Starting phenix.real_space_refine on Thu Jul 31 17:12:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eop_28451/07_2025/8eop_28451.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eop_28451/07_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_28451/07_2025/8eop_28451.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eop_28451/07_2025/8eop_28451.map" model { file = "/net/cci-nas-00/data/ceres_data/8eop_28451/07_2025/8eop_28451.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eop_28451/07_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-5711/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: 9.25, per 1000 atoms: 0.70 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: 3.38 Conformation dependent library (CDL) restraints added in 1.6 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: 2.08 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: 5.28 Time building geometry restraints manager: 3.86 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: 4.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.610 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 34.910 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.080 ------------------------------------------------------------------------------- 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 : 1.420 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: 0.3087 time to fit residues: 105.3192 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 : 1.437 ------------------------------------------------------------------------------- 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 = 0.172929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.135828 restraints weight = 18999.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.136241 restraints weight = 18584.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.137440 restraints weight = 14574.171| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 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 9.415 18515 Z= 0.294 Chirality : 0.040 0.271 2128 Planarity : 0.005 0.097 2344 Dihedral : 9.409 70.407 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 3.11559 ( 24) link_BETA1-4 : bond 0.00421 ( 3) link_BETA1-4 : angle 2.01594 ( 9) hydrogen bonds : bond 0.04114 ( 659) hydrogen bonds : angle 3.98353 ( 1929) SS BOND : bond 0.00239 ( 4) SS BOND : angle 1.11474 ( 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 : 1.435 Fit side-chains revert: symmetry clash REVERT: A 8 MET cc_start: 0.6938 (tmm) cc_final: 0.5299 (mmm) REVERT: A 16 MET cc_start: 0.8171 (mmp) cc_final: 0.7909 (mmp) REVERT: A 291 ILE cc_start: 0.6301 (mm) cc_final: 0.5932 (mm) REVERT: A 292 LEU cc_start: 0.6740 (mt) cc_final: 0.6378 (mp) REVERT: A 581 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.8149 (mtp) REVERT: A 615 LYS cc_start: 0.7162 (tptt) cc_final: 0.6819 (tptp) REVERT: A 1615 ASN cc_start: 0.6518 (p0) cc_final: 0.5737 (m-40) REVERT: A 1686 GLN cc_start: 0.7489 (mm-40) cc_final: 0.6787 (tt0) REVERT: A 1750 LEU cc_start: 0.7503 (tt) cc_final: 0.6578 (mt) REVERT: A 1799 THR cc_start: 0.8058 (t) cc_final: 0.7774 (m) REVERT: A 1962 ARG cc_start: 0.7858 (ttm110) cc_final: 0.7479 (ptp-170) REVERT: A 2011 HIS cc_start: 0.7189 (t70) cc_final: 0.6862 (t-90) outliers start: 15 outliers final: 10 residues processed: 174 average time/residue: 0.2708 time to fit residues: 68.2988 Evaluate side-chains 150 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 139 time to evaluate : 1.299 ------------------------------------------------------------------------------- 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: 0.7980 chunk 123 optimal weight: 0.7980 chunk 15 optimal weight: 9.9990 chunk 66 optimal weight: 0.0470 chunk 87 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 143 optimal weight: 7.9990 chunk 161 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 137 optimal weight: 0.9990 overall best weight: 0.9282 ------------------------------------------------------------------------------- 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 = 0.4044 r_free = 0.4044 target = 0.175202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.140584 restraints weight = 19414.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.139681 restraints weight = 23540.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.141083 restraints weight = 22346.146| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13593 Z= 0.128 Angle : 0.598 9.639 18515 Z= 0.289 Chirality : 0.040 0.248 2128 Planarity : 0.004 0.045 2344 Dihedral : 7.421 59.952 2129 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.87 % Allowed : 12.09 % Favored : 86.04 % 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: 0.41 (0.21), residues: 1667 helix: 1.90 (0.17), residues: 931 sheet: -1.70 (0.53), residues: 114 loop : -1.97 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 484 HIS 0.006 0.001 HIS A 44 PHE 0.016 0.001 PHE A 303 TYR 0.021 0.001 TYR A1926 ARG 0.005 0.000 ARG A1210 Details of bonding type rmsd link_NAG-ASN : bond 0.00636 ( 8) link_NAG-ASN : angle 2.56718 ( 24) link_BETA1-4 : bond 0.00481 ( 3) link_BETA1-4 : angle 1.78280 ( 9) hydrogen bonds : bond 0.04107 ( 659) hydrogen bonds : angle 3.80098 ( 1929) SS BOND : bond 0.00367 ( 4) SS BOND : angle 1.17955 ( 8) covalent geometry : bond 0.00296 (13578) covalent geometry : angle 0.58925 (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 174 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 MET cc_start: 0.6867 (tmm) cc_final: 0.5313 (mmm) REVERT: A 16 MET cc_start: 0.8126 (mmp) cc_final: 0.7769 (mmt) REVERT: A 30 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.7771 (mp) REVERT: A 291 ILE cc_start: 0.6336 (mm) cc_final: 0.6079 (mm) REVERT: A 581 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.8226 (mtp) REVERT: A 615 LYS cc_start: 0.7242 (tptt) cc_final: 0.6865 (tptp) REVERT: A 1615 ASN cc_start: 0.6451 (p0) cc_final: 0.5735 (m-40) REVERT: A 1686 GLN cc_start: 0.7390 (mm-40) cc_final: 0.6738 (tt0) REVERT: A 1750 LEU cc_start: 0.7572 (tt) cc_final: 0.6755 (mt) REVERT: A 1799 THR cc_start: 0.8227 (t) cc_final: 0.7827 (m) REVERT: A 1962 ARG cc_start: 0.7723 (ttm110) cc_final: 0.7403 (ptp-170) outliers start: 26 outliers final: 18 residues processed: 165 average time/residue: 0.2519 time to fit residues: 61.4407 Evaluate side-chains 160 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 1.302 ------------------------------------------------------------------------------- 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: 9.9990 chunk 111 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 154 optimal weight: 3.9990 chunk 107 optimal weight: 0.0170 chunk 16 optimal weight: 9.9990 chunk 86 optimal weight: 7.9990 overall best weight: 0.7620 ------------------------------------------------------------------------------- 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 = 0.4045 r_free = 0.4045 target = 0.175513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.140738 restraints weight = 19075.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.139649 restraints weight = 24076.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.141040 restraints weight = 21207.379| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13593 Z= 0.115 Angle : 0.570 9.658 18515 Z= 0.275 Chirality : 0.039 0.233 2128 Planarity : 0.005 0.062 2344 Dihedral : 6.546 59.793 2129 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.09 % Allowed : 14.17 % Favored : 83.74 % 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: 1.98 (0.17), residues: 931 sheet: -1.70 (0.52), residues: 114 loop : -1.97 (0.23), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 558 HIS 0.006 0.001 HIS A2011 PHE 0.014 0.001 PHE A 303 TYR 0.020 0.001 TYR A1926 ARG 0.007 0.000 ARG A1349 Details of bonding type rmsd link_NAG-ASN : bond 0.00530 ( 8) link_NAG-ASN : angle 2.13566 ( 24) link_BETA1-4 : bond 0.00492 ( 3) link_BETA1-4 : angle 1.53670 ( 9) hydrogen bonds : bond 0.03699 ( 659) hydrogen bonds : angle 3.68701 ( 1929) SS BOND : bond 0.00420 ( 4) SS BOND : angle 1.32673 ( 8) covalent geometry : bond 0.00264 (13578) covalent geometry : angle 0.56419 (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 180 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 151 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 MET cc_start: 0.6858 (tmm) cc_final: 0.5290 (mmm) REVERT: A 16 MET cc_start: 0.8082 (mmp) cc_final: 0.7781 (mmt) REVERT: A 30 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.7789 (mp) REVERT: A 291 ILE cc_start: 0.6373 (mm) cc_final: 0.6149 (mm) REVERT: A 312 ASN cc_start: 0.6517 (t0) cc_final: 0.6302 (t0) REVERT: A 581 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.8183 (mtp) REVERT: A 615 LYS cc_start: 0.7216 (tptt) cc_final: 0.6866 (tptp) REVERT: A 876 MET cc_start: 0.7452 (ppp) cc_final: 0.7176 (ppp) REVERT: A 899 ASP cc_start: 0.6446 (t0) cc_final: 0.6161 (t0) REVERT: A 1210 ARG cc_start: 0.6457 (mtt-85) cc_final: 0.6239 (mmt90) REVERT: A 1615 ASN cc_start: 0.6325 (p0) cc_final: 0.5687 (m-40) REVERT: A 1686 GLN cc_start: 0.7406 (mm-40) cc_final: 0.6759 (tt0) REVERT: A 1750 LEU cc_start: 0.7593 (tt) cc_final: 0.6775 (mt) REVERT: A 1799 THR cc_start: 0.8117 (t) cc_final: 0.7809 (m) REVERT: A 1852 VAL cc_start: 0.8317 (OUTLIER) cc_final: 0.8097 (m) REVERT: A 1962 ARG cc_start: 0.7740 (ttm110) cc_final: 0.7436 (ptp-170) outliers start: 29 outliers final: 18 residues processed: 167 average time/residue: 0.2570 time to fit residues: 63.5942 Evaluate side-chains 159 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 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 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 1432 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 1837 PHE Chi-restraints excluded: chain A residue 1852 VAL 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: 6.9990 chunk 124 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 1 optimal weight: 0.0470 chunk 71 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 108 optimal weight: 0.1980 overall best weight: 0.6280 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.175698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.140865 restraints weight = 19348.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.139389 restraints weight = 24341.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.140819 restraints weight = 21448.996| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 13593 Z= 0.108 Angle : 0.553 9.658 18515 Z= 0.267 Chirality : 0.038 0.229 2128 Planarity : 0.004 0.049 2344 Dihedral : 6.174 56.244 2129 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.66 % Allowed : 14.46 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.21), residues: 1667 helix: 2.14 (0.17), residues: 928 sheet: -1.63 (0.55), residues: 104 loop : -1.96 (0.23), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 558 HIS 0.005 0.001 HIS A 44 PHE 0.013 0.001 PHE A 542 TYR 0.019 0.001 TYR A1926 ARG 0.009 0.000 ARG A1349 Details of bonding type rmsd link_NAG-ASN : bond 0.00487 ( 8) link_NAG-ASN : angle 2.06854 ( 24) link_BETA1-4 : bond 0.00493 ( 3) link_BETA1-4 : angle 1.32940 ( 9) hydrogen bonds : bond 0.03472 ( 659) hydrogen bonds : angle 3.60401 ( 1929) SS BOND : bond 0.00397 ( 4) SS BOND : angle 1.22299 ( 8) covalent geometry : bond 0.00246 (13578) covalent geometry : angle 0.54716 (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 182 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 145 time to evaluate : 1.302 Fit side-chains revert: symmetry clash REVERT: A 16 MET cc_start: 0.8063 (mmp) cc_final: 0.7785 (tpp) REVERT: A 30 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.7777 (mp) REVERT: A 291 ILE cc_start: 0.6483 (mm) cc_final: 0.5989 (mm) REVERT: A 292 LEU cc_start: 0.6778 (mt) cc_final: 0.6121 (mt) REVERT: A 477 ASN cc_start: 0.7372 (OUTLIER) cc_final: 0.7094 (m110) REVERT: A 581 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.8142 (mtp) REVERT: A 615 LYS cc_start: 0.7107 (tptt) cc_final: 0.6815 (tptp) REVERT: A 876 MET cc_start: 0.7521 (ppp) cc_final: 0.7230 (ppp) REVERT: A 1353 ARG cc_start: 0.5684 (OUTLIER) cc_final: 0.3851 (ptt180) REVERT: A 1615 ASN cc_start: 0.6125 (p0) cc_final: 0.5697 (m-40) REVERT: A 1750 LEU cc_start: 0.7615 (tt) cc_final: 0.6799 (mt) REVERT: A 1799 THR cc_start: 0.8207 (t) cc_final: 0.7807 (m) REVERT: A 1962 ARG cc_start: 0.7729 (ttm110) cc_final: 0.7419 (ptp-170) outliers start: 37 outliers final: 22 residues processed: 169 average time/residue: 0.2623 time to fit residues: 65.9224 Evaluate side-chains 159 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 1.326 ------------------------------------------------------------------------------- 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 477 ASN 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 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 1541 CYS 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 130 optimal weight: 0.4980 chunk 34 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 137 optimal weight: 0.7980 chunk 156 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4076 r_free = 0.4076 target = 0.178130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.146777 restraints weight = 19334.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.145447 restraints weight = 25383.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.146152 restraints weight = 24241.035| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13593 Z= 0.115 Angle : 0.566 10.215 18515 Z= 0.273 Chirality : 0.039 0.226 2128 Planarity : 0.005 0.083 2344 Dihedral : 6.105 56.663 2129 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.59 % Allowed : 15.11 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.22), residues: 1667 helix: 2.14 (0.17), residues: 928 sheet: -1.68 (0.52), residues: 114 loop : -1.94 (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 A1486 TYR 0.018 0.001 TYR A1926 ARG 0.004 0.000 ARG A1210 Details of bonding type rmsd link_NAG-ASN : bond 0.00471 ( 8) link_NAG-ASN : angle 2.00076 ( 24) link_BETA1-4 : bond 0.00490 ( 3) link_BETA1-4 : angle 1.28309 ( 9) hydrogen bonds : bond 0.03576 ( 659) hydrogen bonds : angle 3.60141 ( 1929) SS BOND : bond 0.00439 ( 4) SS BOND : angle 1.34389 ( 8) covalent geometry : bond 0.00267 (13578) covalent geometry : angle 0.56066 (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 177 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 141 time to evaluate : 1.346 Fit side-chains REVERT: A 8 MET cc_start: 0.6767 (tmm) cc_final: 0.5262 (mmm) REVERT: A 30 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.7837 (mp) REVERT: A 291 ILE cc_start: 0.6452 (mm) cc_final: 0.6052 (mm) REVERT: A 292 LEU cc_start: 0.6861 (mt) cc_final: 0.6584 (mt) REVERT: A 477 ASN cc_start: 0.7313 (OUTLIER) cc_final: 0.7037 (m110) REVERT: A 581 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.8178 (mtp) REVERT: A 615 LYS cc_start: 0.7132 (tptt) cc_final: 0.6826 (tptp) REVERT: A 876 MET cc_start: 0.7535 (ppp) cc_final: 0.7246 (ppp) REVERT: A 1353 ARG cc_start: 0.5597 (OUTLIER) cc_final: 0.3558 (ptt180) REVERT: A 1372 VAL cc_start: 0.6119 (t) cc_final: 0.5459 (m) REVERT: A 1615 ASN cc_start: 0.6078 (p0) cc_final: 0.5665 (m-40) REVERT: A 1750 LEU cc_start: 0.7630 (tt) cc_final: 0.6802 (mt) REVERT: A 1799 THR cc_start: 0.8230 (t) cc_final: 0.7822 (m) REVERT: A 1953 THR cc_start: 0.8585 (OUTLIER) cc_final: 0.8336 (m) REVERT: A 1962 ARG cc_start: 0.7681 (ttm110) cc_final: 0.7384 (ptp-170) outliers start: 36 outliers final: 24 residues processed: 166 average time/residue: 0.2652 time to fit residues: 64.7302 Evaluate side-chains 161 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 1.334 ------------------------------------------------------------------------------- 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 477 ASN 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 1142 ILE 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 1456 LYS Chi-restraints excluded: chain A residue 1458 LEU Chi-restraints excluded: chain A residue 1541 CYS 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 94 optimal weight: 0.9990 chunk 80 optimal weight: 0.2980 chunk 127 optimal weight: 2.9990 chunk 102 optimal weight: 8.9990 chunk 115 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 163 optimal weight: 0.4980 chunk 61 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- 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 = 0.174024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.139362 restraints weight = 19337.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.138563 restraints weight = 21477.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.140469 restraints weight = 18087.916| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2626 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= 0.112 Angle : 0.574 11.352 18515 Z= 0.275 Chirality : 0.039 0.226 2128 Planarity : 0.005 0.076 2344 Dihedral : 6.050 56.229 2129 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.66 % Allowed : 16.12 % 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: 0.67 (0.22), residues: 1667 helix: 2.18 (0.17), residues: 928 sheet: -1.74 (0.51), residues: 114 loop : -1.93 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 979 HIS 0.003 0.001 HIS A 717 PHE 0.012 0.001 PHE A1486 TYR 0.017 0.001 TYR A1926 ARG 0.008 0.000 ARG A 922 Details of bonding type rmsd link_NAG-ASN : bond 0.00480 ( 8) link_NAG-ASN : angle 1.95168 ( 24) link_BETA1-4 : bond 0.00508 ( 3) link_BETA1-4 : angle 1.25519 ( 9) hydrogen bonds : bond 0.03479 ( 659) hydrogen bonds : angle 3.58534 ( 1929) SS BOND : bond 0.00356 ( 4) SS BOND : angle 1.29446 ( 8) covalent geometry : bond 0.00260 (13578) covalent geometry : angle 0.56896 (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 180 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 143 time to evaluate : 1.337 Fit side-chains REVERT: A 8 MET cc_start: 0.6763 (tmm) cc_final: 0.5205 (mmm) REVERT: A 30 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.7808 (mp) REVERT: A 291 ILE cc_start: 0.6412 (mm) cc_final: 0.6040 (mm) REVERT: A 292 LEU cc_start: 0.6896 (mt) cc_final: 0.6652 (mt) REVERT: A 477 ASN cc_start: 0.7332 (OUTLIER) cc_final: 0.7031 (m110) REVERT: A 581 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.8189 (mtp) REVERT: A 615 LYS cc_start: 0.7091 (tptt) cc_final: 0.6819 (tptp) REVERT: A 876 MET cc_start: 0.7554 (ppp) cc_final: 0.7236 (ppp) REVERT: A 1353 ARG cc_start: 0.5427 (OUTLIER) cc_final: 0.3536 (ptt180) REVERT: A 1372 VAL cc_start: 0.6059 (t) cc_final: 0.5376 (m) REVERT: A 1615 ASN cc_start: 0.6130 (p0) cc_final: 0.5646 (m-40) REVERT: A 1750 LEU cc_start: 0.7615 (tt) cc_final: 0.6782 (mt) REVERT: A 1799 THR cc_start: 0.8228 (t) cc_final: 0.7908 (m) REVERT: A 1850 GLU cc_start: 0.5636 (mp0) cc_final: 0.5330 (tp30) REVERT: A 1953 THR cc_start: 0.8559 (OUTLIER) cc_final: 0.8348 (m) REVERT: A 1962 ARG cc_start: 0.7792 (ttm110) cc_final: 0.7424 (ptp-170) outliers start: 37 outliers final: 23 residues processed: 170 average time/residue: 0.2468 time to fit residues: 63.2703 Evaluate side-chains 160 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 1.419 ------------------------------------------------------------------------------- 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 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 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 32 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 12 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 86 optimal weight: 8.9990 chunk 49 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 HIS A1313 HIS A1675 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.168594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.133965 restraints weight = 19439.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.132213 restraints weight = 27237.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.133358 restraints weight = 24005.956| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13593 Z= 0.183 Angle : 0.680 11.336 18515 Z= 0.330 Chirality : 0.042 0.225 2128 Planarity : 0.005 0.047 2344 Dihedral : 6.663 59.651 2129 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 2.59 % Allowed : 16.33 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.32 (0.21), residues: 1667 helix: 1.88 (0.17), residues: 926 sheet: -2.06 (0.50), residues: 114 loop : -1.99 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 328 HIS 0.005 0.001 HIS A1481 PHE 0.020 0.002 PHE A1486 TYR 0.017 0.002 TYR A1926 ARG 0.008 0.000 ARG A1349 Details of bonding type rmsd link_NAG-ASN : bond 0.00482 ( 8) link_NAG-ASN : angle 2.05569 ( 24) link_BETA1-4 : bond 0.00629 ( 3) link_BETA1-4 : angle 1.40402 ( 9) hydrogen bonds : bond 0.05072 ( 659) hydrogen bonds : angle 3.96657 ( 1929) SS BOND : bond 0.00641 ( 4) SS BOND : angle 1.87029 ( 8) covalent geometry : bond 0.00444 (13578) covalent geometry : angle 0.67479 (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 176 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 140 time to evaluate : 1.416 Fit side-chains REVERT: A 8 MET cc_start: 0.6907 (tmm) cc_final: 0.5220 (mmm) REVERT: A 291 ILE cc_start: 0.6585 (mm) cc_final: 0.6349 (mm) REVERT: A 485 ASP cc_start: 0.7571 (m-30) cc_final: 0.7235 (t0) REVERT: A 615 LYS cc_start: 0.7725 (tptt) cc_final: 0.7272 (tptp) REVERT: A 1353 ARG cc_start: 0.5493 (OUTLIER) cc_final: 0.3611 (ptt180) REVERT: A 1372 VAL cc_start: 0.6153 (t) cc_final: 0.5490 (m) REVERT: A 1588 MET cc_start: 0.8219 (tpt) cc_final: 0.7905 (tpt) REVERT: A 1615 ASN cc_start: 0.6252 (p0) cc_final: 0.5812 (m-40) REVERT: A 1799 THR cc_start: 0.8346 (t) cc_final: 0.7887 (m) REVERT: A 1962 ARG cc_start: 0.7845 (ttm110) cc_final: 0.7449 (ptp-170) outliers start: 36 outliers final: 25 residues processed: 167 average time/residue: 0.2491 time to fit residues: 61.8753 Evaluate side-chains 156 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 1.403 ------------------------------------------------------------------------------- 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 519 SER 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 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 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: 0.4980 chunk 107 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 127 optimal weight: 0.9990 chunk 142 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4007 r_free = 0.4007 target = 0.171780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.136995 restraints weight = 19317.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.136124 restraints weight = 22478.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.137256 restraints weight = 20346.766| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.3003 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 : 0.608 13.738 18515 Z= 0.292 Chirality : 0.039 0.227 2128 Planarity : 0.005 0.066 2344 Dihedral : 6.294 59.431 2129 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.37 % Allowed : 17.27 % Favored : 80.36 % 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: -1.92 (0.53), residues: 104 loop : -1.99 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP A 979 HIS 0.003 0.001 HIS A 717 PHE 0.013 0.001 PHE A 553 TYR 0.018 0.001 TYR A1926 ARG 0.008 0.000 ARG A 922 Details of bonding type rmsd link_NAG-ASN : bond 0.00488 ( 8) link_NAG-ASN : angle 2.03088 ( 24) link_BETA1-4 : bond 0.00563 ( 3) link_BETA1-4 : angle 1.28289 ( 9) hydrogen bonds : bond 0.03836 ( 659) hydrogen bonds : angle 3.73813 ( 1929) SS BOND : bond 0.00353 ( 4) SS BOND : angle 1.42264 ( 8) covalent geometry : bond 0.00279 (13578) covalent geometry : angle 0.60328 (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 168 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 135 time to evaluate : 1.431 Fit side-chains REVERT: A 8 MET cc_start: 0.6888 (tmm) cc_final: 0.5303 (mmm) REVERT: A 291 ILE cc_start: 0.6544 (mm) cc_final: 0.6338 (mm) REVERT: A 485 ASP cc_start: 0.7373 (m-30) cc_final: 0.7166 (t0) REVERT: A 876 MET cc_start: 0.7661 (ppp) cc_final: 0.7388 (ppp) REVERT: A 1353 ARG cc_start: 0.5397 (OUTLIER) cc_final: 0.3606 (ptt180) REVERT: A 1372 VAL cc_start: 0.6025 (t) cc_final: 0.5385 (m) REVERT: A 1615 ASN cc_start: 0.6082 (p0) cc_final: 0.5756 (m-40) REVERT: A 1798 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8323 (mp) REVERT: A 1799 THR cc_start: 0.8248 (t) cc_final: 0.7830 (m) REVERT: A 1962 ARG cc_start: 0.7793 (ttm110) cc_final: 0.7414 (ptp-170) outliers start: 33 outliers final: 25 residues processed: 160 average time/residue: 0.2417 time to fit residues: 58.4888 Evaluate side-chains 158 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 1.309 ------------------------------------------------------------------------------- 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 519 SER Chi-restraints excluded: chain A residue 581 MET 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 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 1798 LEU 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 82 optimal weight: 0.7980 chunk 142 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 59 optimal weight: 0.3980 chunk 146 optimal weight: 5.9990 chunk 153 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 29 optimal weight: 8.9990 chunk 55 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 HIS A1607 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.172091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.137274 restraints weight = 19369.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.136320 restraints weight = 21328.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.137081 restraints weight = 19180.057| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13593 Z= 0.122 Angle : 0.614 13.663 18515 Z= 0.293 Chirality : 0.039 0.232 2128 Planarity : 0.005 0.065 2344 Dihedral : 6.225 56.634 2129 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.16 % Allowed : 17.41 % 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: 0.55 (0.22), residues: 1667 helix: 2.10 (0.17), residues: 927 sheet: -1.88 (0.53), residues: 104 loop : -1.98 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP A 979 HIS 0.003 0.001 HIS A 717 PHE 0.016 0.001 PHE A 553 TYR 0.018 0.001 TYR A1926 ARG 0.008 0.000 ARG A 922 Details of bonding type rmsd link_NAG-ASN : bond 0.00479 ( 8) link_NAG-ASN : angle 2.02706 ( 24) link_BETA1-4 : bond 0.00567 ( 3) link_BETA1-4 : angle 1.26758 ( 9) hydrogen bonds : bond 0.03746 ( 659) hydrogen bonds : angle 3.68977 ( 1929) SS BOND : bond 0.00353 ( 4) SS BOND : angle 1.44124 ( 8) covalent geometry : bond 0.00286 (13578) covalent geometry : angle 0.60844 (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 166 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 1.298 Fit side-chains REVERT: A 8 MET cc_start: 0.6859 (tmm) cc_final: 0.5307 (mmm) REVERT: A 291 ILE cc_start: 0.6566 (mm) cc_final: 0.6286 (mm) REVERT: A 485 ASP cc_start: 0.7373 (m-30) cc_final: 0.7169 (t0) REVERT: A 876 MET cc_start: 0.7747 (ppp) cc_final: 0.7480 (ppp) REVERT: A 1353 ARG cc_start: 0.5425 (OUTLIER) cc_final: 0.3628 (ptt180) REVERT: A 1372 VAL cc_start: 0.6042 (t) cc_final: 0.5405 (m) REVERT: A 1615 ASN cc_start: 0.5960 (p0) cc_final: 0.5682 (m-40) REVERT: A 1750 LEU cc_start: 0.7561 (tt) cc_final: 0.6822 (mt) REVERT: A 1962 ARG cc_start: 0.7789 (ttm110) cc_final: 0.7402 (ptp-170) outliers start: 30 outliers final: 25 residues processed: 161 average time/residue: 0.2367 time to fit residues: 57.7139 Evaluate side-chains 157 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 1.513 ------------------------------------------------------------------------------- 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 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 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 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 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: 1.9990 chunk 127 optimal weight: 0.9980 chunk 103 optimal weight: 0.0970 chunk 17 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 102 optimal weight: 8.9990 chunk 143 optimal weight: 0.5980 chunk 125 optimal weight: 0.9980 chunk 139 optimal weight: 8.9990 chunk 144 optimal weight: 4.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 HIS ** A1523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.172742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.137680 restraints weight = 19442.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.136686 restraints weight = 22372.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.138200 restraints weight = 18960.889| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13593 Z= 0.115 Angle : 0.609 13.194 18515 Z= 0.290 Chirality : 0.039 0.231 2128 Planarity : 0.005 0.064 2344 Dihedral : 6.168 56.597 2129 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.09 % Allowed : 17.55 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.22), residues: 1667 helix: 2.16 (0.17), residues: 927 sheet: -1.83 (0.51), residues: 114 loop : -1.95 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.001 TRP A 979 HIS 0.003 0.001 HIS A 717 PHE 0.012 0.001 PHE A1486 TYR 0.018 0.001 TYR A1926 ARG 0.008 0.000 ARG A 922 Details of bonding type rmsd link_NAG-ASN : bond 0.00484 ( 8) link_NAG-ASN : angle 2.00350 ( 24) link_BETA1-4 : bond 0.00587 ( 3) link_BETA1-4 : angle 1.27762 ( 9) hydrogen bonds : bond 0.03553 ( 659) hydrogen bonds : angle 3.63510 ( 1929) SS BOND : bond 0.00337 ( 4) SS BOND : angle 1.40891 ( 8) covalent geometry : bond 0.00269 (13578) covalent geometry : angle 0.60362 (18474) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4159.64 seconds wall clock time: 72 minutes 42.20 seconds (4362.20 seconds total)