Starting phenix.real_space_refine on Thu Jun 12 10:15:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tbz_25802/06_2025/7tbz_25802.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tbz_25802/06_2025/7tbz_25802.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tbz_25802/06_2025/7tbz_25802.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tbz_25802/06_2025/7tbz_25802.map" model { file = "/net/cci-nas-00/data/ceres_data/7tbz_25802/06_2025/7tbz_25802.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tbz_25802/06_2025/7tbz_25802.cif" } resolution = 4.3 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 70 5.16 5 C 8585 2.51 5 N 2233 2.21 5 O 2387 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 13275 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 13130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1788, 13130 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: 8.30, per 1000 atoms: 0.63 Number of scatterers: 13275 At special positions: 0 Unit cell: (81.674, 100.198, 215.552, 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 70 16.00 O 2387 8.00 N 2233 7.00 C 8585 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=2.04 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 A2601 " - " ASN A1637 " " NAG A2602 " - " ASN A 98 " " NAG B 1 " - " ASN A 400 " " NAG C 1 " - " ASN A1504 " Time building additional restraints: 3.84 Conformation dependent library (CDL) restraints added in 1.7 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 59.7% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.00 Creating SS restraints... Processing helix chain 'A' and resid 3 through 22 removed outlier: 3.676A pdb=" N GLN A 21 " --> pdb=" O PHE A 17 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N THR A 22 " --> pdb=" O ARG A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 45 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: 3.539A 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 117 Processing helix chain 'A' and resid 120 through 134 Processing helix chain 'A' and resid 252 through 273 removed outlier: 4.280A pdb=" N GLU A 256 " --> pdb=" O LYS A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 289 Processing helix chain 'A' and resid 297 through 309 Processing helix chain 'A' and resid 346 through 350 Processing helix chain 'A' and resid 352 through 365 removed outlier: 3.841A 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: 4.398A pdb=" N PHE A 409 " --> pdb=" O LEU A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 429 removed outlier: 3.621A pdb=" N MET A 415 " --> pdb=" O ASP A 411 " (cutoff:3.500A) Proline residue: A 421 - end of helix Processing helix chain 'A' and resid 430 through 441 removed outlier: 3.664A pdb=" N ASP A 441 " --> pdb=" O ARG A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 454 removed outlier: 3.663A pdb=" N PHE A 448 " --> pdb=" O ASP A 444 " (cutoff:3.500A) removed outlier: 3.629A 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: 3.758A pdb=" N ALA A 487 " --> pdb=" O THR A 483 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N CYS A 504 " --> pdb=" O ARG A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 529 Processing helix chain 'A' and resid 559 through 563 removed outlier: 3.730A pdb=" N ASN A 562 " --> pdb=" O ASP A 559 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL A 563 " --> pdb=" O ILE A 560 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 559 through 563' Processing helix chain 'A' and resid 586 through 591 removed outlier: 3.530A pdb=" N TRP A 590 " --> pdb=" O MET A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 609 Processing helix chain 'A' and resid 630 through 639 Processing helix chain 'A' and resid 640 through 665 removed outlier: 4.775A pdb=" N ALA A 647 " --> pdb=" O PHE A 643 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N TRP A 648 " --> pdb=" O MET A 644 " (cutoff:3.500A) removed outlier: 3.558A 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: 3.746A 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: 3.773A pdb=" N VAL A 718 " --> pdb=" O ASP A 714 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N THR A 738 " --> pdb=" O PHE A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 767 removed outlier: 4.704A pdb=" N GLY A 751 " --> pdb=" O ALA A 747 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ILE A 752 " --> pdb=" O ALA A 748 " (cutoff:3.500A) Proline residue: A 760 - end of helix removed outlier: 4.032A pdb=" N ALA A 766 " --> pdb=" O VAL A 762 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N TRP A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 771 removed outlier: 3.930A pdb=" N VAL A 771 " --> pdb=" O ARG A 768 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 768 through 771' Processing helix chain 'A' and resid 772 through 780 Processing helix chain 'A' and resid 782 through 799 removed outlier: 3.672A pdb=" N ALA A 786 " --> pdb=" O LEU A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 846 removed outlier: 3.994A pdb=" N ALA A 844 " --> pdb=" O TRP A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 947 removed outlier: 3.537A pdb=" N SER A 944 " --> pdb=" O THR A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 975 removed outlier: 4.028A 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: 3.924A 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: 3.890A 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: 3.760A pdb=" N ALA A1094 " --> pdb=" O HIS A1090 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1122 removed outlier: 3.989A 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: 3.763A pdb=" N GLU A1220 " --> pdb=" O GLY A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1243 through 1252 removed outlier: 4.029A 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 1366 removed outlier: 4.393A 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: 3.587A pdb=" N MET A1383 " --> pdb=" O GLN A1380 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TYR A1384 " --> pdb=" O PRO A1381 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1380 through 1384' 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 removed outlier: 3.541A pdb=" N HIS A1561 " --> pdb=" O GLN A1557 " (cutoff:3.500A) Processing helix chain 'A' and resid 1570 through 1582 Processing helix chain 'A' and resid 1601 through 1618 Processing helix chain 'A' and resid 1639 through 1650 removed outlier: 3.533A pdb=" N THR A1650 " --> pdb=" O VAL A1646 " (cutoff:3.500A) Processing helix chain 'A' and resid 1650 through 1666 removed outlier: 3.791A pdb=" N ASP A1654 " --> pdb=" O THR A1650 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N CYS A1660 " --> pdb=" O LEU A1656 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A1661 " --> pdb=" O VAL A1657 " (cutoff:3.500A) Processing helix chain 'A' and resid 1667 through 1679 removed outlier: 3.971A pdb=" N SER A1671 " --> pdb=" O PHE A1667 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE A1672 " --> pdb=" O VAL A1668 " (cutoff:3.500A) Processing helix chain 'A' and resid 1684 through 1691 removed outlier: 4.038A pdb=" N SER A1691 " --> pdb=" O LEU A1687 " (cutoff:3.500A) Processing helix chain 'A' and resid 1694 through 1724 removed outlier: 4.158A pdb=" N VAL A1712 " --> pdb=" O CYS A1708 " (cutoff:3.500A) Proline residue: A1713 - end of helix removed outlier: 3.955A pdb=" N PHE A1724 " --> pdb=" O ILE A1720 " (cutoff:3.500A) Processing helix chain 'A' and resid 1726 through 1731 removed outlier: 3.754A 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 1784 removed outlier: 4.012A 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: 3.651A pdb=" N GLN A1871 " --> pdb=" O THR A1867 " (cutoff:3.500A) removed outlier: 3.696A 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 Processing helix chain 'A' and resid 2020 through 2032 removed outlier: 3.641A 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: 4.114A pdb=" N CYS A2107 " --> pdb=" O SER A2103 " (cutoff:3.500A) Processing helix chain 'A' and resid 2127 through 2135 Processing helix chain 'A' and resid 2152 through 2163 removed outlier: 3.959A pdb=" N GLN A2156 " --> pdb=" O LEU A2152 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE A2163 " --> pdb=" O PHE A2159 " (cutoff:3.500A) Processing helix chain 'A' and resid 2186 through 2201 removed outlier: 4.487A pdb=" N LYS A2199 " --> pdb=" O SER A2195 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ARG A2200 " --> pdb=" O GLN A2196 " (cutoff:3.500A) Processing helix chain 'A' and resid 2212 through 2223 removed outlier: 3.806A pdb=" N VAL A2216 " --> pdb=" O THR A2212 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP A2223 " --> pdb=" O ASN A2219 " (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: 6.430A pdb=" N GLY A 616 " --> pdb=" O VAL A1590 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N VAL A1592 " --> pdb=" O GLY A 616 " (cutoff:3.500A) removed outlier: 6.674A 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: 6.149A pdb=" N GLN A 620 " --> pdb=" O PHE A1594 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N TYR A1388 " --> pdb=" O GLY A1533 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N PHE A1535 " --> pdb=" O TYR A1388 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N PHE A1390 " --> pdb=" O PHE A1535 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N LEU A1537 " --> pdb=" O PHE A1390 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N SER A1392 " --> pdb=" O LEU A1537 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N VAL A1539 " --> pdb=" O SER A1392 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A1391 " --> pdb=" O GLN A1498 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR A1437 " --> pdb=" O GLN A1488 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 383 through 385 removed outlier: 6.466A 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: 6.351A pdb=" N VAL A 552 " --> pdb=" O THR A1630 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N PHE A1632 " --> pdb=" O VAL A 552 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N TYR A 554 " --> pdb=" O PHE A1632 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ALA A1631 " --> pdb=" O LEU A1379 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 922 through 924 removed outlier: 3.525A pdb=" N VAL A 899 " --> pdb=" O PHE A 923 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER A 900 " --> pdb=" O TYR A 958 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR A 958 " --> pdb=" O SER A 900 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 929 through 930 removed outlier: 7.048A pdb=" N THR A 929 " --> pdb=" O LEU A1086 " (cutoff:3.500A) removed outlier: 7.401A 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: 5.954A pdb=" N SER A1105 " --> pdb=" O LEU A1109 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N LEU A1109 " --> pdb=" O SER A1105 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1195 through 1200 removed outlier: 6.415A pdb=" N LEU A1196 " --> pdb=" O VAL A1207 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL A1207 " --> pdb=" O LEU A1196 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER A1236 " --> pdb=" O VAL A1131 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1944 through 1946 removed outlier: 7.230A pdb=" N LEU A1945 " --> pdb=" O MET A2117 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1988 through 1990 removed outlier: 5.857A pdb=" N GLY A1989 " --> pdb=" O PHE A2067 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL A2066 " --> pdb=" O VAL A2098 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 2167 through 2171 removed outlier: 3.813A pdb=" N LYS A2169 " --> pdb=" O GLN A2177 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N GLN A2177 " --> pdb=" O LYS A2169 " (cutoff:3.500A) 743 hydrogen bonds defined for protein. 2160 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: 5.82 Time building geometry restraints manager: 4.50 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: 3198 1.46 - 1.58: 6028 1.58 - 1.70: 0 1.70 - 1.81: 111 Bond restraints: 13578 Sorted by residual: bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 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 B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.57e+01 bond pdb=" C THR A 386 " pdb=" N PRO A 387 " ideal model delta sigma weight residual 1.331 1.360 -0.028 1.21e-02 6.83e+03 5.50e+00 bond pdb=" C1 NAG A2602 " pdb=" O5 NAG A2602 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.53e+00 bond pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.43e+00 ... (remaining 13573 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 18118 1.50 - 2.99: 290 2.99 - 4.49: 58 4.49 - 5.98: 42 5.98 - 7.48: 10 Bond angle restraints: 18518 Sorted by residual: angle pdb=" N VAL A 380 " pdb=" CA VAL A 380 " pdb=" C VAL A 380 " ideal model delta sigma weight residual 113.53 108.88 4.65 9.80e-01 1.04e+00 2.25e+01 angle pdb=" CA VAL A 380 " pdb=" C VAL A 380 " pdb=" N GLY A 381 " ideal model delta sigma weight residual 119.31 116.53 2.78 1.15e+00 7.56e-01 5.85e+00 angle pdb=" C HIS A 934 " pdb=" N ASN A 935 " pdb=" CA ASN A 935 " ideal model delta sigma weight residual 121.54 126.14 -4.60 1.91e+00 2.74e-01 5.79e+00 angle pdb=" C LYS A 613 " pdb=" N LYS A 614 " pdb=" CA LYS A 614 " ideal model delta sigma weight residual 121.54 125.93 -4.39 1.91e+00 2.74e-01 5.29e+00 angle pdb=" C20 CLR A2603 " pdb=" C22 CLR A2603 " pdb=" C23 CLR A2603 " ideal model delta sigma weight residual 115.57 109.24 6.33 3.00e+00 1.11e-01 4.45e+00 ... (remaining 18513 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.43: 7720 23.43 - 46.87: 325 46.87 - 70.30: 33 70.30 - 93.74: 28 93.74 - 117.17: 18 Dihedral angle restraints: 8124 sinusoidal: 2951 harmonic: 5173 Sorted by residual: dihedral pdb=" CB CYS A 626 " pdb=" SG CYS A 626 " pdb=" SG CYS A1465 " pdb=" CB CYS A1465 " ideal model delta sinusoidal sigma weight residual 93.00 175.96 -82.96 1 1.00e+01 1.00e-02 8.42e+01 dihedral pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " pdb=" SG CYS A 81 " pdb=" CB CYS A 81 " ideal model delta sinusoidal sigma weight residual 93.00 22.31 70.69 1 1.00e+01 1.00e-02 6.43e+01 dihedral pdb=" CA PRO A 625 " pdb=" C PRO A 625 " pdb=" N CYS A 626 " pdb=" CA CYS A 626 " ideal model delta harmonic sigma weight residual 180.00 155.95 24.05 0 5.00e+00 4.00e-02 2.31e+01 ... (remaining 8121 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1966 0.068 - 0.135: 192 0.135 - 0.203: 4 0.203 - 0.271: 2 0.271 - 0.338: 4 Chirality restraints: 2168 Sorted by residual: chirality pdb=" C14 CLR A2603 " pdb=" C13 CLR A2603 " pdb=" C15 CLR A2603 " pdb=" C8 CLR A2603 " both_signs ideal model delta sigma weight residual False -2.32 -2.66 0.34 2.00e-01 2.50e+01 2.86e+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 -2.55 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C5 BMA C 5 " pdb=" C4 BMA C 5 " pdb=" C6 BMA C 5 " pdb=" O5 BMA C 5 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 2165 not shown) Planarity restraints: 2347 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 759 " 0.035 5.00e-02 4.00e+02 5.25e-02 4.42e+00 pdb=" N PRO A 760 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 760 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 760 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A2076 " -0.021 5.00e-02 4.00e+02 3.21e-02 1.64e+00 pdb=" N PRO A2077 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO A2077 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A2077 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A1721 " -0.008 2.00e-02 2.50e+03 8.90e-03 1.39e+00 pdb=" CG PHE A1721 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE A1721 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A1721 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A1721 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A1721 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A1721 " -0.000 2.00e-02 2.50e+03 ... (remaining 2344 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1388 2.75 - 3.28: 13499 3.28 - 3.82: 21717 3.82 - 4.36: 23031 4.36 - 4.90: 40112 Nonbonded interactions: 99747 Sorted by model distance: nonbonded pdb=" OD2 ASP A1706 " pdb=" OH TYR A1754 " model vdw 2.207 3.040 nonbonded pdb=" OG1 THR A1493 " pdb=" OD1 ASP A1495 " model vdw 2.255 3.040 nonbonded pdb=" OE1 GLU A 925 " pdb=" OG1 THR A1083 " model vdw 2.256 3.040 nonbonded pdb=" NE2 GLN A1464 " pdb=" O VAL A1476 " model vdw 2.267 3.120 nonbonded pdb=" OD2 ASP A1507 " pdb=" O6 NAG C 1 " model vdw 2.287 3.040 ... (remaining 99742 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: 1.860 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: 0.610 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 35.710 Find NCS groups from input model: 0.170 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: 0.010 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 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 : 0.002 0.081 13593 Z= 0.129 Angle : 0.567 7.477 18557 Z= 0.282 Chirality : 0.042 0.338 2168 Planarity : 0.003 0.053 2343 Dihedral : 14.926 117.173 4760 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.76 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % 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: -2.61 (0.18), residues: 1756 helix: -0.64 (0.15), residues: 978 sheet: -1.91 (0.36), residues: 166 loop : -3.44 (0.20), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.000 TRP A1705 HIS 0.001 0.000 HIS A1626 PHE 0.021 0.001 PHE A1721 TYR 0.008 0.001 TYR A 793 ARG 0.003 0.000 ARG A1336 Details of bonding type rmsd link_NAG-ASN : bond 0.00323 ( 4) link_NAG-ASN : angle 1.81778 ( 12) link_BETA1-4 : bond 0.00479 ( 3) link_BETA1-4 : angle 1.10609 ( 9) hydrogen bonds : bond 0.12998 ( 743) hydrogen bonds : angle 4.93136 ( 2160) link_BETA1-6 : bond 0.00395 ( 1) link_BETA1-6 : angle 1.21662 ( 3) SS BOND : bond 0.00286 ( 6) SS BOND : angle 1.12294 ( 12) link_BETA1-3 : bond 0.00281 ( 1) link_BETA1-3 : angle 1.27687 ( 3) covalent geometry : bond 0.00245 (13578) covalent geometry : angle 0.56437 (18518) *********************** 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 260 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 1.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.9676 (tt) cc_final: 0.9475 (pp) REVERT: A 18 ARG cc_start: 0.9263 (mmt90) cc_final: 0.8823 (mmm160) REVERT: A 112 LEU cc_start: 0.9422 (tt) cc_final: 0.8996 (mp) REVERT: A 286 MET cc_start: 0.9409 (ptp) cc_final: 0.9029 (ptt) REVERT: A 396 MET cc_start: 0.9570 (mmm) cc_final: 0.9341 (mmm) REVERT: A 605 ILE cc_start: 0.9628 (mm) cc_final: 0.9319 (tp) REVERT: A 622 MET cc_start: 0.8335 (mtt) cc_final: 0.7739 (mtt) REVERT: A 640 MET cc_start: 0.9173 (tpp) cc_final: 0.8835 (tpp) REVERT: A 683 PHE cc_start: 0.8936 (t80) cc_final: 0.8596 (m-10) REVERT: A 724 VAL cc_start: 0.8793 (m) cc_final: 0.8559 (p) REVERT: A 735 LEU cc_start: 0.8767 (tp) cc_final: 0.8495 (tp) REVERT: A 827 MET cc_start: 0.8625 (tpt) cc_final: 0.8355 (tpp) REVERT: A 839 THR cc_start: 0.7987 (m) cc_final: 0.7733 (m) REVERT: A 921 LEU cc_start: 0.9354 (tt) cc_final: 0.8924 (mm) REVERT: A 927 GLN cc_start: 0.9132 (mt0) cc_final: 0.8902 (mp10) REVERT: A 1037 MET cc_start: 0.9419 (mmm) cc_final: 0.9190 (mpp) REVERT: A 1086 LEU cc_start: 0.9257 (mt) cc_final: 0.8958 (tt) REVERT: A 1333 LEU cc_start: 0.9326 (mp) cc_final: 0.9125 (mp) REVERT: A 1610 ASN cc_start: 0.9327 (m-40) cc_final: 0.8977 (m-40) REVERT: A 1662 ILE cc_start: 0.9148 (mt) cc_final: 0.8883 (mt) REVERT: A 1665 MET cc_start: 0.9570 (tpp) cc_final: 0.9299 (tpp) REVERT: A 1707 MET cc_start: 0.9428 (mmm) cc_final: 0.9142 (mmp) REVERT: A 1710 TYR cc_start: 0.9025 (t80) cc_final: 0.8589 (t80) REVERT: A 1776 PHE cc_start: 0.9164 (t80) cc_final: 0.8823 (m-10) REVERT: A 1822 MET cc_start: 0.9319 (ttt) cc_final: 0.8876 (tmm) outliers start: 0 outliers final: 0 residues processed: 260 average time/residue: 0.2438 time to fit residues: 93.0909 Evaluate side-chains 155 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 1.491 ------------------------------------------------------------------------------- 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: 10.0000 chunk 134 optimal weight: 0.9990 chunk 74 optimal weight: 30.0000 chunk 46 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 chunk 103 optimal weight: 0.3980 chunk 161 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 52 HIS A 79 ASN A 551 HIS A 621 GLN A 820 ASN A1121 GLN A1327 GLN A1385 ASN A1422 ASN A1443 GLN A1515 GLN A1617 ASN ** A1642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1812 HIS ** A1825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.062350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.050547 restraints weight = 79405.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.051997 restraints weight = 50073.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.053158 restraints weight = 36484.483| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13593 Z= 0.114 Angle : 0.592 9.440 18557 Z= 0.283 Chirality : 0.041 0.218 2168 Planarity : 0.004 0.058 2343 Dihedral : 10.579 99.145 2137 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.08 % Allowed : 4.64 % Favored : 95.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.27 (0.20), residues: 1756 helix: 0.57 (0.17), residues: 979 sheet: -1.51 (0.39), residues: 165 loop : -3.05 (0.22), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1705 HIS 0.002 0.001 HIS A1626 PHE 0.026 0.001 PHE A 403 TYR 0.015 0.001 TYR A1754 ARG 0.005 0.000 ARG A 530 Details of bonding type rmsd link_NAG-ASN : bond 0.00287 ( 4) link_NAG-ASN : angle 1.82290 ( 12) link_BETA1-4 : bond 0.00304 ( 3) link_BETA1-4 : angle 2.79212 ( 9) hydrogen bonds : bond 0.03156 ( 743) hydrogen bonds : angle 3.76763 ( 2160) link_BETA1-6 : bond 0.00885 ( 1) link_BETA1-6 : angle 2.75401 ( 3) SS BOND : bond 0.00386 ( 6) SS BOND : angle 1.22531 ( 12) link_BETA1-3 : bond 0.00789 ( 1) link_BETA1-3 : angle 2.36305 ( 3) covalent geometry : bond 0.00246 (13578) covalent geometry : angle 0.58491 (18518) *********************** 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 187 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 186 time to evaluate : 1.663 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.9668 (tt) cc_final: 0.9455 (pp) REVERT: A 18 ARG cc_start: 0.9113 (mmt90) cc_final: 0.8678 (mmm160) REVERT: A 112 LEU cc_start: 0.9414 (tt) cc_final: 0.9009 (mp) REVERT: A 275 MET cc_start: 0.7444 (ppp) cc_final: 0.5992 (ppp) REVERT: A 286 MET cc_start: 0.9499 (ptp) cc_final: 0.8923 (ptt) REVERT: A 558 MET cc_start: 0.8019 (mtp) cc_final: 0.7749 (mtm) REVERT: A 622 MET cc_start: 0.8344 (mtt) cc_final: 0.7817 (mtt) REVERT: A 683 PHE cc_start: 0.8994 (t80) cc_final: 0.8610 (m-10) REVERT: A 724 VAL cc_start: 0.8960 (m) cc_final: 0.8758 (p) REVERT: A 735 LEU cc_start: 0.9009 (tp) cc_final: 0.8742 (tp) REVERT: A 827 MET cc_start: 0.8667 (tpt) cc_final: 0.8454 (tpp) REVERT: A 921 LEU cc_start: 0.9262 (tt) cc_final: 0.8889 (mm) REVERT: A 987 MET cc_start: 0.8710 (mpp) cc_final: 0.8367 (mpp) REVERT: A 1086 LEU cc_start: 0.9326 (mt) cc_final: 0.9085 (tt) REVERT: A 1473 MET cc_start: 0.9007 (tmm) cc_final: 0.8734 (tmm) REVERT: A 1707 MET cc_start: 0.9494 (mmm) cc_final: 0.9135 (mmp) REVERT: A 1708 CYS cc_start: 0.9415 (m) cc_final: 0.9025 (p) REVERT: A 1710 TYR cc_start: 0.9065 (t80) cc_final: 0.8660 (t80) REVERT: A 1822 MET cc_start: 0.9360 (ttt) cc_final: 0.8789 (tmm) REVERT: A 2057 MET cc_start: 0.9022 (mmt) cc_final: 0.8541 (mmt) outliers start: 1 outliers final: 0 residues processed: 187 average time/residue: 0.2015 time to fit residues: 60.7497 Evaluate side-chains 139 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 145 optimal weight: 2.9990 chunk 108 optimal weight: 30.0000 chunk 165 optimal weight: 8.9990 chunk 172 optimal weight: 5.9990 chunk 93 optimal weight: 40.0000 chunk 159 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 chunk 115 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 175 optimal weight: 7.9990 chunk 119 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 744 ASN A1121 GLN A1600 HIS ** A1619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1641 GLN ** A1642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2049 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.054243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.043188 restraints weight = 86813.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.044450 restraints weight = 53678.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.045360 restraints weight = 38621.233| |-----------------------------------------------------------------------------| r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 13593 Z= 0.279 Angle : 0.786 11.833 18557 Z= 0.399 Chirality : 0.045 0.244 2168 Planarity : 0.005 0.054 2343 Dihedral : 8.295 88.042 2137 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.69 % Favored : 94.25 % Rotamer: Outliers : 0.16 % Allowed : 7.25 % Favored : 92.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.71 (0.20), residues: 1756 helix: 0.92 (0.17), residues: 992 sheet: -1.37 (0.44), residues: 148 loop : -2.62 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 533 HIS 0.006 0.002 HIS A1600 PHE 0.030 0.002 PHE A 683 TYR 0.023 0.002 TYR A 754 ARG 0.036 0.001 ARG A1572 Details of bonding type rmsd link_NAG-ASN : bond 0.00439 ( 4) link_NAG-ASN : angle 1.68984 ( 12) link_BETA1-4 : bond 0.00695 ( 3) link_BETA1-4 : angle 3.48373 ( 9) hydrogen bonds : bond 0.04181 ( 743) hydrogen bonds : angle 4.22599 ( 2160) link_BETA1-6 : bond 0.02231 ( 1) link_BETA1-6 : angle 4.71109 ( 3) SS BOND : bond 0.00606 ( 6) SS BOND : angle 1.57649 ( 12) link_BETA1-3 : bond 0.00408 ( 1) link_BETA1-3 : angle 2.59766 ( 3) covalent geometry : bond 0.00577 (13578) covalent geometry : angle 0.77804 (18518) *********************** 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 155 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 153 time to evaluate : 1.474 Fit side-chains REVERT: A 275 MET cc_start: 0.8021 (ppp) cc_final: 0.7319 (ppp) REVERT: A 286 MET cc_start: 0.9489 (ptp) cc_final: 0.8995 (ptt) REVERT: A 396 MET cc_start: 0.9418 (mmm) cc_final: 0.9137 (mmm) REVERT: A 622 MET cc_start: 0.9067 (mtt) cc_final: 0.8558 (mtt) REVERT: A 827 MET cc_start: 0.8772 (tpt) cc_final: 0.8430 (tpp) REVERT: A 830 PHE cc_start: 0.9182 (t80) cc_final: 0.8616 (t80) REVERT: A 987 MET cc_start: 0.9106 (mpp) cc_final: 0.8786 (mpp) REVERT: A 1057 ASP cc_start: 0.8613 (t0) cc_final: 0.8016 (t0) REVERT: A 1456 MET cc_start: 0.8890 (tpt) cc_final: 0.8673 (tpp) REVERT: A 1468 ASP cc_start: 0.8424 (t0) cc_final: 0.8058 (p0) REVERT: A 1473 MET cc_start: 0.9197 (tmm) cc_final: 0.8951 (tmm) REVERT: A 1656 LEU cc_start: 0.9204 (tt) cc_final: 0.8951 (pp) REVERT: A 1665 MET cc_start: 0.9453 (tpp) cc_final: 0.9201 (tpp) REVERT: A 1707 MET cc_start: 0.9448 (mmm) cc_final: 0.9087 (mmp) REVERT: A 1710 TYR cc_start: 0.9287 (t80) cc_final: 0.8997 (t80) REVERT: A 1744 LEU cc_start: 0.9563 (mm) cc_final: 0.9302 (mm) REVERT: A 1776 PHE cc_start: 0.9193 (t80) cc_final: 0.8877 (m-10) REVERT: A 1822 MET cc_start: 0.9294 (ttt) cc_final: 0.8793 (tmm) REVERT: A 1856 MET cc_start: 0.9056 (mtp) cc_final: 0.8319 (ttm) REVERT: A 2057 MET cc_start: 0.9262 (mmt) cc_final: 0.8771 (mmt) outliers start: 2 outliers final: 1 residues processed: 154 average time/residue: 0.2028 time to fit residues: 51.5445 Evaluate side-chains 110 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 158 optimal weight: 0.7980 chunk 108 optimal weight: 0.0670 chunk 137 optimal weight: 4.9990 chunk 28 optimal weight: 20.0000 chunk 40 optimal weight: 0.8980 chunk 151 optimal weight: 1.9990 chunk 152 optimal weight: 40.0000 chunk 75 optimal weight: 0.1980 chunk 22 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 128 optimal weight: 7.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1610 ASN ** A1642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1825 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.056948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.045729 restraints weight = 83119.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.047163 restraints weight = 50939.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.048127 restraints weight = 36123.403| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 13593 Z= 0.114 Angle : 0.621 11.292 18557 Z= 0.297 Chirality : 0.042 0.208 2168 Planarity : 0.004 0.057 2343 Dihedral : 7.043 67.485 2137 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % 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: -0.15 (0.21), residues: 1756 helix: 1.43 (0.17), residues: 988 sheet: -1.27 (0.43), residues: 152 loop : -2.43 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.001 TRP A 533 HIS 0.004 0.001 HIS A1626 PHE 0.032 0.001 PHE A 755 TYR 0.011 0.001 TYR A1745 ARG 0.010 0.000 ARG A1572 Details of bonding type rmsd link_NAG-ASN : bond 0.00616 ( 4) link_NAG-ASN : angle 1.99530 ( 12) link_BETA1-4 : bond 0.00651 ( 3) link_BETA1-4 : angle 3.61694 ( 9) hydrogen bonds : bond 0.03370 ( 743) hydrogen bonds : angle 3.68657 ( 2160) link_BETA1-6 : bond 0.00963 ( 1) link_BETA1-6 : angle 2.24138 ( 3) SS BOND : bond 0.00652 ( 6) SS BOND : angle 1.17720 ( 12) link_BETA1-3 : bond 0.00509 ( 1) link_BETA1-3 : angle 1.96006 ( 3) covalent geometry : bond 0.00246 (13578) covalent geometry : angle 0.61232 (18518) *********************** 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 162 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 1.633 Fit side-chains REVERT: A 112 LEU cc_start: 0.9153 (pp) cc_final: 0.8829 (mt) REVERT: A 275 MET cc_start: 0.8791 (ppp) cc_final: 0.8180 (ppp) REVERT: A 286 MET cc_start: 0.9503 (ptp) cc_final: 0.9165 (ptt) REVERT: A 622 MET cc_start: 0.9003 (mtt) cc_final: 0.8676 (mtt) REVERT: A 830 PHE cc_start: 0.9146 (t80) cc_final: 0.8786 (m-10) REVERT: A 987 MET cc_start: 0.9012 (mpp) cc_final: 0.8712 (mpp) REVERT: A 1468 ASP cc_start: 0.8294 (t0) cc_final: 0.7858 (p0) REVERT: A 1610 ASN cc_start: 0.9277 (m110) cc_final: 0.8802 (m110) REVERT: A 1656 LEU cc_start: 0.9162 (tt) cc_final: 0.8916 (pp) REVERT: A 1665 MET cc_start: 0.9450 (tpp) cc_final: 0.9167 (tpp) REVERT: A 1707 MET cc_start: 0.9357 (mmm) cc_final: 0.9003 (mmp) REVERT: A 1708 CYS cc_start: 0.9506 (m) cc_final: 0.9262 (m) REVERT: A 1744 LEU cc_start: 0.9499 (mm) cc_final: 0.9244 (mm) REVERT: A 1776 PHE cc_start: 0.9181 (t80) cc_final: 0.8886 (m-10) REVERT: A 1822 MET cc_start: 0.9254 (ttt) cc_final: 0.8870 (tmm) REVERT: A 1856 MET cc_start: 0.8970 (mtp) cc_final: 0.8171 (ttm) REVERT: A 2057 MET cc_start: 0.9184 (mmt) cc_final: 0.8674 (mmt) REVERT: A 2104 MET cc_start: 0.8332 (mmm) cc_final: 0.8076 (mtp) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.1986 time to fit residues: 52.1554 Evaluate side-chains 118 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 62 optimal weight: 1.9990 chunk 13 optimal weight: 0.3980 chunk 72 optimal weight: 7.9990 chunk 126 optimal weight: 3.9990 chunk 139 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 28 optimal weight: 20.0000 chunk 87 optimal weight: 10.0000 chunk 96 optimal weight: 20.0000 chunk 37 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1619 GLN A1688 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.055265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.044005 restraints weight = 83681.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.045373 restraints weight = 51801.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.046304 restraints weight = 36973.394| |-----------------------------------------------------------------------------| r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13593 Z= 0.136 Angle : 0.603 8.480 18557 Z= 0.298 Chirality : 0.041 0.215 2168 Planarity : 0.004 0.056 2343 Dihedral : 6.322 58.419 2137 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.08 % Allowed : 2.93 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.02 (0.21), residues: 1756 helix: 1.56 (0.17), residues: 989 sheet: -1.18 (0.43), residues: 152 loop : -2.34 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP A 533 HIS 0.003 0.001 HIS A1626 PHE 0.024 0.001 PHE A 403 TYR 0.014 0.001 TYR A 997 ARG 0.005 0.000 ARG A 530 Details of bonding type rmsd link_NAG-ASN : bond 0.00187 ( 4) link_NAG-ASN : angle 1.81968 ( 12) link_BETA1-4 : bond 0.00658 ( 3) link_BETA1-4 : angle 3.17811 ( 9) hydrogen bonds : bond 0.03375 ( 743) hydrogen bonds : angle 3.69591 ( 2160) link_BETA1-6 : bond 0.00872 ( 1) link_BETA1-6 : angle 1.91937 ( 3) SS BOND : bond 0.00595 ( 6) SS BOND : angle 1.38698 ( 12) link_BETA1-3 : bond 0.00523 ( 1) link_BETA1-3 : angle 1.94366 ( 3) covalent geometry : bond 0.00298 (13578) covalent geometry : angle 0.59529 (18518) *********************** 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 146 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 145 time to evaluate : 1.927 Fit side-chains revert: symmetry clash REVERT: A 7 LEU cc_start: 0.9706 (tt) cc_final: 0.9469 (pp) REVERT: A 286 MET cc_start: 0.9499 (ptp) cc_final: 0.9147 (ptt) REVERT: A 622 MET cc_start: 0.9082 (mtt) cc_final: 0.8679 (mtt) REVERT: A 674 MET cc_start: 0.9131 (ttt) cc_final: 0.8591 (tmm) REVERT: A 827 MET cc_start: 0.8791 (tpp) cc_final: 0.8066 (tpp) REVERT: A 830 PHE cc_start: 0.9187 (t80) cc_final: 0.8491 (t80) REVERT: A 987 MET cc_start: 0.9103 (mpp) cc_final: 0.8782 (mpp) REVERT: A 1456 MET cc_start: 0.8858 (tpt) cc_final: 0.8422 (tpt) REVERT: A 1468 ASP cc_start: 0.8349 (t0) cc_final: 0.7869 (p0) REVERT: A 1473 MET cc_start: 0.9240 (tmm) cc_final: 0.8971 (tmm) REVERT: A 1610 ASN cc_start: 0.9064 (m110) cc_final: 0.8623 (m110) REVERT: A 1665 MET cc_start: 0.9493 (tpp) cc_final: 0.9178 (tpp) REVERT: A 1707 MET cc_start: 0.9303 (mmm) cc_final: 0.8945 (mmp) REVERT: A 1776 PHE cc_start: 0.9184 (t80) cc_final: 0.8899 (m-10) REVERT: A 1822 MET cc_start: 0.9297 (ttt) cc_final: 0.8940 (tmm) REVERT: A 2057 MET cc_start: 0.9250 (mmt) cc_final: 0.8743 (mmt) outliers start: 1 outliers final: 0 residues processed: 146 average time/residue: 0.1854 time to fit residues: 44.4952 Evaluate side-chains 113 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 93 optimal weight: 30.0000 chunk 79 optimal weight: 6.9990 chunk 177 optimal weight: 9.9990 chunk 150 optimal weight: 7.9990 chunk 68 optimal weight: 40.0000 chunk 161 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 166 optimal weight: 8.9990 chunk 122 optimal weight: 10.0000 chunk 7 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 732 GLN ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1619 GLN ** A1642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.054167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.043312 restraints weight = 84664.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.044646 restraints weight = 51624.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.045538 restraints weight = 36666.595| |-----------------------------------------------------------------------------| r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13593 Z= 0.149 Angle : 0.609 7.422 18557 Z= 0.302 Chirality : 0.042 0.234 2168 Planarity : 0.004 0.053 2343 Dihedral : 5.974 53.703 2137 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.08 % Allowed : 2.85 % Favored : 97.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.21), residues: 1756 helix: 1.67 (0.17), residues: 989 sheet: -1.09 (0.43), residues: 152 loop : -2.27 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 533 HIS 0.004 0.001 HIS A1812 PHE 0.024 0.001 PHE A1329 TYR 0.013 0.001 TYR A 754 ARG 0.003 0.000 ARG A 672 Details of bonding type rmsd link_NAG-ASN : bond 0.00220 ( 4) link_NAG-ASN : angle 1.77662 ( 12) link_BETA1-4 : bond 0.00456 ( 3) link_BETA1-4 : angle 2.50257 ( 9) hydrogen bonds : bond 0.03371 ( 743) hydrogen bonds : angle 3.73840 ( 2160) link_BETA1-6 : bond 0.00464 ( 1) link_BETA1-6 : angle 1.48989 ( 3) SS BOND : bond 0.00319 ( 6) SS BOND : angle 1.36869 ( 12) link_BETA1-3 : bond 0.00512 ( 1) link_BETA1-3 : angle 1.93732 ( 3) covalent geometry : bond 0.00330 (13578) covalent geometry : angle 0.60407 (18518) *********************** 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 146 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 145 time to evaluate : 1.576 Fit side-chains REVERT: A 286 MET cc_start: 0.9487 (ptp) cc_final: 0.9142 (ptt) REVERT: A 359 MET cc_start: 0.9568 (ppp) cc_final: 0.9357 (ppp) REVERT: A 415 MET cc_start: 0.9476 (mmm) cc_final: 0.9209 (mmm) REVERT: A 622 MET cc_start: 0.9122 (mtt) cc_final: 0.8673 (mtt) REVERT: A 827 MET cc_start: 0.8780 (tpp) cc_final: 0.8226 (tpp) REVERT: A 830 PHE cc_start: 0.9199 (t80) cc_final: 0.8547 (t80) REVERT: A 987 MET cc_start: 0.9158 (mpp) cc_final: 0.8867 (mpp) REVERT: A 1456 MET cc_start: 0.8899 (tpt) cc_final: 0.8693 (tpp) REVERT: A 1468 ASP cc_start: 0.8314 (t0) cc_final: 0.7827 (p0) REVERT: A 1473 MET cc_start: 0.9313 (tmm) cc_final: 0.9027 (tmm) REVERT: A 1610 ASN cc_start: 0.8976 (m110) cc_final: 0.8588 (m110) REVERT: A 1665 MET cc_start: 0.9518 (tpp) cc_final: 0.9210 (tpp) REVERT: A 1707 MET cc_start: 0.9259 (mmm) cc_final: 0.8909 (mmp) REVERT: A 1716 LEU cc_start: 0.9162 (tt) cc_final: 0.8836 (mm) REVERT: A 1776 PHE cc_start: 0.9193 (t80) cc_final: 0.8915 (m-10) REVERT: A 1822 MET cc_start: 0.9294 (ttt) cc_final: 0.8977 (tmm) REVERT: A 2057 MET cc_start: 0.9234 (mmt) cc_final: 0.8739 (mmt) outliers start: 1 outliers final: 0 residues processed: 146 average time/residue: 0.1951 time to fit residues: 46.9497 Evaluate side-chains 108 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 16 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 chunk 159 optimal weight: 8.9990 chunk 21 optimal weight: 0.9980 chunk 103 optimal weight: 0.0670 chunk 142 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 133 optimal weight: 7.9990 chunk 140 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 overall best weight: 2.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1619 GLN ** A1642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1688 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.054161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.043283 restraints weight = 84375.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.044630 restraints weight = 51460.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.045547 restraints weight = 36517.072| |-----------------------------------------------------------------------------| r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13593 Z= 0.137 Angle : 0.628 12.409 18557 Z= 0.309 Chirality : 0.043 0.296 2168 Planarity : 0.004 0.055 2343 Dihedral : 5.803 53.593 2137 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 0.08 % Allowed : 1.71 % Favored : 98.21 % 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: 0.14 (0.21), residues: 1756 helix: 1.62 (0.17), residues: 991 sheet: -1.08 (0.44), residues: 153 loop : -2.27 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.001 TRP A 533 HIS 0.003 0.001 HIS A1626 PHE 0.031 0.001 PHE A 755 TYR 0.010 0.001 TYR A1767 ARG 0.005 0.000 ARG A1572 Details of bonding type rmsd link_NAG-ASN : bond 0.00192 ( 4) link_NAG-ASN : angle 1.61240 ( 12) link_BETA1-4 : bond 0.00502 ( 3) link_BETA1-4 : angle 2.57163 ( 9) hydrogen bonds : bond 0.03389 ( 743) hydrogen bonds : angle 3.78158 ( 2160) link_BETA1-6 : bond 0.00779 ( 1) link_BETA1-6 : angle 1.44172 ( 3) SS BOND : bond 0.00549 ( 6) SS BOND : angle 1.45443 ( 12) link_BETA1-3 : bond 0.00415 ( 1) link_BETA1-3 : angle 1.79782 ( 3) covalent geometry : bond 0.00301 (13578) covalent geometry : angle 0.62249 (18518) *********************** 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 146 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 145 time to evaluate : 1.495 Fit side-chains revert: symmetry clash REVERT: A 286 MET cc_start: 0.9495 (ptp) cc_final: 0.9154 (ptt) REVERT: A 359 MET cc_start: 0.9574 (ppp) cc_final: 0.9362 (ppp) REVERT: A 415 MET cc_start: 0.9473 (mmm) cc_final: 0.9236 (mmm) REVERT: A 622 MET cc_start: 0.9064 (mtt) cc_final: 0.8684 (mtt) REVERT: A 674 MET cc_start: 0.9190 (ttt) cc_final: 0.8679 (tmm) REVERT: A 749 CYS cc_start: 0.8567 (m) cc_final: 0.8195 (t) REVERT: A 827 MET cc_start: 0.8758 (tpp) cc_final: 0.8235 (tpp) REVERT: A 830 PHE cc_start: 0.9200 (t80) cc_final: 0.8561 (t80) REVERT: A 987 MET cc_start: 0.9129 (mpp) cc_final: 0.8885 (mpp) REVERT: A 1419 MET cc_start: 0.7216 (pmm) cc_final: 0.6993 (pmm) REVERT: A 1456 MET cc_start: 0.8925 (tpt) cc_final: 0.8680 (tpp) REVERT: A 1468 ASP cc_start: 0.8350 (t0) cc_final: 0.7836 (p0) REVERT: A 1473 MET cc_start: 0.9332 (tmm) cc_final: 0.9031 (tmm) REVERT: A 1610 ASN cc_start: 0.8698 (m110) cc_final: 0.8441 (m-40) REVERT: A 1665 MET cc_start: 0.9537 (tpp) cc_final: 0.9250 (tpp) REVERT: A 1707 MET cc_start: 0.9210 (mmm) cc_final: 0.8850 (mmp) REVERT: A 1716 LEU cc_start: 0.9169 (tt) cc_final: 0.8867 (mm) REVERT: A 1753 MET cc_start: 0.9503 (mtm) cc_final: 0.9094 (mpp) REVERT: A 1776 PHE cc_start: 0.9187 (t80) cc_final: 0.8910 (m-10) REVERT: A 1822 MET cc_start: 0.9320 (ttt) cc_final: 0.9018 (tmm) REVERT: A 1856 MET cc_start: 0.8732 (ttm) cc_final: 0.8328 (ttm) REVERT: A 2057 MET cc_start: 0.9229 (mmt) cc_final: 0.8701 (mmt) REVERT: A 2067 PHE cc_start: 0.8779 (t80) cc_final: 0.8575 (t80) outliers start: 1 outliers final: 0 residues processed: 146 average time/residue: 0.2043 time to fit residues: 48.7210 Evaluate side-chains 105 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 19 optimal weight: 8.9990 chunk 151 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 105 optimal weight: 8.9990 chunk 163 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 chunk 117 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1619 GLN ** A1642 GLN ** 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 = 0.3144 r_free = 0.3144 target = 0.053704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.042964 restraints weight = 86561.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.044328 restraints weight = 52140.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.045175 restraints weight = 36360.309| |-----------------------------------------------------------------------------| r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.4586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 13593 Z= 0.147 Angle : 0.629 14.724 18557 Z= 0.308 Chirality : 0.042 0.215 2168 Planarity : 0.004 0.055 2343 Dihedral : 5.756 54.139 2137 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 0.08 % Allowed : 0.81 % Favored : 99.10 % 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: 1.67 (0.17), residues: 992 sheet: -1.02 (0.44), residues: 153 loop : -2.27 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.095 0.001 TRP A 533 HIS 0.003 0.001 HIS A1626 PHE 0.029 0.001 PHE A1329 TYR 0.008 0.001 TYR A1745 ARG 0.004 0.000 ARG A 530 Details of bonding type rmsd link_NAG-ASN : bond 0.00195 ( 4) link_NAG-ASN : angle 1.56007 ( 12) link_BETA1-4 : bond 0.00506 ( 3) link_BETA1-4 : angle 2.56774 ( 9) hydrogen bonds : bond 0.03374 ( 743) hydrogen bonds : angle 3.75084 ( 2160) link_BETA1-6 : bond 0.00679 ( 1) link_BETA1-6 : angle 1.43052 ( 3) SS BOND : bond 0.00419 ( 6) SS BOND : angle 1.49360 ( 12) link_BETA1-3 : bond 0.00489 ( 1) link_BETA1-3 : angle 1.83679 ( 3) covalent geometry : bond 0.00330 (13578) covalent geometry : angle 0.62366 (18518) *********************** 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 137 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 136 time to evaluate : 1.613 Fit side-chains REVERT: A 61 MET cc_start: 0.9209 (mmm) cc_final: 0.8814 (mmm) REVERT: A 286 MET cc_start: 0.9494 (ptp) cc_final: 0.9154 (ptt) REVERT: A 359 MET cc_start: 0.9587 (ppp) cc_final: 0.9374 (ppp) REVERT: A 396 MET cc_start: 0.9090 (mmm) cc_final: 0.8833 (mmm) REVERT: A 415 MET cc_start: 0.9465 (mmm) cc_final: 0.9198 (mmm) REVERT: A 622 MET cc_start: 0.9046 (mtt) cc_final: 0.8655 (mtt) REVERT: A 671 MET cc_start: 0.9645 (mmp) cc_final: 0.9390 (mmp) REVERT: A 674 MET cc_start: 0.9153 (ttt) cc_final: 0.8689 (tmm) REVERT: A 749 CYS cc_start: 0.8579 (m) cc_final: 0.8192 (t) REVERT: A 827 MET cc_start: 0.8732 (tpp) cc_final: 0.8200 (tpp) REVERT: A 830 PHE cc_start: 0.9173 (t80) cc_final: 0.8530 (t80) REVERT: A 987 MET cc_start: 0.9163 (mpp) cc_final: 0.8924 (mpp) REVERT: A 1091 MET cc_start: 0.9247 (mmp) cc_final: 0.9018 (mmp) REVERT: A 1456 MET cc_start: 0.8921 (tpt) cc_final: 0.8617 (tpp) REVERT: A 1473 MET cc_start: 0.9335 (tmm) cc_final: 0.9029 (tmm) REVERT: A 1707 MET cc_start: 0.9188 (mmm) cc_final: 0.8850 (mmp) REVERT: A 1710 TYR cc_start: 0.9294 (t80) cc_final: 0.8637 (t80) REVERT: A 1716 LEU cc_start: 0.9201 (tt) cc_final: 0.8907 (mm) REVERT: A 1753 MET cc_start: 0.9453 (mtm) cc_final: 0.9142 (pmm) REVERT: A 1776 PHE cc_start: 0.9184 (t80) cc_final: 0.8907 (m-10) REVERT: A 1822 MET cc_start: 0.9252 (ttt) cc_final: 0.9009 (tmm) REVERT: A 1856 MET cc_start: 0.8821 (ttm) cc_final: 0.8386 (ttm) REVERT: A 2057 MET cc_start: 0.9215 (mmt) cc_final: 0.8696 (mmt) REVERT: A 2067 PHE cc_start: 0.8794 (t80) cc_final: 0.8546 (t80) outliers start: 1 outliers final: 0 residues processed: 137 average time/residue: 0.2175 time to fit residues: 48.8922 Evaluate side-chains 105 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 111 optimal weight: 8.9990 chunk 34 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 148 optimal weight: 8.9990 chunk 176 optimal weight: 5.9990 chunk 144 optimal weight: 0.0010 chunk 41 optimal weight: 0.0980 chunk 66 optimal weight: 9.9990 chunk 21 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 overall best weight: 1.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1619 GLN ** A1642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1688 GLN ** 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 = 0.3163 r_free = 0.3163 target = 0.054247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.043420 restraints weight = 85525.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.044758 restraints weight = 52045.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.045677 restraints weight = 36836.683| |-----------------------------------------------------------------------------| r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.4647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 13593 Z= 0.110 Angle : 0.613 10.842 18557 Z= 0.295 Chirality : 0.041 0.223 2168 Planarity : 0.003 0.058 2343 Dihedral : 5.642 54.387 2137 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.08 % Allowed : 0.73 % Favored : 99.19 % 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: 0.27 (0.21), residues: 1756 helix: 1.69 (0.17), residues: 993 sheet: -0.84 (0.44), residues: 152 loop : -2.20 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.078 0.001 TRP A 533 HIS 0.003 0.001 HIS A2006 PHE 0.017 0.001 PHE A 686 TYR 0.010 0.001 TYR A1745 ARG 0.004 0.000 ARG A 530 Details of bonding type rmsd link_NAG-ASN : bond 0.00176 ( 4) link_NAG-ASN : angle 1.51728 ( 12) link_BETA1-4 : bond 0.00394 ( 3) link_BETA1-4 : angle 2.53758 ( 9) hydrogen bonds : bond 0.03179 ( 743) hydrogen bonds : angle 3.62275 ( 2160) link_BETA1-6 : bond 0.00942 ( 1) link_BETA1-6 : angle 1.34163 ( 3) SS BOND : bond 0.00350 ( 6) SS BOND : angle 1.40068 ( 12) link_BETA1-3 : bond 0.00479 ( 1) link_BETA1-3 : angle 1.61101 ( 3) covalent geometry : bond 0.00246 (13578) covalent geometry : angle 0.60821 (18518) *********************** 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 142 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 141 time to evaluate : 1.539 Fit side-chains REVERT: A 7 LEU cc_start: 0.9733 (tt) cc_final: 0.9504 (pp) REVERT: A 61 MET cc_start: 0.9131 (mmm) cc_final: 0.8671 (mmm) REVERT: A 286 MET cc_start: 0.9499 (ptp) cc_final: 0.9139 (ptt) REVERT: A 359 MET cc_start: 0.9596 (ppp) cc_final: 0.9370 (ppp) REVERT: A 415 MET cc_start: 0.9470 (mmm) cc_final: 0.9179 (mmm) REVERT: A 622 MET cc_start: 0.9003 (mtt) cc_final: 0.8653 (mtt) REVERT: A 674 MET cc_start: 0.9129 (ttt) cc_final: 0.8661 (tmm) REVERT: A 749 CYS cc_start: 0.8551 (m) cc_final: 0.8185 (t) REVERT: A 827 MET cc_start: 0.8690 (tpp) cc_final: 0.8091 (tpp) REVERT: A 830 PHE cc_start: 0.9194 (t80) cc_final: 0.8518 (t80) REVERT: A 987 MET cc_start: 0.9148 (mpp) cc_final: 0.8912 (mpp) REVERT: A 1456 MET cc_start: 0.8908 (tpt) cc_final: 0.8621 (tpp) REVERT: A 1473 MET cc_start: 0.9328 (tmm) cc_final: 0.9007 (tmm) REVERT: A 1665 MET cc_start: 0.9381 (tpp) cc_final: 0.9004 (tpp) REVERT: A 1707 MET cc_start: 0.9156 (mmm) cc_final: 0.8797 (mmp) REVERT: A 1710 TYR cc_start: 0.9169 (t80) cc_final: 0.8951 (t80) REVERT: A 1716 LEU cc_start: 0.9174 (tt) cc_final: 0.8893 (mm) REVERT: A 1753 MET cc_start: 0.9367 (mtm) cc_final: 0.9140 (pmm) REVERT: A 1776 PHE cc_start: 0.9180 (t80) cc_final: 0.8906 (m-10) REVERT: A 1822 MET cc_start: 0.9273 (ttt) cc_final: 0.9035 (tmm) REVERT: A 1856 MET cc_start: 0.8784 (ttm) cc_final: 0.8353 (ttm) REVERT: A 2057 MET cc_start: 0.9154 (mmt) cc_final: 0.8906 (mmt) REVERT: A 2067 PHE cc_start: 0.8763 (t80) cc_final: 0.8546 (t80) outliers start: 1 outliers final: 0 residues processed: 142 average time/residue: 0.2078 time to fit residues: 48.2645 Evaluate side-chains 106 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 159 optimal weight: 7.9990 chunk 144 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 25 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 chunk 148 optimal weight: 20.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1619 GLN ** A1642 GLN ** 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 = 0.3137 r_free = 0.3137 target = 0.053353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.042598 restraints weight = 87034.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.043945 restraints weight = 52942.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.044839 restraints weight = 37301.568| |-----------------------------------------------------------------------------| r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13593 Z= 0.141 Angle : 0.623 10.866 18557 Z= 0.306 Chirality : 0.042 0.232 2168 Planarity : 0.004 0.058 2343 Dihedral : 5.641 53.754 2137 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 0.08 % Allowed : 0.24 % Favored : 99.67 % 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: 0.30 (0.21), residues: 1756 helix: 1.70 (0.17), residues: 1000 sheet: -0.81 (0.45), residues: 151 loop : -2.21 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.001 TRP A 533 HIS 0.004 0.001 HIS A1626 PHE 0.027 0.001 PHE A1329 TYR 0.012 0.001 TYR A1745 ARG 0.004 0.000 ARG A 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00180 ( 4) link_NAG-ASN : angle 1.46996 ( 12) link_BETA1-4 : bond 0.00452 ( 3) link_BETA1-4 : angle 2.52140 ( 9) hydrogen bonds : bond 0.03331 ( 743) hydrogen bonds : angle 3.69387 ( 2160) link_BETA1-6 : bond 0.00721 ( 1) link_BETA1-6 : angle 1.45829 ( 3) SS BOND : bond 0.00344 ( 6) SS BOND : angle 1.33423 ( 12) link_BETA1-3 : bond 0.00369 ( 1) link_BETA1-3 : angle 1.70029 ( 3) covalent geometry : bond 0.00316 (13578) covalent geometry : angle 0.61848 (18518) ********************** 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 135 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 1.602 Fit side-chains revert: symmetry clash REVERT: A 7 LEU cc_start: 0.9736 (tt) cc_final: 0.9515 (pp) REVERT: A 286 MET cc_start: 0.9489 (ptp) cc_final: 0.9135 (ptt) REVERT: A 359 MET cc_start: 0.9596 (ppp) cc_final: 0.9355 (ppp) REVERT: A 396 MET cc_start: 0.9350 (mmm) cc_final: 0.9127 (mmm) REVERT: A 415 MET cc_start: 0.9476 (mmm) cc_final: 0.9181 (mmm) REVERT: A 622 MET cc_start: 0.9048 (mtt) cc_final: 0.8625 (mtt) REVERT: A 674 MET cc_start: 0.9106 (ttt) cc_final: 0.8640 (tmm) REVERT: A 749 CYS cc_start: 0.8525 (m) cc_final: 0.8165 (t) REVERT: A 794 PHE cc_start: 0.9288 (t80) cc_final: 0.9036 (t80) REVERT: A 827 MET cc_start: 0.8737 (tpp) cc_final: 0.8071 (tpp) REVERT: A 830 PHE cc_start: 0.9196 (t80) cc_final: 0.8498 (t80) REVERT: A 987 MET cc_start: 0.9149 (mpp) cc_final: 0.8943 (mpp) REVERT: A 1456 MET cc_start: 0.8981 (tpt) cc_final: 0.8639 (tpp) REVERT: A 1473 MET cc_start: 0.9338 (tmm) cc_final: 0.9023 (tmm) REVERT: A 1665 MET cc_start: 0.9324 (tpp) cc_final: 0.9069 (tpp) REVERT: A 1707 MET cc_start: 0.9141 (mmm) cc_final: 0.8814 (mmp) REVERT: A 1716 LEU cc_start: 0.9198 (tt) cc_final: 0.8895 (mm) REVERT: A 1776 PHE cc_start: 0.9185 (t80) cc_final: 0.8913 (m-10) REVERT: A 1822 MET cc_start: 0.9264 (ttt) cc_final: 0.8966 (tmm) REVERT: A 2057 MET cc_start: 0.9176 (mmt) cc_final: 0.8927 (mmt) REVERT: A 2067 PHE cc_start: 0.8852 (t80) cc_final: 0.8610 (t80) outliers start: 1 outliers final: 0 residues processed: 135 average time/residue: 0.2207 time to fit residues: 50.6804 Evaluate side-chains 104 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 7 optimal weight: 0.0770 chunk 92 optimal weight: 9.9990 chunk 164 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 59 optimal weight: 0.5980 chunk 90 optimal weight: 5.9990 chunk 134 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 45 optimal weight: 0.9980 overall best weight: 1.1140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1387 GLN A1619 GLN ** A1642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.054150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.043278 restraints weight = 87366.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.044651 restraints weight = 51973.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.045596 restraints weight = 36204.719| |-----------------------------------------------------------------------------| r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.4928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 13593 Z= 0.107 Angle : 0.609 9.502 18557 Z= 0.293 Chirality : 0.041 0.209 2168 Planarity : 0.003 0.059 2343 Dihedral : 5.593 54.829 2137 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.08 % Allowed : 0.33 % Favored : 99.59 % 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: 1.71 (0.17), residues: 999 sheet: -0.77 (0.43), residues: 163 loop : -2.16 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.001 TRP A 533 HIS 0.002 0.001 HIS A1626 PHE 0.017 0.001 PHE A 686 TYR 0.009 0.001 TYR A 997 ARG 0.003 0.000 ARG A 530 Details of bonding type rmsd link_NAG-ASN : bond 0.00172 ( 4) link_NAG-ASN : angle 1.45150 ( 12) link_BETA1-4 : bond 0.00286 ( 3) link_BETA1-4 : angle 2.51255 ( 9) hydrogen bonds : bond 0.03120 ( 743) hydrogen bonds : angle 3.55445 ( 2160) link_BETA1-6 : bond 0.00880 ( 1) link_BETA1-6 : angle 1.23202 ( 3) SS BOND : bond 0.00322 ( 6) SS BOND : angle 1.19791 ( 12) link_BETA1-3 : bond 0.00571 ( 1) link_BETA1-3 : angle 1.59449 ( 3) covalent geometry : bond 0.00242 (13578) covalent geometry : angle 0.60487 (18518) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3987.26 seconds wall clock time: 70 minutes 2.47 seconds (4202.47 seconds total)