Starting phenix.real_space_refine on Fri Jul 3 10:53:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tby_25801/07_2026/7tby_25801.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tby_25801/07_2026/7tby_25801.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7tby_25801/07_2026/7tby_25801.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tby_25801/07_2026/7tby_25801.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tby_25801/07_2026/7tby_25801.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tby_25801/07_2026/7tby_25801.map" model { file = "/net/cci-nas-00/data/ceres_data/7tby_25801/07_2026/7tby_25801.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tby_25801/07_2026/7tby_25801.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 69 5.16 5 C 8591 2.51 5 N 2233 2.21 5 O 2388 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13281 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 13136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1788, 13136 Classifications: {'peptide': 1788} Incomplete info: {'truncation_to_alanine': 343} Link IDs: {'PTRANS': 87, 'TRANS': 1700} Chain breaks: 15 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 1118 Unresolved non-hydrogen angles: 1399 Unresolved non-hydrogen dihedrals: 901 Unresolved non-hydrogen chiralities: 117 Planarities with less than four sites: {'ASP:plan': 22, 'ARG:plan': 17, 'GLN:plan1': 19, 'GLU:plan': 29, 'HIS:plan': 12, 'ASN:plan1': 13, 'PHE:plan': 9, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 517 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {'CLR': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.91, per 1000 atoms: 0.22 Number of scatterers: 13281 At special positions: 0 Unit cell: (81.674, 93.462, 216.394, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 69 16.00 O 2388 8.00 N 2233 7.00 C 8591 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 81 " distance=2.03 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 309 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 504 " distance=2.03 Simple disulfide: pdb=" SG CYS A 626 " - pdb=" SG CYS A1465 " distance=2.03 Simple disulfide: pdb=" SG CYS A1418 " - pdb=" SG CYS A1429 " distance=2.03 Simple disulfide: pdb=" SG CYS A1463 " - pdb=" SG CYS A1477 " distance=2.03 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 BETA1-3 " BMA C 3 " - " BMA C 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " BETA1-6 " BMA C 3 " - " BMA C 5 " NAG-ASN " NAG A2502 " - " ASN A1637 " " NAG A2503 " - " ASN A 98 " " NAG B 1 " - " ASN A 400 " " NAG C 1 " - " ASN A1504 " Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 677.7 milliseconds 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3346 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 11 sheets defined 60.2% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 3 through 22 removed outlier: 3.850A pdb=" N GLN A 21 " --> pdb=" O PHE A 17 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N THR A 22 " --> pdb=" O ARG A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 44 removed outlier: 4.245A pdb=" N LEU A 27 " --> pdb=" O CYS A 23 " (cutoff:3.500A) Proline residue: A 32 - end of helix Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 65 through 75 removed outlier: 3.566A pdb=" N CYS A 75 " --> pdb=" O GLN A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 90 Processing helix chain 'A' and resid 100 through 118 Processing helix chain 'A' and resid 120 through 134 Processing helix chain 'A' and resid 252 through 274 removed outlier: 4.063A pdb=" N GLU A 256 " --> pdb=" O LYS A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 289 removed outlier: 4.094A pdb=" N ASP A 280 " --> pdb=" O ARG A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 309 removed outlier: 3.721A pdb=" N TYR A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 350 Processing helix chain 'A' and resid 352 through 365 removed outlier: 3.753A pdb=" N ASN A 356 " --> pdb=" O THR A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 380 Proline residue: A 377 - end of helix Processing helix chain 'A' and resid 389 through 405 Processing helix chain 'A' and resid 406 through 410 removed outlier: 4.419A pdb=" N PHE A 409 " --> pdb=" O LEU A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 430 removed outlier: 3.537A pdb=" N MET A 415 " --> pdb=" O ASP A 411 " (cutoff:3.500A) Proline residue: A 421 - end of helix removed outlier: 3.860A pdb=" N SER A 430 " --> pdb=" O PHE A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 441 removed outlier: 3.648A pdb=" N ASP A 441 " --> pdb=" O ARG A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 454 removed outlier: 3.517A pdb=" N PHE A 448 " --> pdb=" O ASP A 444 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 468 Processing helix chain 'A' and resid 483 through 504 removed outlier: 3.824A pdb=" N ALA A 487 " --> pdb=" O THR A 483 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N CYS A 504 " --> pdb=" O ARG A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 529 Processing helix chain 'A' and resid 559 through 563 removed outlier: 3.591A pdb=" N ASN A 562 " --> pdb=" O ASP A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 591 Processing helix chain 'A' and resid 592 through 609 Processing helix chain 'A' and resid 630 through 638 Processing helix chain 'A' and resid 640 through 665 removed outlier: 4.733A pdb=" N ALA A 647 " --> pdb=" O PHE A 643 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N TRP A 648 " --> pdb=" O MET A 644 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA A 665 " --> pdb=" O TYR A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 674 Processing helix chain 'A' and resid 677 through 707 removed outlier: 3.704A pdb=" N LEU A 681 " --> pdb=" O ASP A 677 " (cutoff:3.500A) Proline residue: A 692 - end of helix Processing helix chain 'A' and resid 714 through 738 removed outlier: 3.524A pdb=" N VAL A 718 " --> pdb=" O ASP A 714 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N THR A 738 " --> pdb=" O PHE A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 766 removed outlier: 4.602A pdb=" N GLY A 751 " --> pdb=" O ALA A 747 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ILE A 752 " --> pdb=" O ALA A 748 " (cutoff:3.500A) Proline residue: A 760 - end of helix removed outlier: 3.842A pdb=" N ALA A 766 " --> pdb=" O VAL A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 771 removed outlier: 3.635A pdb=" N TYR A 770 " --> pdb=" O TRP A 767 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL A 771 " --> pdb=" O ARG A 768 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 767 through 771' Processing helix chain 'A' and resid 772 through 780 Processing helix chain 'A' and resid 782 through 800 removed outlier: 3.792A pdb=" N ALA A 786 " --> pdb=" O LEU A 782 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLN A 800 " --> pdb=" O LEU A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 846 removed outlier: 4.145A pdb=" N ALA A 844 " --> pdb=" O TRP A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 947 Processing helix chain 'A' and resid 971 through 975 removed outlier: 4.072A pdb=" N LEU A 975 " --> pdb=" O ARG A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1002 Processing helix chain 'A' and resid 1004 through 1020 removed outlier: 3.944A pdb=" N GLY A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1028 Processing helix chain 'A' and resid 1034 through 1046 removed outlier: 3.886A pdb=" N ALA A1046 " --> pdb=" O SER A1042 " (cutoff:3.500A) Processing helix chain 'A' and resid 1064 through 1077 Processing helix chain 'A' and resid 1090 through 1098 removed outlier: 3.716A pdb=" N ALA A1094 " --> pdb=" O HIS A1090 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1122 removed outlier: 3.805A pdb=" N LEU A1122 " --> pdb=" O LEU A1118 " (cutoff:3.500A) Processing helix chain 'A' and resid 1181 through 1191 Processing helix chain 'A' and resid 1216 through 1228 removed outlier: 3.581A pdb=" N GLU A1220 " --> pdb=" O GLY A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1243 through 1252 removed outlier: 3.840A pdb=" N ILE A1247 " --> pdb=" O THR A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1323 through 1342 Processing helix chain 'A' and resid 1348 through 1365 removed outlier: 4.150A pdb=" N VAL A1352 " --> pdb=" O PHE A1348 " (cutoff:3.500A) Proline residue: A1354 - end of helix Processing helix chain 'A' and resid 1380 through 1384 removed outlier: 3.871A pdb=" N TYR A1384 " --> pdb=" O PRO A1381 " (cutoff:3.500A) Processing helix chain 'A' and resid 1401 through 1409 Processing helix chain 'A' and resid 1444 through 1451 Processing helix chain 'A' and resid 1504 through 1522 Processing helix chain 'A' and resid 1549 through 1561 Processing helix chain 'A' and resid 1570 through 1583 Processing helix chain 'A' and resid 1601 through 1618 Processing helix chain 'A' and resid 1639 through 1650 Processing helix chain 'A' and resid 1650 through 1666 removed outlier: 3.827A pdb=" N CYS A1660 " --> pdb=" O LEU A1656 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A1661 " --> pdb=" O VAL A1657 " (cutoff:3.500A) Processing helix chain 'A' and resid 1667 through 1681 removed outlier: 4.062A pdb=" N SER A1671 " --> pdb=" O PHE A1667 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE A1672 " --> pdb=" O VAL A1668 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL A1681 " --> pdb=" O ILE A1677 " (cutoff:3.500A) Processing helix chain 'A' and resid 1684 through 1691 removed outlier: 3.674A pdb=" N SER A1691 " --> pdb=" O LEU A1687 " (cutoff:3.500A) Processing helix chain 'A' and resid 1694 through 1724 removed outlier: 3.829A pdb=" N TYR A1698 " --> pdb=" O LYS A1694 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL A1712 " --> pdb=" O CYS A1708 " (cutoff:3.500A) Proline residue: A1713 - end of helix removed outlier: 3.916A pdb=" N PHE A1724 " --> pdb=" O ILE A1720 " (cutoff:3.500A) Processing helix chain 'A' and resid 1726 through 1731 removed outlier: 3.707A pdb=" N SER A1731 " --> pdb=" O LYS A1727 " (cutoff:3.500A) Processing helix chain 'A' and resid 1734 through 1753 Proline residue: A1751 - end of helix Processing helix chain 'A' and resid 1754 through 1758 Processing helix chain 'A' and resid 1765 through 1787 removed outlier: 3.827A pdb=" N VAL A1769 " --> pdb=" O THR A1765 " (cutoff:3.500A) Processing helix chain 'A' and resid 1800 through 1807 Processing helix chain 'A' and resid 1810 through 1836 Processing helix chain 'A' and resid 1850 through 1873 removed outlier: 3.671A pdb=" N GLN A1871 " --> pdb=" O THR A1867 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR A1872 " --> pdb=" O VAL A1868 " (cutoff:3.500A) Processing helix chain 'A' and resid 1951 through 1960 Processing helix chain 'A' and resid 2002 through 2015 removed outlier: 3.820A pdb=" N VAL A2007 " --> pdb=" O GLY A2003 " (cutoff:3.500A) Processing helix chain 'A' and resid 2020 through 2032 removed outlier: 3.609A pdb=" N LEU A2032 " --> pdb=" O ALA A2028 " (cutoff:3.500A) Processing helix chain 'A' and resid 2041 through 2045 Processing helix chain 'A' and resid 2046 through 2058 Processing helix chain 'A' and resid 2079 through 2093 Processing helix chain 'A' and resid 2103 through 2111 removed outlier: 3.540A pdb=" N CYS A2107 " --> pdb=" O SER A2103 " (cutoff:3.500A) Processing helix chain 'A' and resid 2127 through 2135 removed outlier: 3.554A pdb=" N PHE A2135 " --> pdb=" O LEU A2131 " (cutoff:3.500A) Processing helix chain 'A' and resid 2152 through 2163 removed outlier: 4.138A pdb=" N GLN A2156 " --> pdb=" O LEU A2152 " (cutoff:3.500A) Processing helix chain 'A' and resid 2186 through 2201 removed outlier: 4.603A pdb=" N LYS A2199 " --> pdb=" O SER A2195 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ARG A2200 " --> pdb=" O GLN A2196 " (cutoff:3.500A) Processing helix chain 'A' and resid 2212 through 2223 removed outlier: 3.539A pdb=" N VAL A2216 " --> pdb=" O THR A2212 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 50 Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.410A pdb=" N GLY A 616 " --> pdb=" O VAL A1590 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N VAL A1592 " --> pdb=" O GLY A 616 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N TYR A 618 " --> pdb=" O VAL A1592 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N PHE A1594 " --> pdb=" O TYR A 618 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLN A 620 " --> pdb=" O PHE A1594 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N TYR A1388 " --> pdb=" O GLY A1533 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N PHE A1535 " --> pdb=" O TYR A1388 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N PHE A1390 " --> pdb=" O PHE A1535 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N LEU A1537 " --> pdb=" O PHE A1390 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N SER A1392 " --> pdb=" O LEU A1537 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N VAL A1539 " --> pdb=" O SER A1392 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL A1391 " --> pdb=" O GLN A1498 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 383 through 385 removed outlier: 6.557A pdb=" N ILE A 383 " --> pdb=" O GLU A 511 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 535 through 537 removed outlier: 6.405A pdb=" N VAL A 552 " --> pdb=" O THR A1630 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N PHE A1632 " --> pdb=" O VAL A 552 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N TYR A 554 " --> pdb=" O PHE A1632 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 922 through 924 removed outlier: 3.864A pdb=" N SER A 900 " --> pdb=" O TYR A 958 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR A 958 " --> pdb=" O SER A 900 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1054 through 1055 removed outlier: 7.370A pdb=" N VAL A1054 " --> pdb=" O ILE A1085 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 1101 through 1105 removed outlier: 6.723A pdb=" N ILE A1101 " --> pdb=" O VAL A1112 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL A1112 " --> pdb=" O ILE A1101 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE A1103 " --> pdb=" O CYS A1110 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1195 through 1200 removed outlier: 6.253A pdb=" N LEU A1196 " --> pdb=" O VAL A1207 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL A1207 " --> pdb=" O LEU A1196 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU A1198 " --> pdb=" O THR A1205 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER A1236 " --> pdb=" O VAL A1131 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1988 through 1990 removed outlier: 5.798A pdb=" N GLY A1989 " --> pdb=" O PHE A2067 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL A2066 " --> pdb=" O VAL A2098 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 2114 through 2117 removed outlier: 6.370A pdb=" N MET A2114 " --> pdb=" O LEU A2125 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU A2125 " --> pdb=" O MET A2114 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE A2116 " --> pdb=" O ARG A2123 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2167 through 2171 removed outlier: 6.124A pdb=" N LEU A2168 " --> pdb=" O GLN A2179 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N GLN A2179 " --> pdb=" O LEU A2168 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU A2170 " --> pdb=" O GLN A2177 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN A2177 " --> pdb=" O GLU A2170 " (cutoff:3.500A) 747 hydrogen bonds defined for protein. 2169 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: 2.78 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4241 1.34 - 1.46: 2922 1.46 - 1.58: 6312 1.58 - 1.69: 0 1.69 - 1.81: 110 Bond restraints: 13585 Sorted by residual: bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.487 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" C1 NAG A2503 " pdb=" O5 NAG A2503 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.11e+00 bond pdb=" C13 CLR A2501 " pdb=" C17 CLR A2501 " ideal model delta sigma weight residual 1.550 1.518 0.032 2.00e-02 2.50e+03 2.62e+00 bond pdb=" C LEU A 759 " pdb=" N PRO A 760 " ideal model delta sigma weight residual 1.333 1.355 -0.022 1.44e-02 4.82e+03 2.36e+00 ... (remaining 13580 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 18057 1.57 - 3.14: 364 3.14 - 4.71: 67 4.71 - 6.27: 34 6.27 - 7.84: 6 Bond angle restraints: 18528 Sorted by residual: angle pdb=" N VAL A1681 " pdb=" CA VAL A1681 " pdb=" C VAL A1681 " ideal model delta sigma weight residual 106.21 110.43 -4.22 1.07e+00 8.73e-01 1.56e+01 angle pdb=" N VAL A1693 " pdb=" CA VAL A1693 " pdb=" C VAL A1693 " ideal model delta sigma weight residual 113.71 109.98 3.73 9.50e-01 1.11e+00 1.55e+01 angle pdb=" C TYR A 385 " pdb=" N THR A 386 " pdb=" CA THR A 386 " ideal model delta sigma weight residual 122.29 127.84 -5.55 1.48e+00 4.57e-01 1.41e+01 angle pdb=" C SER A 639 " pdb=" N MET A 640 " pdb=" CA MET A 640 " ideal model delta sigma weight residual 120.09 124.46 -4.37 1.25e+00 6.40e-01 1.22e+01 angle pdb=" CA THR A 386 " pdb=" C THR A 386 " pdb=" N PRO A 387 " ideal model delta sigma weight residual 117.69 120.45 -2.76 9.30e-01 1.16e+00 8.79e+00 ... (remaining 18523 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 7263 17.66 - 35.32: 490 35.32 - 52.99: 113 52.99 - 70.65: 14 70.65 - 88.31: 7 Dihedral angle restraints: 7887 sinusoidal: 2713 harmonic: 5174 Sorted by residual: dihedral pdb=" CB CYS A 355 " pdb=" SG CYS A 355 " pdb=" SG CYS A 504 " pdb=" CB CYS A 504 " ideal model delta sinusoidal sigma weight residual 93.00 143.54 -50.54 1 1.00e+01 1.00e-02 3.50e+01 dihedral pdb=" CB CYS A 75 " pdb=" SG CYS A 75 " pdb=" SG CYS A 309 " pdb=" CB CYS A 309 " ideal model delta sinusoidal sigma weight residual 93.00 141.10 -48.10 1 1.00e+01 1.00e-02 3.19e+01 dihedral pdb=" CA PHE A1721 " pdb=" C PHE A1721 " pdb=" N ILE A1722 " pdb=" CA ILE A1722 " ideal model delta harmonic sigma weight residual 180.00 160.31 19.69 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 7884 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1848 0.056 - 0.113: 289 0.113 - 0.169: 24 0.169 - 0.225: 2 0.225 - 0.281: 5 Chirality restraints: 2168 Sorted by residual: chirality pdb=" C13 CLR A2501 " pdb=" C12 CLR A2501 " pdb=" C14 CLR A2501 " pdb=" C17 CLR A2501 " both_signs ideal model delta sigma weight residual False -2.93 -2.65 -0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" C5 BMA C 4 " pdb=" C4 BMA C 4 " pdb=" C6 BMA C 4 " pdb=" O5 BMA C 4 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 2165 not shown) Planarity restraints: 2348 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 759 " 0.026 5.00e-02 4.00e+02 3.94e-02 2.49e+00 pdb=" N PRO A 760 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 760 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 760 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A2076 " -0.025 5.00e-02 4.00e+02 3.82e-02 2.33e+00 pdb=" N PRO A2077 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A2077 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A2077 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A1064 " 0.021 5.00e-02 4.00e+02 3.22e-02 1.66e+00 pdb=" N PRO A1065 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO A1065 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A1065 " 0.018 5.00e-02 4.00e+02 ... (remaining 2345 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 302 2.70 - 3.25: 13658 3.25 - 3.80: 20626 3.80 - 4.35: 24882 4.35 - 4.90: 41227 Nonbonded interactions: 100695 Sorted by model distance: nonbonded pdb=" OD2 ASP A1706 " pdb=" OH TYR A1754 " model vdw 2.155 3.040 nonbonded pdb=" O PRO A 641 " pdb=" OG1 THR A 645 " model vdw 2.173 3.040 nonbonded pdb=" OD2 ASP A 108 " pdb=" OG SER A 277 " model vdw 2.234 3.040 nonbonded pdb=" O ASN A 361 " pdb=" OG SER A 365 " model vdw 2.259 3.040 nonbonded pdb=" OG1 THR A1493 " pdb=" OD1 ASP A1495 " model vdw 2.268 3.040 ... (remaining 100690 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.450 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: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.720 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 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 0.081 13600 Z= 0.151 Angle : 0.622 13.167 18567 Z= 0.335 Chirality : 0.042 0.281 2168 Planarity : 0.003 0.039 2344 Dihedral : 12.897 88.311 4523 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.45 (0.18), residues: 1756 helix: -0.44 (0.15), residues: 977 sheet: -2.22 (0.37), residues: 161 loop : -3.38 (0.21), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1336 TYR 0.007 0.001 TYR A1237 PHE 0.015 0.001 PHE A1721 TRP 0.011 0.001 TRP A1705 HIS 0.002 0.000 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.15 (13585) covalent geometry : angle 0.60830 / 0.33 (18528) SS BOND : bond 0.00159 / 0.08 ( 6) SS BOND : angle 0.84401 / 0.47 ( 12) hydrogen bonds : bond 0.12412 / 8.03 ( 747) hydrogen bonds : angle 5.03499 / 3.62 ( 2169) link_BETA1-3 : bond 0.00192 / 0.10 ( 1) link_BETA1-3 : angle 1.31589 / 0.67 ( 3) link_BETA1-4 : bond 0.00521 / 0.26 ( 3) link_BETA1-4 : angle 1.24130 / 0.69 ( 9) link_BETA1-6 : bond 0.00464 / 0.24 ( 1) link_BETA1-6 : angle 1.28586 / 0.66 ( 3) link_NAG-ASN : bond 0.00496 / 0.26 ( 4) link_NAG-ASN : angle 5.00852 / 3.04 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 LYS cc_start: 0.8836 (mmtt) cc_final: 0.8604 (mtpt) REVERT: A 586 MET cc_start: 0.9262 (tpp) cc_final: 0.8940 (mmt) REVERT: A 640 MET cc_start: 0.9188 (tpp) cc_final: 0.8866 (tpp) REVERT: A 1649 MET cc_start: 0.5336 (ppp) cc_final: 0.4694 (ppp) REVERT: A 1716 LEU cc_start: 0.8993 (tp) cc_final: 0.8630 (tt) REVERT: A 1720 ILE cc_start: 0.8675 (mt) cc_final: 0.8412 (mt) REVERT: A 1821 ASP cc_start: 0.8805 (m-30) cc_final: 0.8597 (m-30) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.0892 time to fit residues: 30.1445 Evaluate side-chains 133 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.2980 chunk 91 optimal weight: 0.4980 chunk 149 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 HIS A 551 HIS A 800 GLN A 820 ASN A1106 HIS A1121 GLN A1422 ASN A1450 GLN A1600 HIS A1626 HIS A1688 GLN A1774 ASN A2049 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.076711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.062730 restraints weight = 54352.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.064640 restraints weight = 28511.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.065830 restraints weight = 19094.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.066671 restraints weight = 14831.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.067123 restraints weight = 12523.654| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13600 Z= 0.113 Angle : 0.585 10.508 18567 Z= 0.282 Chirality : 0.041 0.206 2168 Planarity : 0.003 0.042 2344 Dihedral : 4.048 54.410 1899 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.22 % Allowed : 13.27 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.20), residues: 1756 helix: 0.77 (0.17), residues: 986 sheet: -1.71 (0.39), residues: 164 loop : -2.83 (0.23), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 530 TYR 0.014 0.001 TYR A 997 PHE 0.020 0.001 PHE A1530 TRP 0.014 0.001 TRP A1705 HIS 0.003 0.000 HIS A2006 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (13585) covalent geometry : angle 0.57364 / 0.28 (18528) SS BOND : bond 0.00228 / 0.11 ( 6) SS BOND : angle 0.95795 / 0.54 ( 12) hydrogen bonds : bond 0.03411 / 2.24 ( 747) hydrogen bonds : angle 3.95145 / 2.83 ( 2169) link_BETA1-3 : bond 0.00533 / 0.28 ( 1) link_BETA1-3 : angle 1.66827 / 0.89 ( 3) link_BETA1-4 : bond 0.00671 / 0.34 ( 3) link_BETA1-4 : angle 1.59703 / 0.91 ( 9) link_BETA1-6 : bond 0.00493 / 0.26 ( 1) link_BETA1-6 : angle 2.01588 / 1.05 ( 3) link_NAG-ASN : bond 0.00345 / 0.18 ( 4) link_NAG-ASN : angle 4.00428 / 2.42 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 LYS cc_start: 0.9003 (mmtt) cc_final: 0.8769 (mtpt) REVERT: A 640 MET cc_start: 0.9200 (tpp) cc_final: 0.8872 (tpp) REVERT: A 1419 MET cc_start: 0.7372 (pmm) cc_final: 0.6848 (pmm) REVERT: A 1649 MET cc_start: 0.5497 (ppp) cc_final: 0.4874 (ppp) REVERT: A 2069 ASP cc_start: 0.8721 (t0) cc_final: 0.7303 (p0) outliers start: 15 outliers final: 9 residues processed: 147 average time/residue: 0.0916 time to fit residues: 21.8585 Evaluate side-chains 126 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 1721 PHE Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 2073 THR Chi-restraints excluded: chain A residue 2099 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 48 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 166 optimal weight: 0.3980 chunk 70 optimal weight: 8.9990 chunk 162 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1443 GLN A1451 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.075890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.061924 restraints weight = 54742.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.063745 restraints weight = 29807.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.064936 restraints weight = 20354.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.065694 restraints weight = 15992.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.065987 restraints weight = 13682.128| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13600 Z= 0.103 Angle : 0.562 9.328 18567 Z= 0.270 Chirality : 0.040 0.193 2168 Planarity : 0.003 0.041 2344 Dihedral : 4.037 56.875 1899 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.22 % Allowed : 16.04 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.21), residues: 1756 helix: 1.33 (0.17), residues: 988 sheet: -1.49 (0.39), residues: 164 loop : -2.58 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 565 TYR 0.011 0.001 TYR A 770 PHE 0.022 0.001 PHE A1530 TRP 0.015 0.001 TRP A1705 HIS 0.002 0.000 HIS A2006 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 (13585) covalent geometry : angle 0.55260 / 0.27 (18528) SS BOND : bond 0.00212 / 0.10 ( 6) SS BOND : angle 0.89064 / 0.48 ( 12) hydrogen bonds : bond 0.03190 / 2.11 ( 747) hydrogen bonds : angle 3.71435 / 2.67 ( 2169) link_BETA1-3 : bond 0.00369 / 0.19 ( 1) link_BETA1-3 : angle 1.60142 / 0.83 ( 3) link_BETA1-4 : bond 0.00587 / 0.30 ( 3) link_BETA1-4 : angle 1.52525 / 0.86 ( 9) link_BETA1-6 : bond 0.00435 / 0.23 ( 1) link_BETA1-6 : angle 1.73619 / 0.90 ( 3) link_NAG-ASN : bond 0.00301 / 0.16 ( 4) link_NAG-ASN : angle 3.63678 / 2.18 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 MET cc_start: 0.8096 (tmm) cc_final: 0.7854 (tmm) REVERT: A 640 MET cc_start: 0.9181 (tpp) cc_final: 0.8866 (tpp) REVERT: A 742 ARG cc_start: 0.5263 (mtm180) cc_final: 0.4813 (mpp80) REVERT: A 759 LEU cc_start: 0.8482 (mt) cc_final: 0.8009 (tp) REVERT: A 1649 MET cc_start: 0.5604 (ppp) cc_final: 0.5285 (ppp) REVERT: A 1707 MET cc_start: 0.9015 (mmm) cc_final: 0.8656 (mmm) REVERT: A 2069 ASP cc_start: 0.8691 (t0) cc_final: 0.7389 (p0) outliers start: 15 outliers final: 7 residues processed: 143 average time/residue: 0.0925 time to fit residues: 21.2418 Evaluate side-chains 126 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 119 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 1721 PHE Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 2073 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 17 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 141 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 123 optimal weight: 0.9990 chunk 159 optimal weight: 0.9980 chunk 100 optimal weight: 0.4980 chunk 28 optimal weight: 50.0000 chunk 165 optimal weight: 3.9990 chunk 129 optimal weight: 6.9990 chunk 138 optimal weight: 9.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.074353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.060099 restraints weight = 54689.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.061884 restraints weight = 29618.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.063046 restraints weight = 20240.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.063820 restraints weight = 15913.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.064145 restraints weight = 13675.417| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13600 Z= 0.120 Angle : 0.569 8.932 18567 Z= 0.275 Chirality : 0.041 0.196 2168 Planarity : 0.003 0.039 2344 Dihedral : 4.045 54.105 1899 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.20 % Allowed : 17.18 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.21), residues: 1756 helix: 1.70 (0.17), residues: 988 sheet: -1.38 (0.39), residues: 167 loop : -2.41 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 565 TYR 0.011 0.001 TYR A 770 PHE 0.023 0.001 PHE A1663 TRP 0.027 0.001 TRP A 533 HIS 0.001 0.000 HIS A1600 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (13585) covalent geometry : angle 0.56091 / 0.27 (18528) SS BOND : bond 0.00232 / 0.11 ( 6) SS BOND : angle 1.06592 / 0.57 ( 12) hydrogen bonds : bond 0.03342 / 2.20 ( 747) hydrogen bonds : angle 3.61505 / 2.60 ( 2169) link_BETA1-3 : bond 0.00309 / 0.16 ( 1) link_BETA1-3 : angle 1.58208 / 0.82 ( 3) link_BETA1-4 : bond 0.00552 / 0.28 ( 3) link_BETA1-4 : angle 1.56804 / 0.90 ( 9) link_BETA1-6 : bond 0.00420 / 0.22 ( 1) link_BETA1-6 : angle 1.80023 / 0.94 ( 3) link_NAG-ASN : bond 0.00253 / 0.13 ( 4) link_NAG-ASN : angle 3.39656 / 2.03 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 502 MET cc_start: 0.8403 (tmm) cc_final: 0.8164 (tmm) REVERT: A 601 GLU cc_start: 0.8430 (mm-30) cc_final: 0.8159 (mm-30) REVERT: A 640 MET cc_start: 0.9242 (tpp) cc_final: 0.8835 (tpp) REVERT: A 1446 MET cc_start: 0.7403 (mpp) cc_final: 0.6838 (mpp) REVERT: A 1456 MET cc_start: 0.8868 (tpp) cc_final: 0.8532 (tpt) REVERT: A 1665 MET cc_start: 0.9204 (tpp) cc_final: 0.8908 (tpp) REVERT: A 2069 ASP cc_start: 0.8717 (t0) cc_final: 0.7301 (p0) outliers start: 27 outliers final: 16 residues processed: 141 average time/residue: 0.0929 time to fit residues: 21.3537 Evaluate side-chains 132 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1414 PHE Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1721 PHE Chi-restraints excluded: chain A residue 1740 LEU Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 2073 THR Chi-restraints excluded: chain A residue 2099 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 33 optimal weight: 0.1980 chunk 93 optimal weight: 30.0000 chunk 107 optimal weight: 0.9990 chunk 151 optimal weight: 5.9990 chunk 147 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 chunk 143 optimal weight: 7.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.073903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.059614 restraints weight = 55308.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.061449 restraints weight = 29516.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.062598 restraints weight = 19934.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.063408 restraints weight = 15603.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.063845 restraints weight = 13295.938| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13600 Z= 0.107 Angle : 0.567 9.251 18567 Z= 0.271 Chirality : 0.040 0.194 2168 Planarity : 0.003 0.039 2344 Dihedral : 4.008 52.053 1899 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.95 % Allowed : 18.08 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.21), residues: 1756 helix: 1.89 (0.17), residues: 987 sheet: -1.27 (0.40), residues: 169 loop : -2.33 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 565 TYR 0.011 0.001 TYR A 770 PHE 0.025 0.001 PHE A1663 TRP 0.017 0.001 TRP A 533 HIS 0.001 0.000 HIS A1626 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (13585) covalent geometry : angle 0.55946 / 0.27 (18528) SS BOND : bond 0.00219 / 0.11 ( 6) SS BOND : angle 0.97792 / 0.52 ( 12) hydrogen bonds : bond 0.03245 / 2.13 ( 747) hydrogen bonds : angle 3.52969 / 2.54 ( 2169) link_BETA1-3 : bond 0.00300 / 0.16 ( 1) link_BETA1-3 : angle 1.55222 / 0.81 ( 3) link_BETA1-4 : bond 0.00551 / 0.28 ( 3) link_BETA1-4 : angle 1.50988 / 0.87 ( 9) link_BETA1-6 : bond 0.00393 / 0.21 ( 1) link_BETA1-6 : angle 1.66470 / 0.86 ( 3) link_NAG-ASN : bond 0.00246 / 0.13 ( 4) link_NAG-ASN : angle 3.19337 / 1.90 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 640 MET cc_start: 0.9232 (tpp) cc_final: 0.8816 (tpp) REVERT: A 644 MET cc_start: 0.8566 (tpp) cc_final: 0.8358 (tpp) REVERT: A 755 PHE cc_start: 0.8042 (OUTLIER) cc_final: 0.7681 (t80) REVERT: A 1456 MET cc_start: 0.8870 (tpp) cc_final: 0.8492 (tpt) REVERT: A 1524 LYS cc_start: 0.6726 (mttt) cc_final: 0.5901 (tppt) REVERT: A 1707 MET cc_start: 0.8963 (mmm) cc_final: 0.8705 (mmm) REVERT: A 1856 MET cc_start: 0.7679 (mtp) cc_final: 0.7476 (ttm) REVERT: A 2069 ASP cc_start: 0.8713 (t0) cc_final: 0.7251 (p0) outliers start: 24 outliers final: 16 residues processed: 144 average time/residue: 0.0896 time to fit residues: 20.5910 Evaluate side-chains 132 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1347 PHE Chi-restraints excluded: chain A residue 1414 PHE Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1721 PHE Chi-restraints excluded: chain A residue 1740 LEU Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 2099 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 147 optimal weight: 4.9990 chunk 152 optimal weight: 0.0980 chunk 100 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 87 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 135 optimal weight: 5.9990 chunk 96 optimal weight: 20.0000 chunk 139 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.070795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.056363 restraints weight = 56359.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.058049 restraints weight = 30898.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.059129 restraints weight = 21118.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.059673 restraints weight = 16673.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.060277 restraints weight = 14622.920| |-----------------------------------------------------------------------------| r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 13600 Z= 0.211 Angle : 0.669 17.211 18567 Z= 0.327 Chirality : 0.044 0.331 2168 Planarity : 0.004 0.038 2344 Dihedral : 4.278 52.037 1899 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.85 % Allowed : 18.89 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.21), residues: 1756 helix: 1.86 (0.17), residues: 989 sheet: -1.39 (0.40), residues: 166 loop : -2.33 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1680 TYR 0.016 0.002 TYR A 754 PHE 0.016 0.002 PHE A1663 TRP 0.018 0.001 TRP A1705 HIS 0.003 0.001 HIS A1812 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.21 (13585) covalent geometry : angle 0.64679 / 0.32 (18528) SS BOND : bond 0.00324 / 0.16 ( 6) SS BOND : angle 1.55019 / 0.83 ( 12) hydrogen bonds : bond 0.04161 / 2.73 ( 747) hydrogen bonds : angle 3.78760 / 2.74 ( 2169) link_BETA1-3 : bond 0.00087 / 0.05 ( 1) link_BETA1-3 : angle 1.72012 / 0.90 ( 3) link_BETA1-4 : bond 0.00446 / 0.23 ( 3) link_BETA1-4 : angle 1.80411 / 1.00 ( 9) link_BETA1-6 : bond 0.00492 / 0.26 ( 1) link_BETA1-6 : angle 2.02113 / 1.08 ( 3) link_NAG-ASN : bond 0.01983 / 1.04 ( 4) link_NAG-ASN : angle 6.32892 / 4.23 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 115 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 502 MET cc_start: 0.8666 (tmm) cc_final: 0.8418 (tmm) REVERT: A 588 TYR cc_start: 0.9368 (OUTLIER) cc_final: 0.8678 (m-80) REVERT: A 601 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8323 (mm-30) REVERT: A 640 MET cc_start: 0.9319 (tpp) cc_final: 0.8823 (tpp) REVERT: A 644 MET cc_start: 0.8774 (tpp) cc_final: 0.8442 (tpp) REVERT: A 755 PHE cc_start: 0.8244 (OUTLIER) cc_final: 0.7937 (t80) REVERT: A 1524 LYS cc_start: 0.7096 (mttt) cc_final: 0.6139 (tppt) REVERT: A 1707 MET cc_start: 0.8966 (mmm) cc_final: 0.8685 (mmm) outliers start: 35 outliers final: 26 residues processed: 140 average time/residue: 0.0890 time to fit residues: 19.9994 Evaluate side-chains 134 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 588 TYR Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1362 LEU Chi-restraints excluded: chain A residue 1414 PHE Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1661 VAL Chi-restraints excluded: chain A residue 1721 PHE Chi-restraints excluded: chain A residue 1738 LEU Chi-restraints excluded: chain A residue 1740 LEU Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 2073 THR Chi-restraints excluded: chain A residue 2097 VAL Chi-restraints excluded: chain A residue 2099 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 105 optimal weight: 3.9990 chunk 163 optimal weight: 2.9990 chunk 35 optimal weight: 0.0970 chunk 94 optimal weight: 0.9990 chunk 151 optimal weight: 7.9990 chunk 129 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 167 optimal weight: 4.9990 chunk 87 optimal weight: 8.9990 chunk 173 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1450 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.071721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.057320 restraints weight = 55770.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.059075 restraints weight = 30180.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.060183 restraints weight = 20560.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.060993 restraints weight = 16230.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.061205 restraints weight = 13810.669| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13600 Z= 0.133 Angle : 0.619 17.674 18567 Z= 0.295 Chirality : 0.042 0.424 2168 Planarity : 0.003 0.039 2344 Dihedral : 4.160 51.676 1899 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.93 % Allowed : 18.73 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.21), residues: 1756 helix: 1.99 (0.17), residues: 987 sheet: -1.33 (0.40), residues: 166 loop : -2.26 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 565 TYR 0.011 0.001 TYR A 770 PHE 0.011 0.001 PHE A2010 TRP 0.017 0.001 TRP A1705 HIS 0.003 0.000 HIS A1626 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (13585) covalent geometry : angle 0.59498 / 0.29 (18528) SS BOND : bond 0.00274 / 0.14 ( 6) SS BOND : angle 1.22907 / 0.65 ( 12) hydrogen bonds : bond 0.03694 / 2.43 ( 747) hydrogen bonds : angle 3.65247 / 2.64 ( 2169) link_BETA1-3 : bond 0.00240 / 0.13 ( 1) link_BETA1-3 : angle 1.58852 / 0.83 ( 3) link_BETA1-4 : bond 0.00510 / 0.26 ( 3) link_BETA1-4 : angle 1.59901 / 0.92 ( 9) link_BETA1-6 : bond 0.00384 / 0.20 ( 1) link_BETA1-6 : angle 1.69527 / 0.87 ( 3) link_NAG-ASN : bond 0.01380 / 0.73 ( 4) link_NAG-ASN : angle 6.36832 / 4.24 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 115 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9223 (tt) REVERT: A 281 MET cc_start: 0.8278 (tmm) cc_final: 0.8004 (tmm) REVERT: A 502 MET cc_start: 0.8632 (tmm) cc_final: 0.8384 (tmm) REVERT: A 601 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8239 (mm-30) REVERT: A 640 MET cc_start: 0.9296 (tpp) cc_final: 0.8849 (tpp) REVERT: A 644 MET cc_start: 0.8789 (tpp) cc_final: 0.8415 (tpp) REVERT: A 755 PHE cc_start: 0.8216 (OUTLIER) cc_final: 0.7936 (t80) REVERT: A 1456 MET cc_start: 0.8673 (tpp) cc_final: 0.8432 (tpp) REVERT: A 1524 LYS cc_start: 0.7042 (mttt) cc_final: 0.6132 (tppt) REVERT: A 1707 MET cc_start: 0.8905 (mmm) cc_final: 0.8630 (mmm) outliers start: 36 outliers final: 26 residues processed: 144 average time/residue: 0.0896 time to fit residues: 20.8817 Evaluate side-chains 137 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 109 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 754 TYR Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1358 VAL Chi-restraints excluded: chain A residue 1362 LEU Chi-restraints excluded: chain A residue 1414 PHE Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1721 PHE Chi-restraints excluded: chain A residue 1740 LEU Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 2007 VAL Chi-restraints excluded: chain A residue 2073 THR Chi-restraints excluded: chain A residue 2097 VAL Chi-restraints excluded: chain A residue 2099 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 15 optimal weight: 7.9990 chunk 95 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 134 optimal weight: 7.9990 chunk 114 optimal weight: 0.3980 chunk 90 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 chunk 122 optimal weight: 0.0060 chunk 120 optimal weight: 4.9990 overall best weight: 1.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.071520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.057215 restraints weight = 55781.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.058936 restraints weight = 30131.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.060051 restraints weight = 20603.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.060849 restraints weight = 16234.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.061202 restraints weight = 13819.337| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13600 Z= 0.136 Angle : 0.621 17.982 18567 Z= 0.296 Chirality : 0.042 0.433 2168 Planarity : 0.003 0.041 2344 Dihedral : 4.140 50.877 1899 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.93 % Allowed : 19.54 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.21), residues: 1756 helix: 2.01 (0.17), residues: 987 sheet: -1.28 (0.41), residues: 166 loop : -2.21 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 565 TYR 0.015 0.001 TYR A1388 PHE 0.017 0.001 PHE A1530 TRP 0.018 0.001 TRP A1705 HIS 0.001 0.000 HIS A 993 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (13585) covalent geometry : angle 0.59752 / 0.29 (18528) SS BOND : bond 0.00272 / 0.14 ( 6) SS BOND : angle 1.25854 / 0.68 ( 12) hydrogen bonds : bond 0.03711 / 2.44 ( 747) hydrogen bonds : angle 3.64025 / 2.64 ( 2169) link_BETA1-3 : bond 0.00229 / 0.12 ( 1) link_BETA1-3 : angle 1.57789 / 0.82 ( 3) link_BETA1-4 : bond 0.00540 / 0.28 ( 3) link_BETA1-4 : angle 1.60610 / 0.91 ( 9) link_BETA1-6 : bond 0.00423 / 0.22 ( 1) link_BETA1-6 : angle 1.72612 / 0.91 ( 3) link_NAG-ASN : bond 0.01397 / 0.74 ( 4) link_NAG-ASN : angle 6.32384 / 4.20 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 114 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 MET cc_start: 0.8249 (tmm) cc_final: 0.7968 (tmm) REVERT: A 502 MET cc_start: 0.8628 (tmm) cc_final: 0.8381 (tmm) REVERT: A 588 TYR cc_start: 0.9350 (OUTLIER) cc_final: 0.8630 (m-80) REVERT: A 601 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8197 (mm-30) REVERT: A 640 MET cc_start: 0.9289 (tpp) cc_final: 0.8833 (tpp) REVERT: A 644 MET cc_start: 0.8759 (tpp) cc_final: 0.8386 (tpp) REVERT: A 1357 PHE cc_start: 0.8189 (m-80) cc_final: 0.7889 (m-10) REVERT: A 1456 MET cc_start: 0.8671 (tpp) cc_final: 0.8422 (tpp) REVERT: A 1524 LYS cc_start: 0.7019 (mttt) cc_final: 0.6122 (tppt) outliers start: 36 outliers final: 26 residues processed: 138 average time/residue: 0.0885 time to fit residues: 20.0440 Evaluate side-chains 138 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 588 TYR Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1362 LEU Chi-restraints excluded: chain A residue 1414 PHE Chi-restraints excluded: chain A residue 1446 MET Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1721 PHE Chi-restraints excluded: chain A residue 1740 LEU Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1807 PHE Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 2007 VAL Chi-restraints excluded: chain A residue 2073 THR Chi-restraints excluded: chain A residue 2097 VAL Chi-restraints excluded: chain A residue 2099 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 41 optimal weight: 0.4980 chunk 16 optimal weight: 0.9980 chunk 8 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 76 optimal weight: 0.0070 chunk 136 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 130 optimal weight: 0.0970 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 800 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.072487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.058139 restraints weight = 55880.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.059926 restraints weight = 30130.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.061049 restraints weight = 20484.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.061836 restraints weight = 16083.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.062250 restraints weight = 13721.340| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13600 Z= 0.108 Angle : 0.613 17.820 18567 Z= 0.287 Chirality : 0.042 0.438 2168 Planarity : 0.003 0.041 2344 Dihedral : 4.053 50.024 1899 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.52 % Allowed : 20.20 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.21), residues: 1756 helix: 2.10 (0.17), residues: 987 sheet: -1.27 (0.40), residues: 171 loop : -2.15 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 565 TYR 0.010 0.001 TYR A 770 PHE 0.015 0.001 PHE A1530 TRP 0.017 0.001 TRP A1705 HIS 0.003 0.000 HIS A1626 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (13585) covalent geometry : angle 0.59048 / 0.28 (18528) SS BOND : bond 0.00266 / 0.14 ( 6) SS BOND : angle 0.99392 / 0.53 ( 12) hydrogen bonds : bond 0.03440 / 2.26 ( 747) hydrogen bonds : angle 3.55050 / 2.57 ( 2169) link_BETA1-3 : bond 0.00294 / 0.15 ( 1) link_BETA1-3 : angle 1.51296 / 0.79 ( 3) link_BETA1-4 : bond 0.00604 / 0.31 ( 3) link_BETA1-4 : angle 1.48758 / 0.85 ( 9) link_BETA1-6 : bond 0.00418 / 0.22 ( 1) link_BETA1-6 : angle 1.58219 / 0.81 ( 3) link_NAG-ASN : bond 0.01334 / 0.70 ( 4) link_NAG-ASN : angle 6.27630 / 4.16 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 117 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 MET cc_start: 0.8231 (tmm) cc_final: 0.7961 (tmm) REVERT: A 502 MET cc_start: 0.8561 (tmm) cc_final: 0.8297 (tmm) REVERT: A 588 TYR cc_start: 0.9328 (OUTLIER) cc_final: 0.8508 (m-80) REVERT: A 601 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8176 (mm-30) REVERT: A 640 MET cc_start: 0.9267 (tpp) cc_final: 0.8842 (tpp) REVERT: A 644 MET cc_start: 0.8761 (tpp) cc_final: 0.8364 (tpp) REVERT: A 1414 PHE cc_start: 0.8268 (OUTLIER) cc_final: 0.7598 (t80) REVERT: A 1456 MET cc_start: 0.8662 (tpp) cc_final: 0.8346 (tpt) REVERT: A 1524 LYS cc_start: 0.6964 (mttt) cc_final: 0.6122 (tppt) REVERT: A 1665 MET cc_start: 0.9320 (tpp) cc_final: 0.9091 (tpp) REVERT: A 2106 GLU cc_start: 0.8661 (tt0) cc_final: 0.8190 (tt0) outliers start: 31 outliers final: 25 residues processed: 140 average time/residue: 0.0844 time to fit residues: 19.1042 Evaluate side-chains 142 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 588 TYR Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1358 VAL Chi-restraints excluded: chain A residue 1362 LEU Chi-restraints excluded: chain A residue 1414 PHE Chi-restraints excluded: chain A residue 1446 MET Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1587 LYS Chi-restraints excluded: chain A residue 1721 PHE Chi-restraints excluded: chain A residue 1740 LEU Chi-restraints excluded: chain A residue 1807 PHE Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 2007 VAL Chi-restraints excluded: chain A residue 2073 THR Chi-restraints excluded: chain A residue 2097 VAL Chi-restraints excluded: chain A residue 2099 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 105 optimal weight: 6.9990 chunk 151 optimal weight: 0.8980 chunk 89 optimal weight: 6.9990 chunk 35 optimal weight: 0.0770 chunk 135 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 119 optimal weight: 2.9990 chunk 166 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 overall best weight: 1.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.072554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.058214 restraints weight = 55505.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.059989 restraints weight = 29900.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.061148 restraints weight = 20319.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.061936 restraints weight = 15906.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.062272 restraints weight = 13546.788| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13600 Z= 0.115 Angle : 0.631 17.747 18567 Z= 0.295 Chirality : 0.042 0.441 2168 Planarity : 0.003 0.041 2344 Dihedral : 4.022 49.596 1899 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.36 % Allowed : 21.01 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.21), residues: 1756 helix: 2.05 (0.17), residues: 992 sheet: -1.15 (0.41), residues: 171 loop : -2.10 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 565 TYR 0.010 0.001 TYR A 770 PHE 0.014 0.001 PHE A1530 TRP 0.018 0.001 TRP A1705 HIS 0.002 0.000 HIS A2006 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (13585) covalent geometry : angle 0.60964 / 0.29 (18528) SS BOND : bond 0.00254 / 0.13 ( 6) SS BOND : angle 1.04564 / 0.56 ( 12) hydrogen bonds : bond 0.03458 / 2.27 ( 747) hydrogen bonds : angle 3.56216 / 2.59 ( 2169) link_BETA1-3 : bond 0.00302 / 0.16 ( 1) link_BETA1-3 : angle 1.52298 / 0.79 ( 3) link_BETA1-4 : bond 0.00589 / 0.30 ( 3) link_BETA1-4 : angle 1.50881 / 0.86 ( 9) link_BETA1-6 : bond 0.00412 / 0.22 ( 1) link_BETA1-6 : angle 1.58858 / 0.82 ( 3) link_NAG-ASN : bond 0.01303 / 0.69 ( 4) link_NAG-ASN : angle 6.18951 / 4.10 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 114 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 MET cc_start: 0.8299 (tmm) cc_final: 0.8026 (tmm) REVERT: A 449 TRP cc_start: 0.7529 (m100) cc_final: 0.7097 (m100) REVERT: A 502 MET cc_start: 0.8596 (tmm) cc_final: 0.8351 (tmm) REVERT: A 588 TYR cc_start: 0.9345 (OUTLIER) cc_final: 0.8538 (m-80) REVERT: A 601 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8221 (mm-30) REVERT: A 640 MET cc_start: 0.9250 (tpp) cc_final: 0.8803 (tpp) REVERT: A 644 MET cc_start: 0.8773 (tpp) cc_final: 0.8372 (tpp) REVERT: A 1414 PHE cc_start: 0.8259 (OUTLIER) cc_final: 0.7650 (t80) REVERT: A 1456 MET cc_start: 0.8634 (tpp) cc_final: 0.8312 (tpt) REVERT: A 1524 LYS cc_start: 0.7007 (mttt) cc_final: 0.6174 (tppt) outliers start: 29 outliers final: 25 residues processed: 136 average time/residue: 0.0919 time to fit residues: 20.0815 Evaluate side-chains 137 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 347 TYR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 588 TYR Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1358 VAL Chi-restraints excluded: chain A residue 1362 LEU Chi-restraints excluded: chain A residue 1414 PHE Chi-restraints excluded: chain A residue 1446 MET Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1587 LYS Chi-restraints excluded: chain A residue 1721 PHE Chi-restraints excluded: chain A residue 1740 LEU Chi-restraints excluded: chain A residue 1807 PHE Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 2007 VAL Chi-restraints excluded: chain A residue 2073 THR Chi-restraints excluded: chain A residue 2097 VAL Chi-restraints excluded: chain A residue 2099 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 175 optimal weight: 8.9990 chunk 162 optimal weight: 0.9980 chunk 157 optimal weight: 0.6980 chunk 161 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 142 optimal weight: 0.8980 chunk 54 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 74 optimal weight: 20.0000 chunk 154 optimal weight: 8.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 800 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.073080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.058671 restraints weight = 56174.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.060408 restraints weight = 30623.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.061520 restraints weight = 21070.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.062318 restraints weight = 16694.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.062841 restraints weight = 14246.971| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13600 Z= 0.107 Angle : 0.623 17.568 18567 Z= 0.290 Chirality : 0.042 0.447 2168 Planarity : 0.003 0.041 2344 Dihedral : 3.972 49.055 1899 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.12 % Allowed : 21.58 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.21), residues: 1756 helix: 2.07 (0.17), residues: 994 sheet: -1.10 (0.41), residues: 171 loop : -2.10 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 565 TYR 0.010 0.001 TYR A 770 PHE 0.014 0.001 PHE A1530 TRP 0.017 0.001 TRP A1705 HIS 0.002 0.000 HIS A1626 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (13585) covalent geometry : angle 0.60229 / 0.28 (18528) SS BOND : bond 0.00266 / 0.13 ( 6) SS BOND : angle 1.04618 / 0.57 ( 12) hydrogen bonds : bond 0.03337 / 2.19 ( 747) hydrogen bonds : angle 3.51268 / 2.54 ( 2169) link_BETA1-3 : bond 0.00221 / 0.12 ( 1) link_BETA1-3 : angle 1.44997 / 0.75 ( 3) link_BETA1-4 : bond 0.00649 / 0.33 ( 3) link_BETA1-4 : angle 1.48661 / 0.84 ( 9) link_BETA1-6 : bond 0.00549 / 0.29 ( 1) link_BETA1-6 : angle 1.59145 / 0.82 ( 3) link_NAG-ASN : bond 0.01277 / 0.67 ( 4) link_NAG-ASN : angle 6.10443 / 4.05 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1986.02 seconds wall clock time: 35 minutes 13.61 seconds (2113.61 seconds total)