.74: 20057 3.74 - 4.32: 24867 4.32 - 4.90: 42638 Nonbonded interactions: 98401 Sorted by model distance: nonbonded pdb="MG MG A2208 " pdb=" O1B ATP A2210 " model vdw 2.001 2.170 nonbonded pdb="MG MG A2208 " pdb=" O1G ATP A2210 " model vdw 2.008 2.170 nonbonded pdb=" OE1 GLN A1874 " pdb="MG MG A2209 " model vdw 2.053 2.170 nonbonded pdb=" OG1 THR A1834 " pdb="MG MG A2209 " model vdw 2.057 2.170 nonbonded pdb=" O2G ATP A2207 " pdb="MG MG A2209 " model vdw 2.213 2.170 ... (remaining 98396 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.770 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: 0.490 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 33.310 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 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 0.044 13593 Z= 0.147 Angle : 0.632 9.657 18515 Z= 0.308 Chirality : 0.042 0.444 2128 Planarity : 0.004 0.073 2344 Dihedral : 15.217 108.895 5156 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.64 % Favored : 94.30 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.22), residues: 1667 helix: 1.69 (0.18), residues: 917 sheet: -1.72 (0.51), residues: 114 loop : -1.88 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 979 HIS 0.003 0.001 HIS A 882 PHE 0.011 0.001 PHE A 866 TYR 0.010 0.001 TYR A 17 ARG 0.011 0.000 ARG A 350 Details of bonding type rmsd link_NAG-ASN : bond 0.00929 ( 8) link_NAG-ASN : angle 3.91288 ( 24) link_BETA1-4 : bond 0.00421 ( 3) link_BETA1-4 : angle 1.28350 ( 9) hydrogen bonds : bond 0.14177 ( 659) hydrogen bonds : angle 5.17770 ( 1929) SS BOND : bond 0.00130 ( 4) SS BOND : angle 0.87346 ( 8) covalent geometry : bond 0.00302 (13578) covalent geometry : angle 0.61585 (18474) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.8242 (mmp) cc_final: 0.7990 (mmp) REVERT: A 323 ASP cc_start: 0.6558 (m-30) cc_final: 0.6309 (t70) REVERT: A 386 TRP cc_start: 0.4469 (m-10) cc_final: 0.3752 (m-10) REVERT: A 615 LYS cc_start: 0.7122 (tptt) cc_final: 0.6675 (tptp) REVERT: A 975 ARG cc_start: 0.7136 (mtt180) cc_final: 0.6898 (mtt90) REVERT: A 1372 VAL cc_start: 0.6604 (t) cc_final: 0.6001 (m) REVERT: A 1615 ASN cc_start: 0.6762 (p0) cc_final: 0.6011 (m-40) REVERT: A 1686 GLN cc_start: 0.7534 (mm-40) cc_final: 0.6909 (mt0) REVERT: A 1739 ILE cc_start: 0.8281 (tp) cc_final: 0.8078 (tt) REVERT: A 1750 LEU cc_start: 0.7204 (tt) cc_final: 0.6289 (mt) REVERT: A 1799 THR cc_start: 0.8070 (t) cc_final: 0.7665 (m) REVERT: A 1962 ARG cc_start: 0.7895 (ttm110) cc_final: 0.7561 (ptp-170) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.2969 time to fit residues: 100.4459 Evaluate side-chains 153 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 0.8980 chunk 127 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 85 optimal weight: 9.9990 chunk 68 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 50 optimal weight: 0.1980 chunk 80 optimal weight: 2.9990 chunk 98 optimal weight: 0.0670 chunk 152 optimal weight: 0.9980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN A 353 GLN A 390 HIS A 395 HIS A 477 ASN A 718 ASN A1675 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.172928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.135894 restraints weight = 18999.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.135674 restraints weight = 18598.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.136956 restraints weight = 15415.384| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13593 Z= 0.119 Angle : 0.615 9.416 18515 Z= 0.294 Chirality : 0.040 0.271 2128 Planarity : 0.005 0.097 2344 Dihedral : 9.408 70.377 2129 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.08 % Allowed : 8.85 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.21), residues: 1667 helix: 1.88 (0.18), residues: 925 sheet: -1.63 (0.52), residues: 114 loop : -1.99 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 328 HIS 0.012 0.001 HIS A 395 PHE 0.022 0.001 PHE A 303 TYR 0.014 0.001 TYR A1926 ARG 0.005 0.000 ARG A1210 Details of bonding type rmsd link_NAG-ASN : bond 0.00777 ( 8) link_NAG-ASN : angle 3.11572 ( 24) link_BETA1-4 : bond 0.00422 ( 3) link_BETA1-4 : angle 2.01697 ( 9) hydrogen bonds : bond 0.04113 ( 659) hydrogen bonds : angle 3.98330 ( 1929) SS BOND : bond 0.00239 ( 4) SS BOND : angle 1.11468 ( 8) covalent geometry : bond 0.00258 (13578) covalent geometry : angle 0.60280 (18474) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 164 time to evaluate : 1.492 Fit side-chains revert: symmetry clash REVERT: A 8 MET cc_start: 0.6938 (tmm) cc_final: 0.5307 (mmm) REVERT: A 16 MET cc_start: 0.8161 (mmp) cc_final: 0.7905 (mmp) REVERT: A 291 ILE cc_start: 0.6307 (mm) cc_final: 0.5939 (mm) REVERT: A 292 LEU cc_start: 0.6750 (mt) cc_final: 0.6387 (mp) REVERT: A 581 MET cc_start: 0.8369 (OUTLIER) cc_final: 0.8152 (mtp) REVERT: A 615 LYS cc_start: 0.7169 (tptt) cc_final: 0.6824 (tptp) REVERT: A 1615 ASN cc_start: 0.6521 (p0) cc_final: 0.5741 (m-40) REVERT: A 1686 GLN cc_start: 0.7487 (mm-40) cc_final: 0.6787 (tt0) REVERT: A 1750 LEU cc_start: 0.7507 (tt) cc_final: 0.6585 (mt) REVERT: A 1799 THR cc_start: 0.8056 (t) cc_final: 0.7772 (m) REVERT: A 1962 ARG cc_start: 0.7856 (ttm110) cc_final: 0.7479 (ptp-170) REVERT: A 2011 HIS cc_start: 0.7189 (t70) cc_final: 0.6865 (t-90) outliers start: 15 outliers final: 10 residues processed: 174 average time/residue: 0.2641 time to fit residues: 66.7988 Evaluate side-chains 151 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 140 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1435 SER Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1729 VAL Chi-restraints excluded: chain A residue 1852 VAL Chi-restraints excluded: chain A residue 1910 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 10 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 15 optimal weight: 10.0000 chunk 66 optimal weight: 0.0970 chunk 87 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 143 optimal weight: 6.9990 chunk 161 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 137 optimal weight: 0.1980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 HIS A 395 HIS A 710 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.174614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.140023 restraints weight = 19422.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.138544 restraints weight = 23700.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.140061 restraints weight = 22051.986| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13593 Z= 0.135 Angle : 0.610 9.637 18515 Z= 0.294 Chirality : 0.040 0.241 2128 Planarity : 0.005 0.045 2344 Dihedral : 7.400 59.754 2129 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 1.87 % Allowed : 12.59 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.37 (0.21), residues: 1667 helix: 1.86 (0.17), residues: 931 sheet: -1.75 (0.53), residues: 114 loop : -1.97 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 484 HIS 0.006 0.001 HIS A 44 PHE 0.016 0.001 PHE A 303 TYR 0.022 0.001 TYR A1926 ARG 0.006 0.000 ARG A1210 Details of bonding type rmsd link_NAG-ASN : bond 0.00645 ( 8) link_NAG-ASN : angle 2.50484 ( 24) link_BETA1-4 : bond 0.00513 ( 3) link_BETA1-4 : angle 1.77466 ( 9) hydrogen bonds : bond 0.04272 ( 659) hydrogen bonds : angle 3.83145 ( 1929) SS BOND : bond 0.00380 ( 4) SS BOND : angle 1.22530 ( 8) covalent geometry : bond 0.00317 (13578) covalent geometry : angle 0.60187 (18474) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 MET cc_start: 0.6878 (tmm) cc_final: 0.5321 (mmm) REVERT: A 16 MET cc_start: 0.8119 (mmp) cc_final: 0.7812 (mmt) REVERT: A 30 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.7782 (mp) REVERT: A 291 ILE cc_start: 0.6348 (mm) cc_final: 0.6111 (mm) REVERT: A 581 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.8245 (mtp) REVERT: A 615 LYS cc_start: 0.7289 (tptt) cc_final: 0.6911 (tptp) REVERT: A 1615 ASN cc_start: 0.6472 (p0) cc_final: 0.5750 (m-40) REVERT: A 1686 GLN cc_start: 0.7398 (mm-40) cc_final: 0.6743 (tt0) REVERT: A 1750 LEU cc_start: 0.7612 (tt) cc_final: 0.6766 (mt) REVERT: A 1799 THR cc_start: 0.8187 (t) cc_final: 0.7792 (m) REVERT: A 1852 VAL cc_start: 0.8352 (OUTLIER) cc_final: 0.8103 (m) REVERT: A 1962 ARG cc_start: 0.7723 (ttm110) cc_final: 0.7398 (ptp-170) REVERT: A 2011 HIS cc_start: 0.7089 (t70) cc_final: 0.6883 (t-90) outliers start: 26 outliers final: 17 residues processed: 166 average time/residue: 0.2576 time to fit residues: 63.3019 Evaluate side-chains 159 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1435 SER Chi-restraints excluded: chain A residue 1541 CYS Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1729 VAL Chi-restraints excluded: chain A residue 1837 PHE Chi-restraints excluded: chain A residue 1852 VAL Chi-restraints excluded: chain A residue 1910 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 21 optimal weight: 0.9980 chunk 30 optimal weight: 10.0000 chunk 111 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 103 optimal weight: 0.0770 chunk 60 optimal weight: 0.7980 chunk 154 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 86 optimal weight: 2.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.175636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.140722 restraints weight = 19037.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.139451 restraints weight = 23041.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.140779 restraints weight = 20916.853| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13593 Z= 0.112 Angle : 0.568 9.653 18515 Z= 0.274 Chirality : 0.038 0.234 2128 Planarity : 0.005 0.067 2344 Dihedral : 6.514 59.727 2129 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.30 % Allowed : 14.32 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.21), residues: 1667 helix: 2.00 (0.17), residues: 928 sheet: -1.71 (0.52), residues: 114 loop : -1.98 (0.23), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 558 HIS 0.004 0.001 HIS A 395 PHE 0.014 0.001 PHE A 303 TYR 0.020 0.001 TYR A1926 ARG 0.006 0.000 ARG A 544 Details of bonding type rmsd link_NAG-ASN : bond 0.00535 ( 8) link_NAG-ASN : angle 2.13017 ( 24) link_BETA1-4 : bond 0.00495 ( 3) link_BETA1-4 : angle 1.53037 ( 9) hydrogen bonds : bond 0.03617 ( 659) hydrogen bonds : angle 3.68601 ( 1929) SS BOND : bond 0.00325 ( 4) SS BOND : angle 1.16308 ( 8) covalent geometry : bond 0.00256 (13578) covalent geometry : angle 0.56187 (18474) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 1.397 Fit side-chains revert: symmetry clash REVERT: A 8 MET cc_start: 0.6856 (tmm) cc_final: 0.5291 (mmm) REVERT: A 16 MET cc_start: 0.8081 (mmp) cc_final: 0.7779 (mmt) REVERT: A 30 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.7765 (mp) REVERT: A 291 ILE cc_start: 0.6435 (mm) cc_final: 0.6015 (mm) REVERT: A 292 LEU cc_start: 0.6885 (mt) cc_final: 0.6600 (mt) REVERT: A 312 ASN cc_start: 0.6509 (t0) cc_final: 0.6291 (t0) REVERT: A 581 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.8167 (mtp) REVERT: A 615 LYS cc_start: 0.7214 (tptt) cc_final: 0.6862 (tptp) REVERT: A 876 MET cc_start: 0.7459 (ppp) cc_final: 0.7181 (ppp) REVERT: A 1210 ARG cc_start: 0.6462 (mtt-85) cc_final: 0.6246 (mmt90) REVERT: A 1615 ASN cc_start: 0.6300 (p0) cc_final: 0.5670 (m-40) REVERT: A 1686 GLN cc_start: 0.7399 (mm-40) cc_final: 0.6777 (tt0) REVERT: A 1750 LEU cc_start: 0.7601 (tt) cc_final: 0.6763 (mt) REVERT: A 1799 THR cc_start: 0.8125 (t) cc_final: 0.7801 (m) REVERT: A 1852 VAL cc_start: 0.8307 (OUTLIER) cc_final: 0.8089 (m) REVERT: A 1886 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6651 (mp0) REVERT: A 1962 ARG cc_start: 0.7734 (ttm110) cc_final: 0.7436 (ptp-170) outliers start: 32 outliers final: 17 residues processed: 170 average time/residue: 0.2481 time to fit residues: 63.0566 Evaluate side-chains 158 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1689 LEU Chi-restraints excluded: chain A residue 1729 VAL Chi-restraints excluded: chain A residue 1793 LEU Chi-restraints excluded: chain A residue 1837 PHE Chi-restraints excluded: chain A residue 1852 VAL Chi-restraints excluded: chain A residue 1886 GLU Chi-restraints excluded: chain A residue 1910 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 23 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 chunk 16 optimal weight: 8.9990 chunk 87 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 HIS A 395 HIS A1313 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.173178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.138439 restraints weight = 19352.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.137369 restraints weight = 23524.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.138248 restraints weight = 22569.237| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13593 Z= 0.134 Angle : 0.589 9.713 18515 Z= 0.285 Chirality : 0.039 0.230 2128 Planarity : 0.005 0.068 2344 Dihedral : 6.377 57.421 2129 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.88 % Allowed : 14.68 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.47 (0.21), residues: 1667 helix: 1.98 (0.17), residues: 930 sheet: -1.81 (0.52), residues: 114 loop : -1.97 (0.24), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 558 HIS 0.006 0.001 HIS A 44 PHE 0.015 0.001 PHE A1486 TYR 0.019 0.001 TYR A1926 ARG 0.003 0.000 ARG A2015 Details of bonding type rmsd link_NAG-ASN : bond 0.00480 ( 8) link_NAG-ASN : angle 2.04962 ( 24) link_BETA1-4 : bond 0.00456 ( 3) link_BETA1-4 : angle 1.33583 ( 9) hydrogen bonds : bond 0.04089 ( 659) hydrogen bonds : angle 3.73368 ( 1929) SS BOND : bond 0.00328 ( 4) SS BOND : angle 1.32138 ( 8) covalent geometry : bond 0.00317 (13578) covalent geometry : angle 0.58316 (18474) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 145 time to evaluate : 1.425 Fit side-chains revert: symmetry clash REVERT: A 8 MET cc_start: 0.6876 (tmm) cc_final: 0.5350 (mmm) REVERT: A 30 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.7841 (mp) REVERT: A 291 ILE cc_start: 0.6506 (mm) cc_final: 0.6245 (mm) REVERT: A 477 ASN cc_start: 0.7457 (OUTLIER) cc_final: 0.7180 (m110) REVERT: A 581 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.8251 (mtp) REVERT: A 615 LYS cc_start: 0.7248 (tptt) cc_final: 0.6911 (tptp) REVERT: A 876 MET cc_start: 0.7598 (ppp) cc_final: 0.7268 (ppp) REVERT: A 1372 VAL cc_start: 0.6102 (t) cc_final: 0.5415 (m) REVERT: A 1615 ASN cc_start: 0.6246 (p0) cc_final: 0.5734 (m-40) REVERT: A 1799 THR cc_start: 0.8249 (t) cc_final: 0.7836 (m) REVERT: A 1886 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.6750 (mp0) REVERT: A 1962 ARG cc_start: 0.7754 (ttm110) cc_final: 0.7421 (ptp-170) outliers start: 40 outliers final: 28 residues processed: 172 average time/residue: 0.2602 time to fit residues: 66.0369 Evaluate side-chains 165 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain A residue 925 GLN Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1432 LEU Chi-restraints excluded: chain A residue 1435 SER Chi-restraints excluded: chain A residue 1456 LYS Chi-restraints excluded: chain A residue 1458 LEU Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1689 LEU Chi-restraints excluded: chain A residue 1729 VAL Chi-restraints excluded: chain A residue 1793 LEU Chi-restraints excluded: chain A residue 1798 LEU Chi-restraints excluded: chain A residue 1837 PHE Chi-restraints excluded: chain A residue 1844 THR Chi-restraints excluded: chain A residue 1886 GLU Chi-restraints excluded: chain A residue 1910 LEU Chi-restraints excluded: chain A residue 1969 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 130 optimal weight: 2.9990 chunk 34 optimal weight: 0.1980 chunk 115 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 53 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.173881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.138910 restraints weight = 19520.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.138156 restraints weight = 21293.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.139109 restraints weight = 18895.607| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 13593 Z= 0.108 Angle : 0.560 11.178 18515 Z= 0.271 Chirality : 0.038 0.229 2128 Planarity : 0.005 0.080 2344 Dihedral : 6.107 56.294 2129 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.88 % Allowed : 15.32 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.22), residues: 1667 helix: 2.10 (0.17), residues: 928 sheet: -1.77 (0.51), residues: 114 loop : -1.96 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 558 HIS 0.003 0.001 HIS A 717 PHE 0.012 0.001 PHE A 303 TYR 0.018 0.001 TYR A1926 ARG 0.007 0.000 ARG A 922 Details of bonding type rmsd link_NAG-ASN : bond 0.00482 ( 8) link_NAG-ASN : angle 2.00847 ( 24) link_BETA1-4 : bond 0.00532 ( 3) link_BETA1-4 : angle 1.27989 ( 9) hydrogen bonds : bond 0.03492 ( 659) hydrogen bonds : angle 3.62202 ( 1929) SS BOND : bond 0.00334 ( 4) SS BOND : angle 1.22299 ( 8) covalent geometry : bond 0.00246 (13578) covalent geometry : angle 0.55491 (18474) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 139 time to evaluate : 1.334 Fit side-chains REVERT: A 30 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.7806 (mp) REVERT: A 291 ILE cc_start: 0.6460 (mm) cc_final: 0.6208 (mm) REVERT: A 477 ASN cc_start: 0.7400 (OUTLIER) cc_final: 0.7118 (m110) REVERT: A 581 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.8172 (mtp) REVERT: A 615 LYS cc_start: 0.7202 (tptt) cc_final: 0.6879 (tptp) REVERT: A 876 MET cc_start: 0.7604 (ppp) cc_final: 0.7287 (ppp) REVERT: A 1349 ARG cc_start: 0.5742 (mtt180) cc_final: 0.5473 (mtm180) REVERT: A 1353 ARG cc_start: 0.5756 (OUTLIER) cc_final: 0.3699 (ptt180) REVERT: A 1372 VAL cc_start: 0.6034 (t) cc_final: 0.5356 (m) REVERT: A 1430 GLN cc_start: 0.6650 (tt0) cc_final: 0.6439 (pp30) REVERT: A 1615 ASN cc_start: 0.6239 (p0) cc_final: 0.5727 (m-40) REVERT: A 1750 LEU cc_start: 0.7636 (tt) cc_final: 0.6792 (mt) REVERT: A 1799 THR cc_start: 0.8233 (t) cc_final: 0.7812 (m) REVERT: A 1953 THR cc_start: 0.8621 (OUTLIER) cc_final: 0.8415 (m) REVERT: A 1962 ARG cc_start: 0.7811 (ttm110) cc_final: 0.7435 (ptp-170) outliers start: 40 outliers final: 27 residues processed: 169 average time/residue: 0.2453 time to fit residues: 61.6423 Evaluate side-chains 165 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain A residue 925 GLN Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 1142 ILE Chi-restraints excluded: chain A residue 1353 ARG Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1432 LEU Chi-restraints excluded: chain A residue 1456 LYS Chi-restraints excluded: chain A residue 1541 CYS Chi-restraints excluded: chain A residue 1599 VAL Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1689 LEU Chi-restraints excluded: chain A residue 1729 VAL Chi-restraints excluded: chain A residue 1793 LEU Chi-restraints excluded: chain A residue 1798 LEU Chi-restraints excluded: chain A residue 1837 PHE Chi-restraints excluded: chain A residue 1910 LEU Chi-restraints excluded: chain A residue 1953 THR Chi-restraints excluded: chain A residue 1969 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 94 optimal weight: 1.9990 chunk 80 optimal weight: 0.4980 chunk 127 optimal weight: 2.9990 chunk 102 optimal weight: 0.0970 chunk 115 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 33 optimal weight: 0.0010 chunk 163 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 HIS A1523 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.174496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.139651 restraints weight = 19308.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.138677 restraints weight = 21725.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.140463 restraints weight = 19280.599| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 13593 Z= 0.104 Angle : 0.564 11.039 18515 Z= 0.270 Chirality : 0.038 0.227 2128 Planarity : 0.004 0.066 2344 Dihedral : 6.005 56.096 2129 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.73 % Allowed : 16.04 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.22), residues: 1667 helix: 2.18 (0.17), residues: 929 sheet: -1.73 (0.52), residues: 114 loop : -1.94 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 558 HIS 0.003 0.001 HIS A 717 PHE 0.011 0.001 PHE A 303 TYR 0.018 0.001 TYR A1926 ARG 0.005 0.000 ARG A 922 Details of bonding type rmsd link_NAG-ASN : bond 0.00479 ( 8) link_NAG-ASN : angle 1.95519 ( 24) link_BETA1-4 : bond 0.00533 ( 3) link_BETA1-4 : angle 1.25257 ( 9) hydrogen bonds : bond 0.03295 ( 659) hydrogen bonds : angle 3.54484 ( 1929) SS BOND : bond 0.00364 ( 4) SS BOND : angle 1.27273 ( 8) covalent geometry : bond 0.00237 (13578) covalent geometry : angle 0.55872 (18474) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 145 time to evaluate : 2.496 Fit side-chains REVERT: A 8 MET cc_start: 0.6757 (tmm) cc_final: 0.5210 (mmm) REVERT: A 291 ILE cc_start: 0.6426 (mm) cc_final: 0.6179 (mm) REVERT: A 477 ASN cc_start: 0.7333 (OUTLIER) cc_final: 0.7047 (m110) REVERT: A 581 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.8164 (mtp) REVERT: A 615 LYS cc_start: 0.7185 (tptt) cc_final: 0.6876 (tptp) REVERT: A 876 MET cc_start: 0.7564 (ppp) cc_final: 0.7246 (ppp) REVERT: A 1353 ARG cc_start: 0.5623 (OUTLIER) cc_final: 0.3664 (ptt180) REVERT: A 1372 VAL cc_start: 0.5986 (t) cc_final: 0.5311 (m) REVERT: A 1430 GLN cc_start: 0.6630 (tt0) cc_final: 0.6402 (pp30) REVERT: A 1615 ASN cc_start: 0.6202 (p0) cc_final: 0.5550 (m-40) REVERT: A 1738 VAL cc_start: 0.6982 (t) cc_final: 0.6753 (p) REVERT: A 1750 LEU cc_start: 0.7604 (tt) cc_final: 0.6766 (mt) REVERT: A 1799 THR cc_start: 0.8240 (t) cc_final: 0.7907 (m) REVERT: A 1850 GLU cc_start: 0.5612 (mp0) cc_final: 0.5285 (tp30) REVERT: A 1953 THR cc_start: 0.8605 (OUTLIER) cc_final: 0.8371 (m) REVERT: A 1962 ARG cc_start: 0.7800 (ttm110) cc_final: 0.7424 (ptp-170) outliers start: 38 outliers final: 25 residues processed: 174 average time/residue: 0.2499 time to fit residues: 64.7315 Evaluate side-chains 163 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 1142 ILE Chi-restraints excluded: chain A residue 1353 ARG Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1432 LEU Chi-restraints excluded: chain A residue 1435 SER Chi-restraints excluded: chain A residue 1458 LEU Chi-restraints excluded: chain A residue 1541 CYS Chi-restraints excluded: chain A residue 1599 VAL Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1689 LEU Chi-restraints excluded: chain A residue 1729 VAL Chi-restraints excluded: chain A residue 1837 PHE Chi-restraints excluded: chain A residue 1891 LEU Chi-restraints excluded: chain A residue 1910 LEU Chi-restraints excluded: chain A residue 1953 THR Chi-restraints excluded: chain A residue 1969 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 32 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 49 optimal weight: 0.8980 chunk 81 optimal weight: 0.0170 chunk 148 optimal weight: 3.9990 overall best weight: 1.7824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 HIS A1675 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.168849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.133806 restraints weight = 19516.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.132715 restraints weight = 23755.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.133748 restraints weight = 22181.297| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13593 Z= 0.186 Angle : 0.682 15.473 18515 Z= 0.328 Chirality : 0.042 0.223 2128 Planarity : 0.006 0.132 2344 Dihedral : 6.635 59.544 2129 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 2.81 % Allowed : 16.33 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.21), residues: 1667 helix: 1.91 (0.17), residues: 926 sheet: -2.09 (0.50), residues: 114 loop : -2.01 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 328 HIS 0.004 0.001 HIS A1481 PHE 0.020 0.002 PHE A1486 TYR 0.017 0.002 TYR A1926 ARG 0.009 0.000 ARG A1349 Details of bonding type rmsd link_NAG-ASN : bond 0.00477 ( 8) link_NAG-ASN : angle 2.02139 ( 24) link_BETA1-4 : bond 0.00743 ( 3) link_BETA1-4 : angle 1.36212 ( 9) hydrogen bonds : bond 0.05011 ( 659) hydrogen bonds : angle 3.94337 ( 1929) SS BOND : bond 0.00577 ( 4) SS BOND : angle 1.79709 ( 8) covalent geometry : bond 0.00453 (13578) covalent geometry : angle 0.67717 (18474) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 135 time to evaluate : 1.547 Fit side-chains REVERT: A 8 MET cc_start: 0.6949 (tmm) cc_final: 0.5316 (mmm) REVERT: A 291 ILE cc_start: 0.6563 (mm) cc_final: 0.6322 (mm) REVERT: A 615 LYS cc_start: 0.7665 (tptt) cc_final: 0.7220 (tptp) REVERT: A 1353 ARG cc_start: 0.5711 (OUTLIER) cc_final: 0.3663 (ptt180) REVERT: A 1372 VAL cc_start: 0.6151 (t) cc_final: 0.5492 (m) REVERT: A 1430 GLN cc_start: 0.6777 (tt0) cc_final: 0.6438 (pp30) REVERT: A 1588 MET cc_start: 0.8242 (tpt) cc_final: 0.7894 (tpt) REVERT: A 1615 ASN cc_start: 0.6178 (p0) cc_final: 0.5760 (m-40) REVERT: A 1798 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8327 (mp) REVERT: A 1799 THR cc_start: 0.8340 (t) cc_final: 0.7893 (m) REVERT: A 1850 GLU cc_start: 0.5836 (mp0) cc_final: 0.5501 (tp30) REVERT: A 1962 ARG cc_start: 0.7810 (ttm110) cc_final: 0.7433 (ptp-170) outliers start: 39 outliers final: 28 residues processed: 165 average time/residue: 0.2647 time to fit residues: 65.0270 Evaluate side-chains 161 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 867 ILE Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain A residue 925 GLN Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 1280 VAL Chi-restraints excluded: chain A residue 1353 ARG Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1435 SER Chi-restraints excluded: chain A residue 1458 LEU Chi-restraints excluded: chain A residue 1541 CYS Chi-restraints excluded: chain A residue 1599 VAL Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1689 LEU Chi-restraints excluded: chain A residue 1729 VAL Chi-restraints excluded: chain A residue 1738 VAL Chi-restraints excluded: chain A residue 1798 LEU Chi-restraints excluded: chain A residue 1837 PHE Chi-restraints excluded: chain A residue 1891 LEU Chi-restraints excluded: chain A residue 1910 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 72 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 133 optimal weight: 0.4980 chunk 155 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 HIS A 477 ASN A 843 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.171739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.137402 restraints weight = 19390.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.136381 restraints weight = 23188.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.137710 restraints weight = 20220.589| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13593 Z= 0.120 Angle : 0.599 12.022 18515 Z= 0.288 Chirality : 0.039 0.227 2128 Planarity : 0.005 0.101 2344 Dihedral : 6.312 59.067 2129 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.09 % Allowed : 17.48 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.22), residues: 1667 helix: 2.05 (0.17), residues: 927 sheet: -1.96 (0.52), residues: 104 loop : -1.99 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP A 979 HIS 0.003 0.001 HIS A 717 PHE 0.013 0.001 PHE A1486 TYR 0.018 0.001 TYR A1926 ARG 0.008 0.000 ARG A1349 Details of bonding type rmsd link_NAG-ASN : bond 0.00475 ( 8) link_NAG-ASN : angle 2.00333 ( 24) link_BETA1-4 : bond 0.00581 ( 3) link_BETA1-4 : angle 1.27553 ( 9) hydrogen bonds : bond 0.03848 ( 659) hydrogen bonds : angle 3.73162 ( 1929) SS BOND : bond 0.00375 ( 4) SS BOND : angle 1.36439 ( 8) covalent geometry : bond 0.00281 (13578) covalent geometry : angle 0.59368 (18474) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 1.321 Fit side-chains REVERT: A 8 MET cc_start: 0.6849 (tmm) cc_final: 0.5283 (mmm) REVERT: A 291 ILE cc_start: 0.6533 (mm) cc_final: 0.6311 (mm) REVERT: A 876 MET cc_start: 0.7670 (ppp) cc_final: 0.7401 (ppp) REVERT: A 1353 ARG cc_start: 0.5650 (OUTLIER) cc_final: 0.3678 (ptt180) REVERT: A 1372 VAL cc_start: 0.6038 (t) cc_final: 0.5401 (m) REVERT: A 1430 GLN cc_start: 0.6638 (tt0) cc_final: 0.6311 (pp30) REVERT: A 1615 ASN cc_start: 0.6087 (p0) cc_final: 0.5765 (m-40) REVERT: A 1798 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8336 (mp) REVERT: A 1799 THR cc_start: 0.8293 (t) cc_final: 0.7867 (m) REVERT: A 1850 GLU cc_start: 0.5783 (mp0) cc_final: 0.5412 (tp30) REVERT: A 1953 THR cc_start: 0.8548 (OUTLIER) cc_final: 0.8345 (m) REVERT: A 1962 ARG cc_start: 0.7793 (ttm110) cc_final: 0.7401 (ptp-170) outliers start: 29 outliers final: 24 residues processed: 161 average time/residue: 0.2495 time to fit residues: 60.0102 Evaluate side-chains 155 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 867 ILE Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain A residue 925 GLN Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 1353 ARG Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1432 LEU Chi-restraints excluded: chain A residue 1435 SER Chi-restraints excluded: chain A residue 1458 LEU Chi-restraints excluded: chain A residue 1541 CYS Chi-restraints excluded: chain A residue 1599 VAL Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1689 LEU Chi-restraints excluded: chain A residue 1729 VAL Chi-restraints excluded: chain A residue 1798 LEU Chi-restraints excluded: chain A residue 1891 LEU Chi-restraints excluded: chain A residue 1910 LEU Chi-restraints excluded: chain A residue 1953 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 82 optimal weight: 0.8980 chunk 142 optimal weight: 0.1980 chunk 73 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 153 optimal weight: 0.6980 chunk 3 optimal weight: 0.0370 chunk 29 optimal weight: 8.9990 chunk 55 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 95 optimal weight: 0.3980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.174151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.140034 restraints weight = 19383.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.139413 restraints weight = 22520.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.140901 restraints weight = 19543.157| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 13593 Z= 0.107 Angle : 0.588 14.125 18515 Z= 0.282 Chirality : 0.038 0.230 2128 Planarity : 0.004 0.053 2344 Dihedral : 6.073 56.017 2129 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.01 % Allowed : 17.41 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.22), residues: 1667 helix: 2.19 (0.17), residues: 926 sheet: -1.83 (0.53), residues: 104 loop : -1.95 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP A 979 HIS 0.003 0.000 HIS A1866 PHE 0.011 0.001 PHE A 303 TYR 0.018 0.001 TYR A1926 ARG 0.005 0.000 ARG A 922 Details of bonding type rmsd link_NAG-ASN : bond 0.00484 ( 8) link_NAG-ASN : angle 1.97982 ( 24) link_BETA1-4 : bond 0.00613 ( 3) link_BETA1-4 : angle 1.24510 ( 9) hydrogen bonds : bond 0.03265 ( 659) hydrogen bonds : angle 3.59639 ( 1929) SS BOND : bond 0.00308 ( 4) SS BOND : angle 1.25110 ( 8) covalent geometry : bond 0.00243 (13578) covalent geometry : angle 0.58353 (18474) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 1.349 Fit side-chains REVERT: A 8 MET cc_start: 0.6764 (tmm) cc_final: 0.5235 (mmm) REVERT: A 291 ILE cc_start: 0.6468 (mm) cc_final: 0.6258 (mm) REVERT: A 485 ASP cc_start: 0.7420 (m-30) cc_final: 0.7042 (t0) REVERT: A 876 MET cc_start: 0.7724 (ppp) cc_final: 0.7447 (ppp) REVERT: A 1353 ARG cc_start: 0.5557 (OUTLIER) cc_final: 0.3632 (ptt180) REVERT: A 1372 VAL cc_start: 0.5987 (t) cc_final: 0.5364 (m) REVERT: A 1607 GLN cc_start: 0.7996 (tm-30) cc_final: 0.7722 (tm-30) REVERT: A 1615 ASN cc_start: 0.5809 (p0) cc_final: 0.5552 (m-40) REVERT: A 1739 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.8086 (tt) REVERT: A 1750 LEU cc_start: 0.7583 (tt) cc_final: 0.6833 (mt) REVERT: A 1850 GLU cc_start: 0.5751 (mp0) cc_final: 0.5462 (tp30) REVERT: A 1962 ARG cc_start: 0.7809 (ttm110) cc_final: 0.7440 (ptp-170) REVERT: A 1985 MET cc_start: 0.7099 (ptt) cc_final: 0.6242 (mmp) outliers start: 28 outliers final: 23 residues processed: 160 average time/residue: 0.2508 time to fit residues: 60.1318 Evaluate side-chains 160 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 867 ILE Chi-restraints excluded: chain A residue 925 GLN Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 1280 VAL Chi-restraints excluded: chain A residue 1353 ARG Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1432 LEU Chi-restraints excluded: chain A residue 1435 SER Chi-restraints excluded: chain A residue 1458 LEU Chi-restraints excluded: chain A residue 1541 CYS Chi-restraints excluded: chain A residue 1599 VAL Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1689 LEU Chi-restraints excluded: chain A residue 1729 VAL Chi-restraints excluded: chain A residue 1739 ILE Chi-restraints excluded: chain A residue 1891 LEU Chi-restraints excluded: chain A residue 1910 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 58 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 chunk 103 optimal weight: 0.4980 chunk 17 optimal weight: 0.0980 chunk 159 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 143 optimal weight: 0.7980 chunk 125 optimal weight: 0.7980 chunk 139 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.173794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.139422 restraints weight = 19479.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.138561 restraints weight = 22017.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.140188 restraints weight = 18891.285| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13593 Z= 0.112 Angle : 0.595 12.720 18515 Z= 0.285 Chirality : 0.038 0.229 2128 Planarity : 0.004 0.060 2344 Dihedral : 6.089 57.277 2129 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.87 % Allowed : 18.13 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.69 (0.22), residues: 1667 helix: 2.24 (0.17), residues: 922 sheet: -1.81 (0.50), residues: 124 loop : -1.94 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.001 TRP A 979 HIS 0.003 0.001 HIS A 717 PHE 0.014 0.001 PHE A 553 TYR 0.017 0.001 TYR A1926 ARG 0.005 0.000 ARG A1349 Details of bonding type rmsd link_NAG-ASN : bond 0.00471 ( 8) link_NAG-ASN : angle 1.94307 ( 24) link_BETA1-4 : bond 0.00554 ( 3) link_BETA1-4 : angle 1.27381 ( 9) hydrogen bonds : bond 0.03393 ( 659) hydrogen bonds : angle 3.57848 ( 1929) SS BOND : bond 0.00302 ( 4) SS BOND : angle 1.37815 ( 8) covalent geometry : bond 0.00260 (13578) covalent geometry : angle 0.59059 (18474) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3998.46 seconds wall clock time: 70 minutes 49.21 seconds (4249.21 seconds total)