Starting phenix.real_space_refine on Wed Mar 4 12:54:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tby_25801/03_2026/7tby_25801.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tby_25801/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7tby_25801/03_2026/7tby_25801.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tby_25801/03_2026/7tby_25801.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tby_25801/03_2026/7tby_25801.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tby_25801/03_2026/7tby_25801.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.45, per 1000 atoms: 0.26 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: 1.23 Conformation dependent library (CDL) restraints added in 571.8 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: 0.42 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: 2.44 Time building geometry restraints manager: 1.62 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 - 23.47: 7686 23.47 - 46.95: 357 46.95 - 70.42: 40 70.42 - 93.90: 25 93.90 - 117.37: 18 Dihedral angle restraints: 8126 sinusoidal: 2952 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=" C1 NAG C 2 " pdb=" C5 NAG C 2 " pdb=" O5 NAG C 2 " pdb=" C4 NAG C 2 " ideal model delta sinusoidal sigma weight residual -64.11 53.26 -117.37 1 3.00e+01 1.11e-03 1.56e+01 ... (remaining 8123 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: 2.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 14.290 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 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 : 15.630 117.373 4762 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 covalent geometry : bond 0.00270 (13585) covalent geometry : angle 0.60830 (18528) SS BOND : bond 0.00159 ( 6) SS BOND : angle 0.84401 ( 12) hydrogen bonds : bond 0.12412 ( 747) hydrogen bonds : angle 5.03499 ( 2169) link_BETA1-3 : bond 0.00192 ( 1) link_BETA1-3 : angle 1.31589 ( 3) link_BETA1-4 : bond 0.00521 ( 3) link_BETA1-4 : angle 1.24130 ( 9) link_BETA1-6 : bond 0.00464 ( 1) link_BETA1-6 : angle 1.28586 ( 3) link_NAG-ASN : bond 0.00496 ( 4) link_NAG-ASN : angle 5.00852 ( 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 : 0.454 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: 0.1076 time to fit residues: 36.4647 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 : 0.511 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.076696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.062704 restraints weight = 54577.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.064607 restraints weight = 28640.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.065783 restraints weight = 19232.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.066606 restraints weight = 14921.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.067171 restraints weight = 12665.032| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 13600 Z= 0.114 Angle : 0.600 10.909 18567 Z= 0.285 Chirality : 0.042 0.215 2168 Planarity : 0.003 0.042 2344 Dihedral : 10.790 94.808 2138 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % 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: -1.03 (0.20), residues: 1756 helix: 0.74 (0.17), residues: 986 sheet: -1.73 (0.38), 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 0.013 0.001 TYR A 997 PHE 0.019 0.001 PHE A1530 TRP 0.013 0.001 TRP A1705 HIS 0.002 0.000 HIS A2006 Details of bonding type rmsd covalent geometry : bond 0.00247 (13585) covalent geometry : angle 0.58530 (18528) SS BOND : bond 0.00233 ( 6) SS BOND : angle 0.93398 ( 12) hydrogen bonds : bond 0.03521 ( 747) hydrogen bonds : angle 3.96291 ( 2169) link_BETA1-3 : bond 0.00718 ( 1) link_BETA1-3 : angle 1.96315 ( 3) link_BETA1-4 : bond 0.00481 ( 3) link_BETA1-4 : angle 2.78847 ( 9) link_BETA1-6 : bond 0.00897 ( 1) link_BETA1-6 : angle 2.78735 ( 3) link_NAG-ASN : bond 0.00322 ( 4) link_NAG-ASN : angle 4.18903 ( 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 : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 LYS cc_start: 0.9004 (mmtt) cc_final: 0.8767 (mtpt) REVERT: A 640 MET cc_start: 0.9206 (tpp) cc_final: 0.8881 (tpp) REVERT: A 1419 MET cc_start: 0.7385 (pmm) cc_final: 0.6830 (pmm) REVERT: A 1649 MET cc_start: 0.5503 (ppp) cc_final: 0.4880 (ppp) REVERT: A 1707 MET cc_start: 0.8811 (mmm) cc_final: 0.8581 (mmm) REVERT: A 2069 ASP cc_start: 0.8717 (t0) cc_final: 0.7303 (p0) outliers start: 15 outliers final: 8 residues processed: 147 average time/residue: 0.0894 time to fit residues: 21.2986 Evaluate side-chains 125 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 117 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 22 optimal weight: 0.8980 chunk 166 optimal weight: 0.8980 chunk 70 optimal weight: 8.9990 chunk 162 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3373 r_free = 0.3373 target = 0.075494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.061486 restraints weight = 54891.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.063289 restraints weight = 29921.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.064447 restraints weight = 20551.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.065266 restraints weight = 16163.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.065562 restraints weight = 13772.927| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13600 Z= 0.107 Angle : 0.598 11.148 18567 Z= 0.280 Chirality : 0.041 0.196 2168 Planarity : 0.003 0.039 2344 Dihedral : 8.119 76.867 2138 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.38 % Allowed : 16.12 % Favored : 82.49 % 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: -0.33 (0.21), residues: 1756 helix: 1.34 (0.17), residues: 988 sheet: -1.57 (0.39), residues: 168 loop : -2.55 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 530 TYR 0.011 0.001 TYR A 770 PHE 0.023 0.001 PHE A1530 TRP 0.016 0.001 TRP A1705 HIS 0.002 0.000 HIS A2006 Details of bonding type rmsd covalent geometry : bond 0.00228 (13585) covalent geometry : angle 0.58330 (18528) SS BOND : bond 0.00226 ( 6) SS BOND : angle 0.92067 ( 12) hydrogen bonds : bond 0.03235 ( 747) hydrogen bonds : angle 3.71620 ( 2169) link_BETA1-3 : bond 0.00008 ( 1) link_BETA1-3 : angle 1.72985 ( 3) link_BETA1-4 : bond 0.00405 ( 3) link_BETA1-4 : angle 3.42116 ( 9) link_BETA1-6 : bond 0.01424 ( 1) link_BETA1-6 : angle 3.11132 ( 3) link_NAG-ASN : bond 0.00314 ( 4) link_NAG-ASN : angle 3.85085 ( 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: 17 poor density : 133 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 MET cc_start: 0.8049 (tmm) cc_final: 0.7800 (tmm) REVERT: A 640 MET cc_start: 0.9194 (tpp) cc_final: 0.8863 (tpp) REVERT: A 1419 MET cc_start: 0.7370 (pmm) cc_final: 0.6943 (pmm) REVERT: A 1649 MET cc_start: 0.5656 (ppp) cc_final: 0.5345 (ppp) REVERT: A 1707 MET cc_start: 0.8854 (mmm) cc_final: 0.8614 (mmm) REVERT: A 2069 ASP cc_start: 0.8705 (t0) cc_final: 0.7408 (p0) outliers start: 17 outliers final: 10 residues processed: 141 average time/residue: 0.0925 time to fit residues: 20.9055 Evaluate side-chains 126 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 712 TYR 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 Chi-restraints excluded: chain A residue 2099 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 17 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 141 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 123 optimal weight: 0.8980 chunk 159 optimal weight: 4.9990 chunk 100 optimal weight: 0.6980 chunk 28 optimal weight: 0.0070 chunk 165 optimal weight: 7.9990 chunk 129 optimal weight: 2.9990 chunk 138 optimal weight: 10.0000 overall best weight: 1.3202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.074529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.060357 restraints weight = 54719.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.062083 restraints weight = 30373.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.063005 restraints weight = 20967.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.063880 restraints weight = 17198.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.064297 restraints weight = 14555.366| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 13600 Z= 0.114 Angle : 0.583 9.253 18567 Z= 0.276 Chirality : 0.041 0.183 2168 Planarity : 0.003 0.038 2344 Dihedral : 6.238 59.769 2138 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.12 % Allowed : 17.02 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.06 (0.21), residues: 1756 helix: 1.68 (0.17), residues: 988 sheet: -1.42 (0.39), residues: 167 loop : -2.42 (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 0.029 0.001 PHE A1530 TRP 0.024 0.001 TRP A 533 HIS 0.001 0.000 HIS A2006 Details of bonding type rmsd covalent geometry : bond 0.00248 (13585) covalent geometry : angle 0.56978 (18528) SS BOND : bond 0.00235 ( 6) SS BOND : angle 1.02184 ( 12) hydrogen bonds : bond 0.03315 ( 747) hydrogen bonds : angle 3.61454 ( 2169) link_BETA1-3 : bond 0.00597 ( 1) link_BETA1-3 : angle 1.83803 ( 3) link_BETA1-4 : bond 0.00835 ( 3) link_BETA1-4 : angle 3.53512 ( 9) link_BETA1-6 : bond 0.00951 ( 1) link_BETA1-6 : angle 2.10849 ( 3) link_NAG-ASN : bond 0.00387 ( 4) link_NAG-ASN : angle 3.58345 ( 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 148 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 502 MET cc_start: 0.8379 (tmm) cc_final: 0.8138 (tmm) REVERT: A 640 MET cc_start: 0.9230 (tpp) cc_final: 0.8845 (tpp) REVERT: A 1446 MET cc_start: 0.7463 (mpp) cc_final: 0.7061 (pmm) REVERT: A 1456 MET cc_start: 0.8852 (tpp) cc_final: 0.8529 (tpt) REVERT: A 1665 MET cc_start: 0.9202 (tpp) cc_final: 0.8905 (tpp) REVERT: A 1707 MET cc_start: 0.8899 (mmm) cc_final: 0.8692 (mmm) REVERT: A 2069 ASP cc_start: 0.8720 (t0) cc_final: 0.7399 (p0) outliers start: 26 outliers final: 16 residues processed: 142 average time/residue: 0.0948 time to fit residues: 21.8241 Evaluate side-chains 130 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 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 990 VAL Chi-restraints excluded: chain A residue 1075 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 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: 3.9990 chunk 93 optimal weight: 30.0000 chunk 107 optimal weight: 10.0000 chunk 151 optimal weight: 5.9990 chunk 147 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 143 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1641 GLN A1825 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.070158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.055734 restraints weight = 56527.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.057399 restraints weight = 30817.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.058443 restraints weight = 21197.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.059192 restraints weight = 16902.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.059626 restraints weight = 14530.251| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13600 Z= 0.216 Angle : 0.668 9.201 18567 Z= 0.335 Chirality : 0.044 0.204 2168 Planarity : 0.004 0.035 2344 Dihedral : 5.936 55.132 2138 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 3.01 % Allowed : 18.00 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.08 (0.21), residues: 1756 helix: 1.70 (0.17), residues: 988 sheet: -1.52 (0.40), residues: 166 loop : -2.39 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1680 TYR 0.020 0.002 TYR A 754 PHE 0.025 0.002 PHE A1530 TRP 0.020 0.002 TRP A 533 HIS 0.003 0.001 HIS A 311 Details of bonding type rmsd covalent geometry : bond 0.00478 (13585) covalent geometry : angle 0.65815 (18528) SS BOND : bond 0.00302 ( 6) SS BOND : angle 1.66509 ( 12) hydrogen bonds : bond 0.04449 ( 747) hydrogen bonds : angle 3.92926 ( 2169) link_BETA1-3 : bond 0.00324 ( 1) link_BETA1-3 : angle 1.81432 ( 3) link_BETA1-4 : bond 0.00751 ( 3) link_BETA1-4 : angle 2.50370 ( 9) link_BETA1-6 : bond 0.00862 ( 1) link_BETA1-6 : angle 1.67172 ( 3) link_NAG-ASN : bond 0.00338 ( 4) link_NAG-ASN : angle 3.54280 ( 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 152 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 115 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 MET cc_start: 0.9334 (ptp) cc_final: 0.9079 (ppp) REVERT: A 502 MET cc_start: 0.8512 (tmm) cc_final: 0.8248 (tmm) REVERT: A 588 TYR cc_start: 0.9370 (OUTLIER) cc_final: 0.8845 (m-80) REVERT: A 640 MET cc_start: 0.9353 (tpp) cc_final: 0.8872 (tpp) REVERT: A 644 MET cc_start: 0.8780 (tpp) cc_final: 0.8510 (tpp) REVERT: A 755 PHE cc_start: 0.8263 (OUTLIER) cc_final: 0.7955 (t80) REVERT: A 1446 MET cc_start: 0.8001 (mpp) cc_final: 0.7782 (mpp) REVERT: A 1524 LYS cc_start: 0.6987 (mttt) cc_final: 0.6009 (tppt) REVERT: A 1649 MET cc_start: 0.5905 (ppp) cc_final: 0.5681 (ppp) REVERT: A 1706 ASP cc_start: 0.9063 (m-30) cc_final: 0.8799 (m-30) outliers start: 37 outliers final: 22 residues processed: 141 average time/residue: 0.0989 time to fit residues: 22.0702 Evaluate side-chains 132 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 548 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 755 PHE Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 759 LEU 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 1721 PHE Chi-restraints excluded: chain A residue 1738 LEU Chi-restraints excluded: chain A residue 1740 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 147 optimal weight: 7.9990 chunk 152 optimal weight: 0.0570 chunk 100 optimal weight: 0.0060 chunk 46 optimal weight: 2.9990 chunk 87 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 96 optimal weight: 9.9990 chunk 139 optimal weight: 0.9990 chunk 81 optimal weight: 7.9990 overall best weight: 1.0120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1450 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.072163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.057744 restraints weight = 55892.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.059521 restraints weight = 30245.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.060663 restraints weight = 20452.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.061421 restraints weight = 16026.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.061811 restraints weight = 13720.869| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 13600 Z= 0.113 Angle : 0.615 17.463 18567 Z= 0.292 Chirality : 0.042 0.452 2168 Planarity : 0.003 0.039 2344 Dihedral : 5.567 54.005 2138 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.12 % Allowed : 19.63 % 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: 0.36 (0.21), residues: 1756 helix: 1.96 (0.17), residues: 987 sheet: -1.46 (0.40), residues: 168 loop : -2.31 (0.25), residues: 601 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 0.023 0.001 PHE A1663 TRP 0.018 0.001 TRP A1705 HIS 0.003 0.000 HIS A1626 Details of bonding type rmsd covalent geometry : bond 0.00237 (13585) covalent geometry : angle 0.58832 (18528) SS BOND : bond 0.00276 ( 6) SS BOND : angle 1.07415 ( 12) hydrogen bonds : bond 0.03549 ( 747) hydrogen bonds : angle 3.62953 ( 2169) link_BETA1-3 : bond 0.00550 ( 1) link_BETA1-3 : angle 1.70825 ( 3) link_BETA1-4 : bond 0.00390 ( 3) link_BETA1-4 : angle 2.61590 ( 9) link_BETA1-6 : bond 0.00718 ( 1) link_BETA1-6 : angle 1.15608 ( 3) link_NAG-ASN : bond 0.01768 ( 4) link_NAG-ASN : angle 6.52891 ( 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 145 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 MET cc_start: 0.8285 (tmm) cc_final: 0.8071 (tmm) REVERT: A 640 MET cc_start: 0.9289 (tpp) cc_final: 0.8883 (tpp) REVERT: A 644 MET cc_start: 0.8704 (tpp) cc_final: 0.8342 (tpp) REVERT: A 755 PHE cc_start: 0.8231 (OUTLIER) cc_final: 0.7946 (t80) REVERT: A 1524 LYS cc_start: 0.6948 (mttt) cc_final: 0.6050 (tppt) REVERT: A 1706 ASP cc_start: 0.8981 (m-30) cc_final: 0.8781 (m-30) outliers start: 26 outliers final: 19 residues processed: 139 average time/residue: 0.0944 time to fit residues: 21.0896 Evaluate side-chains 131 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 1807 PHE Chi-restraints excluded: chain A residue 2007 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: 6.9990 chunk 163 optimal weight: 0.2980 chunk 35 optimal weight: 0.4980 chunk 94 optimal weight: 7.9990 chunk 151 optimal weight: 6.9990 chunk 129 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 167 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 173 optimal weight: 0.0370 chunk 81 optimal weight: 8.9990 overall best weight: 0.7662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.072780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.058433 restraints weight = 54926.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.060192 restraints weight = 29684.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.061301 restraints weight = 20153.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.062092 restraints weight = 15903.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.062412 restraints weight = 13554.660| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13600 Z= 0.106 Angle : 0.598 17.501 18567 Z= 0.282 Chirality : 0.042 0.484 2168 Planarity : 0.003 0.039 2344 Dihedral : 5.255 54.616 2138 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.69 % Allowed : 19.30 % Favored : 78.01 % 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: 0.50 (0.21), residues: 1756 helix: 2.03 (0.17), residues: 988 sheet: -1.23 (0.40), residues: 171 loop : -2.22 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 742 TYR 0.010 0.001 TYR A 770 PHE 0.025 0.001 PHE A1663 TRP 0.018 0.001 TRP A1705 HIS 0.002 0.000 HIS A 55 Details of bonding type rmsd covalent geometry : bond 0.00223 (13585) covalent geometry : angle 0.57236 (18528) SS BOND : bond 0.00231 ( 6) SS BOND : angle 1.05809 ( 12) hydrogen bonds : bond 0.03364 ( 747) hydrogen bonds : angle 3.55721 ( 2169) link_BETA1-3 : bond 0.00517 ( 1) link_BETA1-3 : angle 1.58989 ( 3) link_BETA1-4 : bond 0.00310 ( 3) link_BETA1-4 : angle 2.44175 ( 9) link_BETA1-6 : bond 0.00994 ( 1) link_BETA1-6 : angle 1.16300 ( 3) link_NAG-ASN : bond 0.01735 ( 4) link_NAG-ASN : angle 6.35148 ( 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 155 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9215 (tt) REVERT: A 281 MET cc_start: 0.8242 (tmm) cc_final: 0.8028 (tmm) REVERT: A 502 MET cc_start: 0.8560 (tmm) cc_final: 0.8204 (tmm) REVERT: A 640 MET cc_start: 0.9248 (tpp) cc_final: 0.8800 (tpp) REVERT: A 644 MET cc_start: 0.8743 (tpp) cc_final: 0.8372 (tpp) REVERT: A 755 PHE cc_start: 0.8191 (OUTLIER) cc_final: 0.7950 (t80) REVERT: A 1446 MET cc_start: 0.7390 (mpp) cc_final: 0.6963 (pmm) REVERT: A 1456 MET cc_start: 0.8631 (tpp) cc_final: 0.7925 (tpt) REVERT: A 1524 LYS cc_start: 0.6943 (mttt) cc_final: 0.6066 (tppt) REVERT: A 1707 MET cc_start: 0.8805 (mmm) cc_final: 0.8565 (mmm) outliers start: 33 outliers final: 23 residues processed: 148 average time/residue: 0.0925 time to fit residues: 22.4811 Evaluate side-chains 140 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU 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 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 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 1358 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 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 2099 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 15 optimal weight: 0.9990 chunk 95 optimal weight: 8.9990 chunk 65 optimal weight: 6.9990 chunk 100 optimal weight: 0.0470 chunk 132 optimal weight: 0.7980 chunk 134 optimal weight: 8.9990 chunk 114 optimal weight: 9.9990 chunk 90 optimal weight: 0.0970 chunk 98 optimal weight: 9.9990 chunk 122 optimal weight: 0.0670 chunk 120 optimal weight: 5.9990 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 800 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.073755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.059405 restraints weight = 54677.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.061214 restraints weight = 29379.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.062401 restraints weight = 19966.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.063185 restraints weight = 15660.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.063597 restraints weight = 13316.295| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13600 Z= 0.103 Angle : 0.608 17.732 18567 Z= 0.284 Chirality : 0.041 0.447 2168 Planarity : 0.003 0.053 2344 Dihedral : 5.039 54.349 2138 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.04 % Allowed : 20.28 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.62 (0.21), residues: 1756 helix: 2.08 (0.17), residues: 991 sheet: -1.10 (0.41), residues: 171 loop : -2.12 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A2113 TYR 0.010 0.001 TYR A 770 PHE 0.026 0.001 PHE A1663 TRP 0.017 0.001 TRP A1705 HIS 0.003 0.000 HIS A1626 Details of bonding type rmsd covalent geometry : bond 0.00213 (13585) covalent geometry : angle 0.58333 (18528) SS BOND : bond 0.00243 ( 6) SS BOND : angle 0.96227 ( 12) hydrogen bonds : bond 0.03135 ( 747) hydrogen bonds : angle 3.47162 ( 2169) link_BETA1-3 : bond 0.00606 ( 1) link_BETA1-3 : angle 1.56198 ( 3) link_BETA1-4 : bond 0.00275 ( 3) link_BETA1-4 : angle 2.43365 ( 9) link_BETA1-6 : bond 0.01003 ( 1) link_BETA1-6 : angle 1.18662 ( 3) link_NAG-ASN : bond 0.01409 ( 4) link_NAG-ASN : angle 6.32473 ( 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 154 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 MET cc_start: 0.8236 (tmm) cc_final: 0.8018 (tmm) REVERT: A 502 MET cc_start: 0.8529 (tmm) cc_final: 0.8166 (tmm) REVERT: A 640 MET cc_start: 0.9247 (tpp) cc_final: 0.8814 (tpp) REVERT: A 644 MET cc_start: 0.8722 (tpp) cc_final: 0.8355 (tpp) REVERT: A 755 PHE cc_start: 0.8145 (OUTLIER) cc_final: 0.7920 (t80) REVERT: A 1414 PHE cc_start: 0.8182 (OUTLIER) cc_final: 0.7544 (t80) REVERT: A 1446 MET cc_start: 0.7290 (mpp) cc_final: 0.6859 (pmm) REVERT: A 1456 MET cc_start: 0.8589 (tpp) cc_final: 0.7851 (tpt) REVERT: A 1524 LYS cc_start: 0.6960 (mttt) cc_final: 0.6160 (tppt) REVERT: A 1707 MET cc_start: 0.8807 (mmm) cc_final: 0.8551 (mmm) REVERT: A 2106 GLU cc_start: 0.8575 (tt0) cc_final: 0.8170 (tt0) outliers start: 25 outliers final: 19 residues processed: 145 average time/residue: 0.0912 time to fit residues: 21.4964 Evaluate side-chains 143 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.506 ------------------------------------------------------------------------------- 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 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 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 1347 PHE Chi-restraints excluded: chain A residue 1358 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 1807 PHE Chi-restraints excluded: chain A residue 2007 VAL Chi-restraints excluded: chain A residue 2073 THR 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: 4.9990 chunk 16 optimal weight: 8.9990 chunk 8 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 76 optimal weight: 0.1980 chunk 136 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 chunk 12 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 130 optimal weight: 6.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1686 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.071884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.057424 restraints weight = 56187.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.059031 restraints weight = 30280.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.060254 restraints weight = 21113.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.061007 restraints weight = 16339.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.061265 restraints weight = 14031.508| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13600 Z= 0.150 Angle : 0.634 17.784 18567 Z= 0.304 Chirality : 0.043 0.456 2168 Planarity : 0.004 0.040 2344 Dihedral : 5.031 52.752 2138 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.44 % Allowed : 20.52 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.61 (0.21), residues: 1756 helix: 2.07 (0.17), residues: 994 sheet: -1.14 (0.41), residues: 168 loop : -2.13 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1572 TYR 0.015 0.001 TYR A1388 PHE 0.026 0.001 PHE A1663 TRP 0.019 0.001 TRP A1705 HIS 0.002 0.000 HIS A 993 Details of bonding type rmsd covalent geometry : bond 0.00335 (13585) covalent geometry : angle 0.61097 (18528) SS BOND : bond 0.00253 ( 6) SS BOND : angle 1.22337 ( 12) hydrogen bonds : bond 0.03636 ( 747) hydrogen bonds : angle 3.59569 ( 2169) link_BETA1-3 : bond 0.00484 ( 1) link_BETA1-3 : angle 1.58804 ( 3) link_BETA1-4 : bond 0.00393 ( 3) link_BETA1-4 : angle 2.43575 ( 9) link_BETA1-6 : bond 0.00923 ( 1) link_BETA1-6 : angle 1.24036 ( 3) link_NAG-ASN : bond 0.01375 ( 4) link_NAG-ASN : angle 6.21911 ( 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 146 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 MET cc_start: 0.8248 (tmm) cc_final: 0.8017 (tmm) REVERT: A 449 TRP cc_start: 0.7531 (m100) cc_final: 0.7111 (m100) REVERT: A 502 MET cc_start: 0.8587 (tmm) cc_final: 0.8235 (tmm) REVERT: A 588 TYR cc_start: 0.9342 (OUTLIER) cc_final: 0.8689 (m-80) REVERT: A 640 MET cc_start: 0.9275 (tpp) cc_final: 0.8781 (tpp) REVERT: A 644 MET cc_start: 0.8814 (tpp) cc_final: 0.8476 (tpp) REVERT: A 755 PHE cc_start: 0.8278 (OUTLIER) cc_final: 0.8064 (t80) REVERT: A 1414 PHE cc_start: 0.8313 (OUTLIER) cc_final: 0.7668 (t80) REVERT: A 1446 MET cc_start: 0.7290 (mpp) cc_final: 0.6852 (pmm) REVERT: A 1456 MET cc_start: 0.8597 (tpp) cc_final: 0.8104 (tpt) REVERT: A 1524 LYS cc_start: 0.6933 (mttt) cc_final: 0.6146 (tppt) REVERT: A 1707 MET cc_start: 0.8862 (mmm) cc_final: 0.8586 (mmm) outliers start: 30 outliers final: 22 residues processed: 140 average time/residue: 0.0921 time to fit residues: 21.0758 Evaluate side-chains 137 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.501 ------------------------------------------------------------------------------- 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 507 LEU Chi-restraints excluded: chain A residue 548 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 1112 VAL Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1358 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 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: 3.9990 chunk 151 optimal weight: 0.8980 chunk 89 optimal weight: 0.0970 chunk 35 optimal weight: 0.3980 chunk 135 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.073152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.058828 restraints weight = 55446.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.060561 restraints weight = 30734.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.061627 restraints weight = 21206.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.062406 restraints weight = 16904.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.062790 restraints weight = 14480.795| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3160 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= 0.110 Angle : 0.626 17.691 18567 Z= 0.292 Chirality : 0.042 0.456 2168 Planarity : 0.003 0.046 2344 Dihedral : 4.966 53.634 2138 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.71 % Allowed : 21.42 % Favored : 76.87 % 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: 0.67 (0.21), residues: 1756 helix: 2.09 (0.17), residues: 995 sheet: -1.01 (0.41), residues: 171 loop : -2.12 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1572 TYR 0.010 0.001 TYR A 770 PHE 0.048 0.001 PHE A1371 TRP 0.017 0.001 TRP A1705 HIS 0.002 0.000 HIS A1626 Details of bonding type rmsd covalent geometry : bond 0.00238 (13585) covalent geometry : angle 0.60302 (18528) SS BOND : bond 0.00251 ( 6) SS BOND : angle 0.99966 ( 12) hydrogen bonds : bond 0.03347 ( 747) hydrogen bonds : angle 3.50483 ( 2169) link_BETA1-3 : bond 0.00506 ( 1) link_BETA1-3 : angle 1.47836 ( 3) link_BETA1-4 : bond 0.00214 ( 3) link_BETA1-4 : angle 2.39701 ( 9) link_BETA1-6 : bond 0.00994 ( 1) link_BETA1-6 : angle 1.19726 ( 3) link_NAG-ASN : bond 0.01316 ( 4) link_NAG-ASN : angle 6.20775 ( 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 140 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 MET cc_start: 0.8213 (tmm) cc_final: 0.7988 (tmm) REVERT: A 449 TRP cc_start: 0.7486 (m100) cc_final: 0.7078 (m100) REVERT: A 502 MET cc_start: 0.8518 (tmm) cc_final: 0.8148 (tmm) REVERT: A 588 TYR cc_start: 0.9333 (OUTLIER) cc_final: 0.8647 (m-80) REVERT: A 640 MET cc_start: 0.9256 (tpp) cc_final: 0.8822 (tpp) REVERT: A 644 MET cc_start: 0.8760 (tpp) cc_final: 0.8416 (tpp) REVERT: A 755 PHE cc_start: 0.8221 (OUTLIER) cc_final: 0.8019 (t80) REVERT: A 799 GLU cc_start: 0.7357 (mt-10) cc_final: 0.7051 (mt-10) REVERT: A 1414 PHE cc_start: 0.8193 (OUTLIER) cc_final: 0.7591 (t80) REVERT: A 1446 MET cc_start: 0.7291 (mpp) cc_final: 0.6816 (pmm) REVERT: A 1456 MET cc_start: 0.8561 (tpp) cc_final: 0.8237 (tpt) REVERT: A 1524 LYS cc_start: 0.6882 (mttt) cc_final: 0.6133 (tppt) REVERT: A 1707 MET cc_start: 0.8851 (mmm) cc_final: 0.8605 (mmm) outliers start: 21 outliers final: 18 residues processed: 133 average time/residue: 0.0907 time to fit residues: 19.9138 Evaluate side-chains 134 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 TYR 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 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 1112 VAL Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1358 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 1807 PHE Chi-restraints excluded: chain A residue 2007 VAL Chi-restraints excluded: chain A residue 2073 THR 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: 5.9990 chunk 162 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 161 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 142 optimal weight: 0.8980 chunk 54 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 74 optimal weight: 20.0000 chunk 154 optimal weight: 4.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.072149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.057622 restraints weight = 56215.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.059389 restraints weight = 30122.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.060531 restraints weight = 20431.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.061297 restraints weight = 16072.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.061646 restraints weight = 13746.959| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13600 Z= 0.139 Angle : 0.637 17.584 18567 Z= 0.301 Chirality : 0.042 0.458 2168 Planarity : 0.003 0.040 2344 Dihedral : 4.962 52.829 2138 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.28 % Allowed : 21.25 % Favored : 76.47 % 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: 2.09 (0.17), residues: 994 sheet: -1.05 (0.42), residues: 168 loop : -2.14 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1572 TYR 0.012 0.001 TYR A1388 PHE 0.026 0.001 PHE A1663 TRP 0.019 0.001 TRP A1705 HIS 0.002 0.001 HIS A2006 Details of bonding type rmsd covalent geometry : bond 0.00309 (13585) covalent geometry : angle 0.61504 (18528) SS BOND : bond 0.00254 ( 6) SS BOND : angle 1.23063 ( 12) hydrogen bonds : bond 0.03614 ( 747) hydrogen bonds : angle 3.57316 ( 2169) link_BETA1-3 : bond 0.00473 ( 1) link_BETA1-3 : angle 1.60858 ( 3) link_BETA1-4 : bond 0.00323 ( 3) link_BETA1-4 : angle 2.39363 ( 9) link_BETA1-6 : bond 0.00873 ( 1) link_BETA1-6 : angle 1.16354 ( 3) link_NAG-ASN : bond 0.01304 ( 4) link_NAG-ASN : angle 6.09881 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2067.14 seconds wall clock time: 36 minutes 32.56 seconds (2192.56 seconds total)