Starting phenix.real_space_refine on Thu Jun 12 09:17:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tby_25801/06_2025/7tby_25801.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tby_25801/06_2025/7tby_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7tby_25801/06_2025/7tby_25801.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tby_25801/06_2025/7tby_25801.map" model { file = "/net/cci-nas-00/data/ceres_data/7tby_25801/06_2025/7tby_25801.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tby_25801/06_2025/7tby_25801.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 19, 'ASP:plan': 22, 'TYR:plan': 3, 'ASN:plan1': 13, 'HIS:plan': 12, 'PHE:plan': 9, 'GLU:plan': 29, 'ARG:plan': 17} 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: 8.57, per 1000 atoms: 0.65 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: 3.45 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.86 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: 6.14 Time building geometry restraints manager: 4.02 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: 2.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 34.930 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.850 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (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 TRP 0.011 0.001 TRP A1705 HIS 0.002 0.000 HIS A 52 PHE 0.015 0.001 PHE A1721 TYR 0.007 0.001 TYR A1237 ARG 0.002 0.000 ARG A1336 Details of bonding type rmsd link_NAG-ASN : bond 0.00496 ( 4) link_NAG-ASN : angle 5.00852 ( 12) link_BETA1-4 : bond 0.00521 ( 3) link_BETA1-4 : angle 1.24130 ( 9) hydrogen bonds : bond 0.12412 ( 747) hydrogen bonds : angle 5.03499 ( 2169) link_BETA1-6 : bond 0.00464 ( 1) link_BETA1-6 : angle 1.28586 ( 3) SS BOND : bond 0.00159 ( 6) SS BOND : angle 0.84401 ( 12) link_BETA1-3 : bond 0.00192 ( 1) link_BETA1-3 : angle 1.31589 ( 3) covalent geometry : bond 0.00270 (13585) covalent geometry : angle 0.60830 (18528) *********************** 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 : 1.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.9410 (tp) cc_final: 0.9123 (tt) REVERT: A 373 LYS cc_start: 0.8836 (mmtt) cc_final: 0.8603 (mtpt) REVERT: A 586 MET cc_start: 0.9262 (tpp) cc_final: 0.8939 (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: 0.8631 (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: 0.8598 (m-30) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.2577 time to fit residues: 87.5666 Evaluate side-chains 132 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 74 optimal weight: 0.0980 chunk 46 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 72 optimal weight: 20.0000 chunk 139 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 84 optimal weight: 0.6980 chunk 103 optimal weight: 10.0000 chunk 161 optimal weight: 6.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 A1600 HIS A1626 HIS A1688 GLN A1774 ASN A2049 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.075989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.062006 restraints weight = 53950.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.063880 restraints weight = 28564.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.065075 restraints weight = 19146.886| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13600 Z= 0.125 Angle : 0.609 11.012 18567 Z= 0.290 Chirality : 0.042 0.219 2168 Planarity : 0.003 0.042 2344 Dihedral : 10.526 92.452 2138 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.38 % Allowed : 13.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.20), residues: 1756 helix: 0.79 (0.17), residues: 987 sheet: -1.73 (0.39), residues: 164 loop : -2.80 (0.23), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1705 HIS 0.003 0.000 HIS A2006 PHE 0.018 0.001 PHE A1530 TYR 0.014 0.001 TYR A 997 ARG 0.004 0.000 ARG A 530 Details of bonding type rmsd link_NAG-ASN : bond 0.00265 ( 4) link_NAG-ASN : angle 4.20873 ( 12) link_BETA1-4 : bond 0.00402 ( 3) link_BETA1-4 : angle 2.86612 ( 9) hydrogen bonds : bond 0.03482 ( 747) hydrogen bonds : angle 3.95489 ( 2169) link_BETA1-6 : bond 0.00819 ( 1) link_BETA1-6 : angle 2.94119 ( 3) SS BOND : bond 0.00272 ( 6) SS BOND : angle 0.96263 ( 12) link_BETA1-3 : bond 0.00762 ( 1) link_BETA1-3 : angle 2.25379 ( 3) covalent geometry : bond 0.00270 (13585) covalent geometry : angle 0.59440 (18528) *********************** 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 155 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 1.555 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.9463 (tp) cc_final: 0.9225 (tt) REVERT: A 373 LYS cc_start: 0.9046 (mmtt) cc_final: 0.8797 (mtpt) REVERT: A 640 MET cc_start: 0.9224 (tpp) cc_final: 0.8862 (tpp) REVERT: A 1419 MET cc_start: 0.7366 (pmm) cc_final: 0.6910 (pmm) REVERT: A 1649 MET cc_start: 0.5631 (ppp) cc_final: 0.5023 (ppp) REVERT: A 1707 MET cc_start: 0.8797 (mmm) cc_final: 0.8561 (mmm) REVERT: A 2069 ASP cc_start: 0.8737 (t0) cc_final: 0.7292 (p0) outliers start: 17 outliers final: 11 residues processed: 150 average time/residue: 0.1994 time to fit residues: 48.7086 Evaluate side-chains 127 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 1.417 ------------------------------------------------------------------------------- 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 1362 LEU Chi-restraints excluded: chain A residue 1721 PHE Chi-restraints excluded: chain A residue 1775 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 29 optimal weight: 7.9990 chunk 115 optimal weight: 2.9990 chunk 165 optimal weight: 8.9990 chunk 37 optimal weight: 0.9990 chunk 175 optimal weight: 20.0000 chunk 119 optimal weight: 2.9990 chunk 30 optimal weight: 20.0000 chunk 62 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 132 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3345 r_free = 0.3345 target = 0.074311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.060164 restraints weight = 54962.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.061919 restraints weight = 30324.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.063041 restraints weight = 20979.184| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13600 Z= 0.124 Angle : 0.611 11.173 18567 Z= 0.289 Chirality : 0.042 0.220 2168 Planarity : 0.003 0.039 2344 Dihedral : 7.662 70.094 2138 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.47 % Allowed : 16.78 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.21), residues: 1756 helix: 1.41 (0.17), residues: 988 sheet: -1.62 (0.38), residues: 169 loop : -2.51 (0.24), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1705 HIS 0.001 0.000 HIS A1600 PHE 0.017 0.001 PHE A1530 TYR 0.013 0.001 TYR A 770 ARG 0.003 0.000 ARG A 530 Details of bonding type rmsd link_NAG-ASN : bond 0.00342 ( 4) link_NAG-ASN : angle 3.85199 ( 12) link_BETA1-4 : bond 0.00246 ( 3) link_BETA1-4 : angle 3.65732 ( 9) hydrogen bonds : bond 0.03444 ( 747) hydrogen bonds : angle 3.74912 ( 2169) link_BETA1-6 : bond 0.01565 ( 1) link_BETA1-6 : angle 3.55679 ( 3) SS BOND : bond 0.00255 ( 6) SS BOND : angle 1.05124 ( 12) link_BETA1-3 : bond 0.00661 ( 1) link_BETA1-3 : angle 1.96544 ( 3) covalent geometry : bond 0.00268 (13585) covalent geometry : angle 0.59516 (18528) *********************** 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 147 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.9469 (tp) cc_final: 0.9268 (tt) REVERT: A 281 MET cc_start: 0.8044 (tmm) cc_final: 0.7823 (tmm) REVERT: A 640 MET cc_start: 0.9223 (tpp) cc_final: 0.8873 (tpp) REVERT: A 1419 MET cc_start: 0.7398 (pmm) cc_final: 0.7031 (pmm) REVERT: A 1649 MET cc_start: 0.5684 (ppp) cc_final: 0.5347 (ppp) REVERT: A 2069 ASP cc_start: 0.8756 (t0) cc_final: 0.7487 (p0) outliers start: 18 outliers final: 11 residues processed: 140 average time/residue: 0.2189 time to fit residues: 49.0854 Evaluate side-chains 127 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 1.601 ------------------------------------------------------------------------------- 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 560 ILE Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1414 PHE Chi-restraints excluded: chain A residue 1587 LYS 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 11 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 121 optimal weight: 8.9990 chunk 95 optimal weight: 10.0000 chunk 106 optimal weight: 0.9980 chunk 126 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 22 optimal weight: 0.1980 chunk 118 optimal weight: 7.9990 chunk 146 optimal weight: 4.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1641 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.071809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.057342 restraints weight = 55499.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.058979 restraints weight = 31486.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.060068 restraints weight = 22184.655| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13600 Z= 0.181 Angle : 0.633 9.680 18567 Z= 0.311 Chirality : 0.043 0.199 2168 Planarity : 0.004 0.037 2344 Dihedral : 6.352 58.627 2138 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 3.09 % Allowed : 17.43 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.21), residues: 1756 helix: 1.65 (0.17), residues: 989 sheet: -1.58 (0.40), residues: 166 loop : -2.42 (0.24), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 533 HIS 0.003 0.001 HIS A 311 PHE 0.024 0.002 PHE A1530 TYR 0.013 0.001 TYR A 754 ARG 0.004 0.000 ARG A1680 Details of bonding type rmsd link_NAG-ASN : bond 0.00458 ( 4) link_NAG-ASN : angle 3.72037 ( 12) link_BETA1-4 : bond 0.00456 ( 3) link_BETA1-4 : angle 2.83169 ( 9) hydrogen bonds : bond 0.04080 ( 747) hydrogen bonds : angle 3.82908 ( 2169) link_BETA1-6 : bond 0.00661 ( 1) link_BETA1-6 : angle 2.08576 ( 3) SS BOND : bond 0.00290 ( 6) SS BOND : angle 1.41249 ( 12) link_BETA1-3 : bond 0.00212 ( 1) link_BETA1-3 : angle 2.10019 ( 3) covalent geometry : bond 0.00400 (13585) covalent geometry : angle 0.62168 (18528) *********************** 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 156 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 118 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 MET cc_start: 0.8177 (tmm) cc_final: 0.7908 (tmm) REVERT: A 588 TYR cc_start: 0.9301 (OUTLIER) cc_final: 0.8787 (m-80) REVERT: A 640 MET cc_start: 0.9310 (tpp) cc_final: 0.8882 (tpp) REVERT: A 644 MET cc_start: 0.8755 (tpp) cc_final: 0.8498 (tpp) REVERT: A 755 PHE cc_start: 0.8256 (OUTLIER) cc_final: 0.7922 (t80) REVERT: A 1419 MET cc_start: 0.7629 (pmm) cc_final: 0.7376 (pmm) REVERT: A 1456 MET cc_start: 0.8859 (tpp) cc_final: 0.8556 (tpt) REVERT: A 1524 LYS cc_start: 0.6801 (mttt) cc_final: 0.5863 (tppt) REVERT: A 1649 MET cc_start: 0.5855 (ppp) cc_final: 0.5642 (ppp) REVERT: A 1707 MET cc_start: 0.8884 (mmm) cc_final: 0.8649 (mmm) outliers start: 38 outliers final: 23 residues processed: 147 average time/residue: 0.2228 time to fit residues: 52.1993 Evaluate side-chains 133 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU 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 507 LEU Chi-restraints excluded: chain A residue 588 TYR Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 759 LEU 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 1362 LEU Chi-restraints excluded: chain A residue 1414 PHE Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1587 LYS Chi-restraints excluded: chain A residue 1721 PHE Chi-restraints excluded: chain A residue 1738 LEU Chi-restraints excluded: chain A residue 1740 LEU Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 2073 THR Chi-restraints excluded: chain A residue 2097 VAL Chi-restraints excluded: chain A residue 2099 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 79 optimal weight: 8.9990 chunk 167 optimal weight: 8.9990 chunk 97 optimal weight: 9.9990 chunk 88 optimal weight: 9.9990 chunk 35 optimal weight: 0.8980 chunk 175 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 70 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 94 optimal weight: 9.9990 overall best weight: 4.5386 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.069648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.055971 restraints weight = 56767.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.057211 restraints weight = 33214.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.057752 restraints weight = 23535.473| |-----------------------------------------------------------------------------| r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 13600 Z= 0.262 Angle : 0.713 17.242 18567 Z= 0.353 Chirality : 0.045 0.211 2168 Planarity : 0.004 0.036 2344 Dihedral : 6.349 53.606 2138 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 3.91 % Allowed : 18.16 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.21), residues: 1756 helix: 1.63 (0.17), residues: 984 sheet: -1.72 (0.39), residues: 165 loop : -2.51 (0.24), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1705 HIS 0.004 0.001 HIS A 311 PHE 0.017 0.002 PHE A1721 TYR 0.020 0.002 TYR A 754 ARG 0.003 0.000 ARG A1680 Details of bonding type rmsd link_NAG-ASN : bond 0.03191 ( 4) link_NAG-ASN : angle 6.18970 ( 12) link_BETA1-4 : bond 0.01102 ( 3) link_BETA1-4 : angle 2.85426 ( 9) hydrogen bonds : bond 0.04612 ( 747) hydrogen bonds : angle 4.06898 ( 2169) link_BETA1-6 : bond 0.00983 ( 1) link_BETA1-6 : angle 1.69629 ( 3) SS BOND : bond 0.00387 ( 6) SS BOND : angle 1.75749 ( 12) link_BETA1-3 : bond 0.00868 ( 1) link_BETA1-3 : angle 2.01878 ( 3) covalent geometry : bond 0.00572 (13585) covalent geometry : angle 0.69058 (18528) *********************** 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 155 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 107 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 MET cc_start: 0.9350 (ptp) cc_final: 0.9063 (ppp) REVERT: A 449 TRP cc_start: 0.7441 (m100) cc_final: 0.6943 (m100) REVERT: A 502 MET cc_start: 0.8549 (tmm) cc_final: 0.8315 (tmm) REVERT: A 588 TYR cc_start: 0.9344 (OUTLIER) cc_final: 0.8649 (m-80) REVERT: A 640 MET cc_start: 0.9378 (tpp) cc_final: 0.8898 (tpp) REVERT: A 644 MET cc_start: 0.8929 (tpp) cc_final: 0.8583 (tpp) REVERT: A 755 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.8052 (t80) REVERT: A 1456 MET cc_start: 0.8873 (tpp) cc_final: 0.8603 (tpt) REVERT: A 1473 MET cc_start: 0.8887 (ttp) cc_final: 0.8312 (ttp) REVERT: A 1524 LYS cc_start: 0.7061 (mttt) cc_final: 0.5998 (tppt) REVERT: A 1649 MET cc_start: 0.5933 (ppp) cc_final: 0.5633 (ppp) outliers start: 48 outliers final: 29 residues processed: 146 average time/residue: 0.2008 time to fit residues: 47.5535 Evaluate side-chains 135 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 104 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL 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 388 ASP Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 588 TYR Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 730 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 1112 VAL Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1358 VAL Chi-restraints excluded: chain A residue 1362 LEU Chi-restraints excluded: chain A residue 1414 PHE Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1721 PHE Chi-restraints excluded: chain A residue 1738 LEU Chi-restraints excluded: chain A residue 1740 LEU Chi-restraints excluded: chain A residue 1807 PHE Chi-restraints excluded: chain A residue 1867 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 23 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 17 optimal weight: 0.0970 chunk 125 optimal weight: 2.9990 chunk 173 optimal weight: 8.9990 chunk 134 optimal weight: 5.9990 overall best weight: 1.6182 ------------------------------------------------------------------------------- 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 = 0.3277 r_free = 0.3277 target = 0.071382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.057094 restraints weight = 56211.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.058772 restraints weight = 31315.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.059838 restraints weight = 21759.731| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13600 Z= 0.127 Angle : 0.625 16.952 18567 Z= 0.299 Chirality : 0.043 0.468 2168 Planarity : 0.003 0.040 2344 Dihedral : 5.969 54.134 2138 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.01 % Allowed : 20.03 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.21), residues: 1756 helix: 1.89 (0.17), residues: 982 sheet: -1.61 (0.40), residues: 167 loop : -2.37 (0.24), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1705 HIS 0.002 0.001 HIS A1626 PHE 0.022 0.001 PHE A1663 TYR 0.011 0.001 TYR A 770 ARG 0.002 0.000 ARG A 565 Details of bonding type rmsd link_NAG-ASN : bond 0.01620 ( 4) link_NAG-ASN : angle 6.29333 ( 12) link_BETA1-4 : bond 0.00337 ( 3) link_BETA1-4 : angle 2.52390 ( 9) hydrogen bonds : bond 0.03845 ( 747) hydrogen bonds : angle 3.76069 ( 2169) link_BETA1-6 : bond 0.00872 ( 1) link_BETA1-6 : angle 1.31411 ( 3) SS BOND : bond 0.00303 ( 6) SS BOND : angle 1.16887 ( 12) link_BETA1-3 : bond 0.00544 ( 1) link_BETA1-3 : angle 1.76510 ( 3) covalent geometry : bond 0.00276 (13585) covalent geometry : angle 0.60098 (18528) *********************** 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 152 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 115 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 640 MET cc_start: 0.9308 (tpp) cc_final: 0.8910 (tpp) REVERT: A 644 MET cc_start: 0.8794 (tpp) cc_final: 0.8422 (tpp) REVERT: A 755 PHE cc_start: 0.8369 (OUTLIER) cc_final: 0.8066 (t80) REVERT: A 1456 MET cc_start: 0.8825 (tpp) cc_final: 0.8595 (tpt) REVERT: A 1524 LYS cc_start: 0.6813 (mttt) cc_final: 0.5913 (tppt) REVERT: A 1649 MET cc_start: 0.5801 (ppp) cc_final: 0.5598 (ppp) REVERT: A 1760 PHE cc_start: 0.8160 (OUTLIER) cc_final: 0.7817 (m-80) outliers start: 37 outliers final: 23 residues processed: 145 average time/residue: 0.2029 time to fit residues: 47.4605 Evaluate side-chains 136 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 1.387 ------------------------------------------------------------------------------- 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 560 ILE Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 804 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 1587 LYS Chi-restraints excluded: chain A residue 1661 VAL Chi-restraints excluded: chain A residue 1721 PHE Chi-restraints excluded: chain A residue 1740 LEU Chi-restraints excluded: chain A residue 1760 PHE Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1807 PHE Chi-restraints excluded: chain A residue 1812 HIS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 2 optimal weight: 8.9990 chunk 105 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 64 optimal weight: 8.9990 chunk 156 optimal weight: 20.0000 chunk 65 optimal weight: 0.9990 chunk 160 optimal weight: 9.9990 chunk 54 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 92 optimal weight: 30.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.070742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.056363 restraints weight = 56308.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.058028 restraints weight = 31120.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.059147 restraints weight = 21556.284| |-----------------------------------------------------------------------------| r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13600 Z= 0.159 Angle : 0.636 17.744 18567 Z= 0.306 Chirality : 0.044 0.462 2168 Planarity : 0.003 0.041 2344 Dihedral : 5.754 53.025 2138 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.09 % Allowed : 20.52 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.21), residues: 1756 helix: 1.92 (0.17), residues: 983 sheet: -1.52 (0.40), residues: 168 loop : -2.35 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1705 HIS 0.002 0.001 HIS A 311 PHE 0.015 0.001 PHE A1357 TYR 0.014 0.001 TYR A 754 ARG 0.002 0.000 ARG A1680 Details of bonding type rmsd link_NAG-ASN : bond 0.01451 ( 4) link_NAG-ASN : angle 6.24492 ( 12) link_BETA1-4 : bond 0.00471 ( 3) link_BETA1-4 : angle 2.58735 ( 9) hydrogen bonds : bond 0.03952 ( 747) hydrogen bonds : angle 3.77087 ( 2169) link_BETA1-6 : bond 0.00917 ( 1) link_BETA1-6 : angle 1.27597 ( 3) SS BOND : bond 0.00314 ( 6) SS BOND : angle 1.36810 ( 12) link_BETA1-3 : bond 0.00506 ( 1) link_BETA1-3 : angle 1.69987 ( 3) covalent geometry : bond 0.00351 (13585) covalent geometry : angle 0.61280 (18528) *********************** 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 145 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 107 time to evaluate : 1.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 TRP cc_start: 0.7542 (m100) cc_final: 0.7105 (m100) REVERT: A 502 MET cc_start: 0.8626 (tmm) cc_final: 0.8327 (tmm) REVERT: A 588 TYR cc_start: 0.9315 (OUTLIER) cc_final: 0.8649 (m-80) REVERT: A 640 MET cc_start: 0.9344 (tpp) cc_final: 0.8887 (tpp) REVERT: A 644 MET cc_start: 0.8806 (tpp) cc_final: 0.8344 (tpp) REVERT: A 755 PHE cc_start: 0.8346 (OUTLIER) cc_final: 0.8083 (t80) REVERT: A 1357 PHE cc_start: 0.8379 (m-80) cc_final: 0.7974 (m-10) REVERT: A 1456 MET cc_start: 0.8802 (tpp) cc_final: 0.8557 (tpt) REVERT: A 1524 LYS cc_start: 0.7033 (mttt) cc_final: 0.6103 (tppt) REVERT: A 1649 MET cc_start: 0.5902 (ppp) cc_final: 0.5639 (ppp) REVERT: A 1707 MET cc_start: 0.8793 (mmm) cc_final: 0.8572 (mmm) REVERT: A 1760 PHE cc_start: 0.8179 (OUTLIER) cc_final: 0.7877 (m-80) outliers start: 38 outliers final: 29 residues processed: 138 average time/residue: 0.2035 time to fit residues: 45.2611 Evaluate side-chains 135 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 103 time to evaluate : 1.435 ------------------------------------------------------------------------------- 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 347 TYR 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 560 ILE Chi-restraints excluded: chain A residue 588 TYR Chi-restraints excluded: chain A residue 745 LEU 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 771 VAL 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 1587 LYS Chi-restraints excluded: chain A residue 1721 PHE Chi-restraints excluded: chain A residue 1740 LEU Chi-restraints excluded: chain A residue 1760 PHE Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1807 PHE Chi-restraints excluded: chain A residue 1812 HIS Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 2007 VAL Chi-restraints excluded: chain A residue 2073 THR Chi-restraints excluded: chain A residue 2097 VAL Chi-restraints excluded: chain A residue 2099 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 61 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 112 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 800 GLN ** A1634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.070006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.056351 restraints weight = 56321.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.057344 restraints weight = 31224.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.058526 restraints weight = 22738.023| |-----------------------------------------------------------------------------| r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13600 Z= 0.192 Angle : 0.667 17.725 18567 Z= 0.324 Chirality : 0.044 0.471 2168 Planarity : 0.004 0.040 2344 Dihedral : 5.679 52.452 2138 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 3.18 % Allowed : 21.09 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.21), residues: 1756 helix: 1.87 (0.17), residues: 982 sheet: -1.50 (0.40), residues: 168 loop : -2.36 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1705 HIS 0.002 0.001 HIS A 311 PHE 0.017 0.001 PHE A1357 TYR 0.017 0.001 TYR A 754 ARG 0.002 0.000 ARG A1680 Details of bonding type rmsd link_NAG-ASN : bond 0.01409 ( 4) link_NAG-ASN : angle 6.19556 ( 12) link_BETA1-4 : bond 0.00604 ( 3) link_BETA1-4 : angle 2.56864 ( 9) hydrogen bonds : bond 0.04198 ( 747) hydrogen bonds : angle 3.89177 ( 2169) link_BETA1-6 : bond 0.00807 ( 1) link_BETA1-6 : angle 1.26735 ( 3) SS BOND : bond 0.00322 ( 6) SS BOND : angle 1.48979 ( 12) link_BETA1-3 : bond 0.00521 ( 1) link_BETA1-3 : angle 1.76611 ( 3) covalent geometry : bond 0.00424 (13585) covalent geometry : angle 0.64499 (18528) *********************** 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 143 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 104 time to evaluate : 1.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 MET cc_start: 0.8763 (mmt) cc_final: 0.8543 (mmt) REVERT: A 449 TRP cc_start: 0.7554 (m100) cc_final: 0.7121 (m100) REVERT: A 502 MET cc_start: 0.8664 (tmm) cc_final: 0.8429 (tmm) REVERT: A 636 MET cc_start: 0.9004 (ppp) cc_final: 0.8662 (tmm) REVERT: A 640 MET cc_start: 0.9361 (tpp) cc_final: 0.8870 (tpp) REVERT: A 644 MET cc_start: 0.8865 (tpp) cc_final: 0.8392 (tpp) REVERT: A 755 PHE cc_start: 0.8345 (OUTLIER) cc_final: 0.8117 (t80) REVERT: A 1456 MET cc_start: 0.8784 (tpp) cc_final: 0.8538 (tpt) REVERT: A 1524 LYS cc_start: 0.7123 (mttt) cc_final: 0.6215 (tppt) REVERT: A 1649 MET cc_start: 0.5982 (ppp) cc_final: 0.5717 (ppp) REVERT: A 1760 PHE cc_start: 0.8294 (OUTLIER) cc_final: 0.7940 (m-80) outliers start: 39 outliers final: 29 residues processed: 137 average time/residue: 0.2179 time to fit residues: 47.5036 Evaluate side-chains 131 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 347 TYR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 560 ILE 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 759 LEU Chi-restraints excluded: chain A residue 771 VAL 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 1587 LYS Chi-restraints excluded: chain A residue 1721 PHE Chi-restraints excluded: chain A residue 1740 LEU Chi-restraints excluded: chain A residue 1760 PHE Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1807 PHE Chi-restraints excluded: chain A residue 1812 HIS Chi-restraints excluded: chain A residue 1867 THR Chi-restraints excluded: chain A residue 2007 VAL Chi-restraints excluded: chain A residue 2073 THR Chi-restraints excluded: chain A residue 2097 VAL Chi-restraints excluded: chain A residue 2099 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 146 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 27 optimal weight: 20.0000 chunk 25 optimal weight: 9.9990 chunk 140 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 153 optimal weight: 20.0000 chunk 110 optimal weight: 3.9990 chunk 67 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 800 GLN ** A1634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.070740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.057064 restraints weight = 56020.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.058594 restraints weight = 31096.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.058963 restraints weight = 22052.514| |-----------------------------------------------------------------------------| r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13600 Z= 0.147 Angle : 0.641 17.709 18567 Z= 0.307 Chirality : 0.043 0.466 2168 Planarity : 0.003 0.041 2344 Dihedral : 5.507 52.962 2138 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.34 % Allowed : 20.85 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.21), residues: 1756 helix: 1.93 (0.17), residues: 984 sheet: -1.43 (0.41), residues: 168 loop : -2.34 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1705 HIS 0.003 0.001 HIS A1626 PHE 0.014 0.001 PHE A1357 TYR 0.013 0.001 TYR A 754 ARG 0.003 0.000 ARG A 393 Details of bonding type rmsd link_NAG-ASN : bond 0.01362 ( 4) link_NAG-ASN : angle 6.17981 ( 12) link_BETA1-4 : bond 0.00424 ( 3) link_BETA1-4 : angle 2.51422 ( 9) hydrogen bonds : bond 0.03950 ( 747) hydrogen bonds : angle 3.76849 ( 2169) link_BETA1-6 : bond 0.00844 ( 1) link_BETA1-6 : angle 1.14782 ( 3) SS BOND : bond 0.00316 ( 6) SS BOND : angle 1.33944 ( 12) link_BETA1-3 : bond 0.00463 ( 1) link_BETA1-3 : angle 1.61234 ( 3) covalent geometry : bond 0.00325 (13585) covalent geometry : angle 0.61774 (18528) *********************** 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 150 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 109 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 MET cc_start: 0.9175 (ptp) cc_final: 0.8937 (ppp) REVERT: A 449 TRP cc_start: 0.7565 (m100) cc_final: 0.7140 (m100) REVERT: A 502 MET cc_start: 0.8635 (tmm) cc_final: 0.8407 (tmm) REVERT: A 640 MET cc_start: 0.9343 (tpp) cc_final: 0.8868 (tpp) REVERT: A 644 MET cc_start: 0.8860 (tpp) cc_final: 0.8357 (tpp) REVERT: A 1456 MET cc_start: 0.8793 (tpp) cc_final: 0.8560 (tpt) REVERT: A 1524 LYS cc_start: 0.7183 (mttt) cc_final: 0.6176 (tppt) REVERT: A 1649 MET cc_start: 0.5915 (ppp) cc_final: 0.5665 (ppp) REVERT: A 1760 PHE cc_start: 0.8315 (OUTLIER) cc_final: 0.7981 (m-80) outliers start: 41 outliers final: 32 residues processed: 143 average time/residue: 0.2050 time to fit residues: 47.6993 Evaluate side-chains 135 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 102 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 347 TYR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 771 VAL 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 1097 LEU Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1358 VAL Chi-restraints excluded: chain A residue 1414 PHE Chi-restraints excluded: chain A residue 1446 MET Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1587 LYS Chi-restraints excluded: chain A residue 1721 PHE Chi-restraints excluded: chain A residue 1740 LEU Chi-restraints excluded: chain A residue 1760 PHE Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1807 PHE Chi-restraints excluded: chain A residue 1812 HIS Chi-restraints excluded: chain A residue 1867 THR 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 96 optimal weight: 20.0000 chunk 123 optimal weight: 0.8980 chunk 167 optimal weight: 10.0000 chunk 112 optimal weight: 0.9990 chunk 115 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 159 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 67 optimal weight: 0.0020 chunk 33 optimal weight: 4.9990 chunk 28 optimal weight: 20.0000 overall best weight: 1.7794 ------------------------------------------------------------------------------- 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 = 0.3269 r_free = 0.3269 target = 0.071086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.056727 restraints weight = 55396.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.058393 restraints weight = 30532.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.059484 restraints weight = 21129.033| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 13600 Z= 0.137 Angle : 0.645 19.853 18567 Z= 0.308 Chirality : 0.044 0.519 2168 Planarity : 0.004 0.041 2344 Dihedral : 5.409 53.176 2138 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.77 % Allowed : 21.66 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.21), residues: 1756 helix: 1.91 (0.17), residues: 988 sheet: -1.36 (0.41), residues: 171 loop : -2.31 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1705 HIS 0.002 0.000 HIS A1626 PHE 0.017 0.001 PHE A1663 TYR 0.013 0.001 TYR A 754 ARG 0.002 0.000 ARG A 565 Details of bonding type rmsd link_NAG-ASN : bond 0.01388 ( 4) link_NAG-ASN : angle 6.72240 ( 12) link_BETA1-4 : bond 0.00394 ( 3) link_BETA1-4 : angle 2.49084 ( 9) hydrogen bonds : bond 0.03869 ( 747) hydrogen bonds : angle 3.75423 ( 2169) link_BETA1-6 : bond 0.00824 ( 1) link_BETA1-6 : angle 1.10597 ( 3) SS BOND : bond 0.00298 ( 6) SS BOND : angle 1.26703 ( 12) link_BETA1-3 : bond 0.00484 ( 1) link_BETA1-3 : angle 1.63225 ( 3) covalent geometry : bond 0.00305 (13585) covalent geometry : angle 0.61884 (18528) ********************** 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 137 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 103 time to evaluate : 1.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 MET cc_start: 0.9130 (ptp) cc_final: 0.8926 (ppp) REVERT: A 449 TRP cc_start: 0.7600 (m100) cc_final: 0.7173 (m100) REVERT: A 502 MET cc_start: 0.8586 (tmm) cc_final: 0.8338 (tmm) REVERT: A 636 MET cc_start: 0.8973 (ppp) cc_final: 0.8629 (tmm) REVERT: A 640 MET cc_start: 0.9329 (tpp) cc_final: 0.8862 (tpp) REVERT: A 644 MET cc_start: 0.8828 (tpp) cc_final: 0.8345 (tpp) REVERT: A 1456 MET cc_start: 0.8787 (tpp) cc_final: 0.8543 (tpt) REVERT: A 1524 LYS cc_start: 0.7063 (mttt) cc_final: 0.6124 (tppt) REVERT: A 1649 MET cc_start: 0.5941 (ppp) cc_final: 0.5673 (ppp) REVERT: A 1760 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.7963 (m-80) outliers start: 34 outliers final: 30 residues processed: 130 average time/residue: 0.2015 time to fit residues: 42.6449 Evaluate side-chains 133 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 102 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 347 TYR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 771 VAL 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 1207 VAL Chi-restraints excluded: chain A residue 1358 VAL Chi-restraints excluded: chain A residue 1414 PHE Chi-restraints excluded: chain A residue 1446 MET Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1587 LYS Chi-restraints excluded: chain A residue 1721 PHE Chi-restraints excluded: chain A residue 1740 LEU Chi-restraints excluded: chain A residue 1760 PHE Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1807 PHE Chi-restraints excluded: chain A residue 1867 THR 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 40 optimal weight: 3.9990 chunk 138 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 chunk 38 optimal weight: 0.0020 chunk 170 optimal weight: 7.9990 chunk 132 optimal weight: 0.8980 chunk 98 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 93 optimal weight: 9.9990 chunk 103 optimal weight: 7.9990 overall best weight: 1.9392 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.071293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.057718 restraints weight = 55958.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.058689 restraints weight = 32060.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.059442 restraints weight = 23409.657| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13600 Z= 0.140 Angle : 0.657 19.279 18567 Z= 0.309 Chirality : 0.043 0.460 2168 Planarity : 0.003 0.041 2344 Dihedral : 5.300 52.911 2138 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.85 % Allowed : 21.82 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.21), residues: 1756 helix: 1.97 (0.17), residues: 988 sheet: -1.32 (0.41), residues: 171 loop : -2.30 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1705 HIS 0.002 0.001 HIS A1812 PHE 0.017 0.001 PHE A1663 TYR 0.015 0.001 TYR A 754 ARG 0.002 0.000 ARG A1817 Details of bonding type rmsd link_NAG-ASN : bond 0.01185 ( 4) link_NAG-ASN : angle 6.58177 ( 12) link_BETA1-4 : bond 0.00432 ( 3) link_BETA1-4 : angle 2.41689 ( 9) hydrogen bonds : bond 0.03838 ( 747) hydrogen bonds : angle 3.70940 ( 2169) link_BETA1-6 : bond 0.01047 ( 1) link_BETA1-6 : angle 1.24340 ( 3) SS BOND : bond 0.00302 ( 6) SS BOND : angle 1.30143 ( 12) link_BETA1-3 : bond 0.00401 ( 1) link_BETA1-3 : angle 1.56209 ( 3) covalent geometry : bond 0.00311 (13585) covalent geometry : angle 0.63233 (18528) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3882.91 seconds wall clock time: 68 minutes 15.18 seconds (4095.18 seconds total)