Starting phenix.real_space_refine on Mon Dec 30 19:00:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tby_25801/12_2024/7tby_25801.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tby_25801/12_2024/7tby_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_25801/12_2024/7tby_25801.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tby_25801/12_2024/7tby_25801.map" model { file = "/net/cci-nas-00/data/ceres_data/7tby_25801/12_2024/7tby_25801.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tby_25801/12_2024/7tby_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-5532/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: 8.13, per 1000 atoms: 0.61 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: 3.23 Conformation dependent library (CDL) restraints added in 1.8 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: 2.16 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: 5.73 Time building geometry restraints manager: 3.72 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: 5.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 33.860 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.010 ------------------------------------------------------------------------------- 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 13585 Z= 0.180 Angle : 0.608 7.842 18528 Z= 0.333 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 *********************** 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 : 1.454 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: 0.2503 time to fit residues: 84.1455 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 : 1.226 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 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 13585 Z= 0.178 Angle : 0.594 9.778 18528 Z= 0.287 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 *********************** 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 : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.9471 (tp) cc_final: 0.9244 (tt) REVERT: A 373 LYS cc_start: 0.8996 (mmtt) cc_final: 0.8788 (mtpt) REVERT: A 640 MET cc_start: 0.9189 (tpp) cc_final: 0.8803 (tpp) REVERT: A 1419 MET cc_start: 0.7451 (pmm) cc_final: 0.6843 (pmm) REVERT: A 1649 MET cc_start: 0.5559 (ppp) cc_final: 0.4914 (ppp) REVERT: A 1707 MET cc_start: 0.8809 (mmm) cc_final: 0.8572 (mmm) REVERT: A 2069 ASP cc_start: 0.8752 (t0) cc_final: 0.7288 (p0) outliers start: 17 outliers final: 11 residues processed: 150 average time/residue: 0.2062 time to fit residues: 50.4357 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 : 1.463 ------------------------------------------------------------------------------- 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 89 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 134 optimal weight: 4.9990 chunk 110 optimal weight: 9.9990 chunk 44 optimal weight: 0.9990 chunk 161 optimal weight: 0.0270 chunk 174 optimal weight: 9.9990 chunk 144 optimal weight: 7.9990 chunk 160 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 overall best weight: 3.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1443 GLN A1825 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13585 Z= 0.274 Angle : 0.654 11.211 18528 Z= 0.320 Chirality : 0.044 0.221 2168 Planarity : 0.004 0.037 2344 Dihedral : 7.929 67.244 2138 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.28 % Allowed : 16.86 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.21), residues: 1756 helix: 1.33 (0.17), residues: 989 sheet: -1.66 (0.39), residues: 169 loop : -2.54 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1705 HIS 0.003 0.001 HIS A1600 PHE 0.018 0.001 PHE A1530 TYR 0.016 0.001 TYR A 754 ARG 0.004 0.000 ARG A1680 *********************** 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 145 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 1.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 PHE cc_start: 0.8564 (t80) cc_final: 0.8327 (t80) REVERT: A 640 MET cc_start: 0.9268 (tpp) cc_final: 0.8808 (tpp) REVERT: A 1419 MET cc_start: 0.7590 (pmm) cc_final: 0.7159 (pmm) outliers start: 28 outliers final: 19 residues processed: 136 average time/residue: 0.2131 time to fit residues: 46.4105 Evaluate side-chains 127 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE 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 695 VAL Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 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 1865 LEU Chi-restraints excluded: chain A residue 1867 THR 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 159 optimal weight: 8.9990 chunk 121 optimal weight: 10.0000 chunk 84 optimal weight: 0.1980 chunk 17 optimal weight: 10.0000 chunk 77 optimal weight: 0.0980 chunk 108 optimal weight: 0.4980 chunk 162 optimal weight: 2.9990 chunk 172 optimal weight: 5.9990 chunk 154 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 chunk 143 optimal weight: 6.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1450 GLN A1451 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13585 Z= 0.165 Angle : 0.576 7.434 18528 Z= 0.278 Chirality : 0.041 0.225 2168 Planarity : 0.003 0.039 2344 Dihedral : 6.349 59.183 2138 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.44 % Allowed : 17.51 % Favored : 80.05 % 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: 0.04 (0.21), residues: 1756 helix: 1.69 (0.17), residues: 987 sheet: -1.51 (0.40), residues: 169 loop : -2.46 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1705 HIS 0.002 0.000 HIS A2006 PHE 0.014 0.001 PHE A2010 TYR 0.012 0.001 TYR A 770 ARG 0.002 0.000 ARG A 530 *********************** 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 158 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 PHE cc_start: 0.8522 (t80) cc_final: 0.8292 (t80) REVERT: A 502 MET cc_start: 0.8434 (tmm) cc_final: 0.8209 (tmm) REVERT: A 640 MET cc_start: 0.9226 (tpp) cc_final: 0.8812 (tpp) REVERT: A 644 MET cc_start: 0.8645 (tpp) cc_final: 0.8413 (tpp) REVERT: A 755 PHE cc_start: 0.8006 (OUTLIER) cc_final: 0.7650 (t80) REVERT: A 1419 MET cc_start: 0.7531 (pmm) cc_final: 0.7158 (pmm) REVERT: A 1446 MET cc_start: 0.6683 (pmm) cc_final: 0.6015 (pmm) REVERT: A 1456 MET cc_start: 0.8894 (tpp) cc_final: 0.8522 (tpt) REVERT: A 1524 LYS cc_start: 0.6784 (mttt) cc_final: 0.5967 (tppt) REVERT: A 1649 MET cc_start: 0.5633 (ppp) cc_final: 0.5430 (ppp) REVERT: A 1707 MET cc_start: 0.8868 (mmm) cc_final: 0.8625 (mmm) REVERT: A 2069 ASP cc_start: 0.8877 (t0) cc_final: 0.7390 (p0) outliers start: 30 outliers final: 18 residues processed: 148 average time/residue: 0.2128 time to fit residues: 50.9759 Evaluate side-chains 132 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 754 TYR Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1362 LEU Chi-restraints excluded: chain A residue 1414 PHE Chi-restraints excluded: chain A residue 1602 ILE Chi-restraints excluded: chain A residue 1721 PHE Chi-restraints excluded: chain A residue 1740 LEU Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 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 97 optimal weight: 8.9990 chunk 2 optimal weight: 0.9990 chunk 128 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 146 optimal weight: 0.9980 chunk 118 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 154 optimal weight: 7.9990 chunk 43 optimal weight: 0.5980 chunk 57 optimal weight: 4.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13585 Z= 0.222 Angle : 0.593 9.137 18528 Z= 0.294 Chirality : 0.043 0.432 2168 Planarity : 0.003 0.037 2344 Dihedral : 6.119 55.896 2138 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.93 % Allowed : 18.49 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.21), residues: 1756 helix: 1.81 (0.17), residues: 989 sheet: -1.51 (0.40), residues: 166 loop : -2.39 (0.24), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1705 HIS 0.002 0.001 HIS A 311 PHE 0.021 0.001 PHE A1663 TYR 0.012 0.001 TYR A1388 ARG 0.003 0.000 ARG A 565 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 116 time to evaluate : 1.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 PHE cc_start: 0.8545 (t80) cc_final: 0.8283 (t80) REVERT: A 502 MET cc_start: 0.8462 (tmm) cc_final: 0.8210 (tmm) REVERT: A 588 TYR cc_start: 0.9355 (OUTLIER) cc_final: 0.8771 (m-80) REVERT: A 640 MET cc_start: 0.9275 (tpp) cc_final: 0.8791 (tpp) REVERT: A 644 MET cc_start: 0.8743 (tpp) cc_final: 0.8416 (tpp) REVERT: A 755 PHE cc_start: 0.8071 (OUTLIER) cc_final: 0.7720 (t80) REVERT: A 1357 PHE cc_start: 0.8241 (m-80) cc_final: 0.7957 (m-10) REVERT: A 1419 MET cc_start: 0.7641 (pmm) cc_final: 0.7315 (pmm) REVERT: A 1446 MET cc_start: 0.7165 (pmm) cc_final: 0.6932 (pmm) REVERT: A 1456 MET cc_start: 0.8899 (tpp) cc_final: 0.8536 (tpt) REVERT: A 1524 LYS cc_start: 0.6930 (mttt) cc_final: 0.6001 (tppt) REVERT: A 1856 MET cc_start: 0.7788 (mtp) cc_final: 0.7465 (ttm) outliers start: 36 outliers final: 24 residues processed: 143 average time/residue: 0.2161 time to fit residues: 49.0571 Evaluate side-chains 136 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 1.634 ------------------------------------------------------------------------------- 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 507 LEU Chi-restraints excluded: chain A residue 588 TYR Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 754 TYR Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1347 PHE Chi-restraints excluded: chain A residue 1358 VAL Chi-restraints excluded: chain A residue 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 1740 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 154 optimal weight: 10.0000 chunk 34 optimal weight: 0.4980 chunk 101 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 172 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 166 optimal weight: 10.0000 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1450 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13585 Z= 0.232 Angle : 0.609 10.464 18528 Z= 0.299 Chirality : 0.043 0.473 2168 Planarity : 0.003 0.040 2344 Dihedral : 5.822 53.174 2138 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 3.01 % Allowed : 19.06 % 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: 0.28 (0.21), residues: 1756 helix: 1.90 (0.17), residues: 987 sheet: -1.55 (0.40), residues: 168 loop : -2.34 (0.24), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1705 HIS 0.002 0.001 HIS A1626 PHE 0.019 0.001 PHE A1663 TYR 0.013 0.001 TYR A 754 ARG 0.003 0.000 ARG A2113 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 113 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 PHE cc_start: 0.8551 (t80) cc_final: 0.8263 (t80) REVERT: A 281 MET cc_start: 0.8225 (tmm) cc_final: 0.7968 (tmm) REVERT: A 449 TRP cc_start: 0.7553 (m100) cc_final: 0.7026 (m100) REVERT: A 502 MET cc_start: 0.8483 (tmm) cc_final: 0.8215 (tmm) REVERT: A 640 MET cc_start: 0.9292 (tpp) cc_final: 0.8826 (tpp) REVERT: A 644 MET cc_start: 0.8831 (tpp) cc_final: 0.8477 (tpp) REVERT: A 755 PHE cc_start: 0.8120 (OUTLIER) cc_final: 0.7789 (t80) REVERT: A 1419 MET cc_start: 0.7734 (pmm) cc_final: 0.7433 (pmm) REVERT: A 1446 MET cc_start: 0.7167 (pmm) cc_final: 0.6861 (pmm) REVERT: A 1456 MET cc_start: 0.8856 (tpp) cc_final: 0.8604 (tpt) REVERT: A 1524 LYS cc_start: 0.7040 (mttt) cc_final: 0.6018 (tppt) REVERT: A 1656 LEU cc_start: 0.8809 (tt) cc_final: 0.8361 (pp) outliers start: 37 outliers final: 28 residues processed: 141 average time/residue: 0.2140 time to fit residues: 49.3788 Evaluate side-chains 137 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 754 TYR Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 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 1740 LEU Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1807 PHE Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 2007 VAL Chi-restraints excluded: chain A residue 2073 THR Chi-restraints excluded: chain A residue 2097 VAL Chi-restraints excluded: chain A residue 2099 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 19 optimal weight: 7.9990 chunk 98 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 144 optimal weight: 8.9990 chunk 96 optimal weight: 20.0000 chunk 171 optimal weight: 9.9990 chunk 107 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 79 optimal weight: 20.0000 chunk 106 optimal weight: 2.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1641 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13585 Z= 0.296 Angle : 0.637 10.604 18528 Z= 0.320 Chirality : 0.044 0.460 2168 Planarity : 0.004 0.040 2344 Dihedral : 5.815 57.807 2138 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 3.34 % Allowed : 19.79 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.87 (0.17), residues: 983 sheet: -1.48 (0.41), residues: 168 loop : -2.39 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1705 HIS 0.003 0.001 HIS A 311 PHE 0.017 0.001 PHE A1663 TYR 0.017 0.001 TYR A 754 ARG 0.003 0.000 ARG A1680 *********************** 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 154 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 113 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 359 MET cc_start: 0.9287 (ptp) cc_final: 0.9041 (ppp) REVERT: A 449 TRP cc_start: 0.7620 (m100) cc_final: 0.7075 (m100) REVERT: A 502 MET cc_start: 0.8487 (tmm) cc_final: 0.8188 (tmm) REVERT: A 640 MET cc_start: 0.9327 (tpp) cc_final: 0.8829 (tpp) REVERT: A 644 MET cc_start: 0.8876 (tpp) cc_final: 0.8505 (tpp) REVERT: A 755 PHE cc_start: 0.8203 (OUTLIER) cc_final: 0.7862 (t80) REVERT: A 1419 MET cc_start: 0.7817 (pmm) cc_final: 0.7511 (pmm) REVERT: A 1446 MET cc_start: 0.7354 (pmm) cc_final: 0.7132 (pmm) REVERT: A 1456 MET cc_start: 0.8831 (tpp) cc_final: 0.8611 (tpt) REVERT: A 1524 LYS cc_start: 0.7158 (mttt) cc_final: 0.6159 (tppt) REVERT: A 1656 LEU cc_start: 0.8921 (tt) cc_final: 0.8468 (pp) REVERT: A 1760 PHE cc_start: 0.8056 (OUTLIER) cc_final: 0.7851 (m-80) outliers start: 41 outliers final: 28 residues processed: 145 average time/residue: 0.2236 time to fit residues: 51.2388 Evaluate side-chains 135 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 1.719 ------------------------------------------------------------------------------- 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 386 THR Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 754 TYR Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1358 VAL Chi-restraints excluded: chain A residue 1362 LEU Chi-restraints excluded: chain A residue 1414 PHE Chi-restraints excluded: chain A residue 1476 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 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 68 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 109 optimal weight: 7.9990 chunk 116 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 15 optimal weight: 9.9990 chunk 134 optimal weight: 0.5980 chunk 156 optimal weight: 20.0000 chunk 164 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13585 Z= 0.191 Angle : 0.608 10.745 18528 Z= 0.297 Chirality : 0.043 0.451 2168 Planarity : 0.003 0.041 2344 Dihedral : 5.663 58.469 2138 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.93 % Allowed : 20.28 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.21), residues: 1756 helix: 1.98 (0.17), residues: 984 sheet: -1.37 (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 A 533 HIS 0.003 0.000 HIS A1626 PHE 0.029 0.001 PHE A1663 TYR 0.014 0.001 TYR A 754 ARG 0.002 0.000 ARG A 565 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 114 time to evaluate : 1.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 MET cc_start: 0.9164 (ptp) cc_final: 0.8946 (ppp) REVERT: A 449 TRP cc_start: 0.7626 (m100) cc_final: 0.7115 (m100) REVERT: A 502 MET cc_start: 0.8454 (tmm) cc_final: 0.8188 (tmm) REVERT: A 640 MET cc_start: 0.9286 (tpp) cc_final: 0.8850 (tpp) REVERT: A 644 MET cc_start: 0.8837 (tpp) cc_final: 0.8451 (tpp) REVERT: A 755 PHE cc_start: 0.8182 (OUTLIER) cc_final: 0.7849 (t80) REVERT: A 1357 PHE cc_start: 0.8336 (m-80) cc_final: 0.7974 (m-10) REVERT: A 1419 MET cc_start: 0.7802 (pmm) cc_final: 0.7473 (pmm) REVERT: A 1446 MET cc_start: 0.7335 (pmm) cc_final: 0.6973 (pmm) REVERT: A 1456 MET cc_start: 0.8823 (tpp) cc_final: 0.8592 (tpt) REVERT: A 1524 LYS cc_start: 0.7113 (mttt) cc_final: 0.6108 (tppt) REVERT: A 1656 LEU cc_start: 0.8903 (tt) cc_final: 0.8468 (pp) REVERT: A 1760 PHE cc_start: 0.8046 (OUTLIER) cc_final: 0.7829 (m-80) outliers start: 36 outliers final: 28 residues processed: 143 average time/residue: 0.2171 time to fit residues: 50.3341 Evaluate side-chains 137 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 107 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 347 TYR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 754 TYR Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 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 1721 PHE Chi-restraints excluded: chain A residue 1740 LEU Chi-restraints excluded: chain A residue 1760 PHE 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 149 optimal weight: 10.0000 chunk 159 optimal weight: 6.9990 chunk 164 optimal weight: 0.6980 chunk 96 optimal weight: 20.0000 chunk 69 optimal weight: 20.0000 chunk 125 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 144 optimal weight: 20.0000 chunk 151 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 169 optimal weight: 9.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13585 Z= 0.189 Angle : 0.608 11.416 18528 Z= 0.296 Chirality : 0.043 0.453 2168 Planarity : 0.003 0.040 2344 Dihedral : 5.518 55.183 2138 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.69 % Allowed : 21.01 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.39 (0.21), residues: 1756 helix: 1.95 (0.17), residues: 986 sheet: -1.20 (0.41), residues: 169 loop : -2.30 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 533 HIS 0.002 0.001 HIS A2006 PHE 0.030 0.001 PHE A 36 TYR 0.014 0.001 TYR A 754 ARG 0.002 0.000 ARG A 565 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 113 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 TRP cc_start: 0.7629 (m100) cc_final: 0.7155 (m100) REVERT: A 640 MET cc_start: 0.9272 (tpp) cc_final: 0.8811 (tpp) REVERT: A 644 MET cc_start: 0.8857 (tpp) cc_final: 0.8501 (tpp) REVERT: A 755 PHE cc_start: 0.8184 (OUTLIER) cc_final: 0.7854 (t80) REVERT: A 1357 PHE cc_start: 0.8311 (m-80) cc_final: 0.7953 (m-10) REVERT: A 1419 MET cc_start: 0.7788 (pmm) cc_final: 0.7445 (pmm) REVERT: A 1446 MET cc_start: 0.7319 (pmm) cc_final: 0.6941 (pmm) REVERT: A 1456 MET cc_start: 0.8816 (tpp) cc_final: 0.8550 (tpt) REVERT: A 1524 LYS cc_start: 0.7149 (mttt) cc_final: 0.6146 (tppt) REVERT: A 1656 LEU cc_start: 0.8918 (tt) cc_final: 0.8468 (pp) REVERT: A 1760 PHE cc_start: 0.8063 (OUTLIER) cc_final: 0.7829 (m-80) outliers start: 33 outliers final: 29 residues processed: 140 average time/residue: 0.2162 time to fit residues: 48.2665 Evaluate side-chains 137 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 106 time to evaluate : 1.500 ------------------------------------------------------------------------------- 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 548 LEU Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 754 TYR Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 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 1071 ILE Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1358 VAL Chi-restraints excluded: chain A residue 1414 PHE Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1721 PHE Chi-restraints excluded: chain A residue 1740 LEU Chi-restraints excluded: chain A residue 1760 PHE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 103 optimal weight: 0.9990 chunk 80 optimal weight: 8.9990 chunk 117 optimal weight: 0.8980 chunk 177 optimal weight: 10.0000 chunk 163 optimal weight: 0.9980 chunk 141 optimal weight: 0.6980 chunk 14 optimal weight: 6.9990 chunk 109 optimal weight: 6.9990 chunk 86 optimal weight: 8.9990 chunk 112 optimal weight: 20.0000 chunk 150 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 13585 Z= 0.166 Angle : 0.622 12.010 18528 Z= 0.300 Chirality : 0.043 0.574 2168 Planarity : 0.003 0.041 2344 Dihedral : 5.444 54.203 2138 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.20 % Allowed : 22.23 % 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: 0.44 (0.21), residues: 1756 helix: 1.94 (0.17), residues: 991 sheet: -1.11 (0.41), residues: 169 loop : -2.26 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1705 HIS 0.002 0.000 HIS A1626 PHE 0.026 0.001 PHE A 36 TYR 0.012 0.001 TYR A 754 ARG 0.002 0.000 ARG A 565 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 449 TRP cc_start: 0.7451 (m100) cc_final: 0.7088 (m100) REVERT: A 502 MET cc_start: 0.8496 (tmm) cc_final: 0.8121 (tmm) REVERT: A 640 MET cc_start: 0.9257 (tpp) cc_final: 0.8805 (tpp) REVERT: A 644 MET cc_start: 0.8844 (tpp) cc_final: 0.8496 (tpp) REVERT: A 755 PHE cc_start: 0.8104 (OUTLIER) cc_final: 0.7862 (t80) REVERT: A 987 MET cc_start: 0.8531 (ptp) cc_final: 0.8128 (ppp) REVERT: A 1357 PHE cc_start: 0.8286 (m-80) cc_final: 0.7925 (m-10) REVERT: A 1419 MET cc_start: 0.7740 (pmm) cc_final: 0.7370 (pmm) REVERT: A 1446 MET cc_start: 0.7277 (pmm) cc_final: 0.6903 (pmm) REVERT: A 1456 MET cc_start: 0.8793 (tpp) cc_final: 0.8513 (tpt) REVERT: A 1524 LYS cc_start: 0.7041 (mttt) cc_final: 0.6064 (tppt) outliers start: 27 outliers final: 24 residues processed: 134 average time/residue: 0.2107 time to fit residues: 45.6850 Evaluate side-chains 134 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 TYR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 754 TYR Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1071 ILE Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1358 VAL Chi-restraints excluded: chain A residue 1414 PHE Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1721 PHE Chi-restraints excluded: chain A residue 1740 LEU Chi-restraints excluded: chain A residue 1807 PHE Chi-restraints excluded: chain A residue 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 43 optimal weight: 2.9990 chunk 130 optimal weight: 0.1980 chunk 20 optimal weight: 7.9990 chunk 39 optimal weight: 7.9990 chunk 141 optimal weight: 0.0770 chunk 59 optimal weight: 0.7980 chunk 145 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 8 optimal weight: 0.0070 overall best weight: 0.3756 ------------------------------------------------------------------------------- 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 = 0.3318 r_free = 0.3318 target = 0.073076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.058786 restraints weight = 55114.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.060594 restraints weight = 29306.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.061760 restraints weight = 19834.074| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13585 Z= 0.147 Angle : 0.607 11.941 18528 Z= 0.290 Chirality : 0.042 0.462 2168 Planarity : 0.003 0.041 2344 Dihedral : 5.289 54.109 2138 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.20 % Allowed : 22.39 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.21), residues: 1756 helix: 1.98 (0.17), residues: 991 sheet: -0.98 (0.42), residues: 167 loop : -2.24 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1705 HIS 0.002 0.000 HIS A 55 PHE 0.024 0.001 PHE A1663 TYR 0.011 0.001 TYR A 770 ARG 0.002 0.000 ARG A 565 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2499.89 seconds wall clock time: 46 minutes 57.64 seconds (2817.64 seconds total)