Starting phenix.real_space_refine on Wed Mar 4 14:16:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tc0_25803/03_2026/7tc0_25803.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tc0_25803/03_2026/7tc0_25803.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tc0_25803/03_2026/7tc0_25803.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tc0_25803/03_2026/7tc0_25803.map" model { file = "/net/cci-nas-00/data/ceres_data/7tc0_25803/03_2026/7tc0_25803.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tc0_25803/03_2026/7tc0_25803.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 8965 2.51 5 N 2289 2.21 5 O 2471 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13809 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 13636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1781, 13636 Classifications: {'peptide': 1781} Incomplete info: {'truncation_to_alanine': 151} Link IDs: {'PCIS': 2, 'PTRANS': 85, 'TRANS': 1693} Chain breaks: 13 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 531 Unresolved non-hydrogen angles: 663 Unresolved non-hydrogen dihedrals: 451 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'ARG:plan': 8, 'GLN:plan1': 7, 'GLU:plan': 16, 'ASP:plan': 13, 'ASN:plan1': 8, 'HIS:plan': 5, 'TRP:plan': 3, 'TYR:plan': 2, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 285 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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Unusual residues: {'CLR': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.28, per 1000 atoms: 0.24 Number of scatterers: 13809 At special positions: 0 Unit cell: (82.516, 98.514, 218.078, 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 84 16.00 O 2471 8.00 N 2289 7.00 C 8965 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 81 " distance=2.03 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 309 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 504 " distance=2.03 Simple disulfide: pdb=" SG CYS A 626 " - pdb=" SG CYS A1465 " distance=2.03 Simple disulfide: pdb=" SG CYS A1418 " - pdb=" SG CYS A1429 " distance=2.03 Simple disulfide: pdb=" SG CYS A1463 " - pdb=" SG CYS A1477 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Links applied BETA1-3 " BMA C 3 " - " BMA C 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " BETA1-6 " BMA C 3 " - " BMA C 5 " NAG-ASN " NAG A2502 " - " ASN A1637 " " NAG A2503 " - " ASN A 98 " " NAG B 1 " - " ASN A 400 " " NAG C 1 " - " ASN A1504 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.21 Conformation dependent library (CDL) restraints added in 563.2 milliseconds 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3326 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 10 sheets defined 60.5% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 3 through 22 removed outlier: 3.827A pdb=" N GLN A 21 " --> pdb=" O PHE A 17 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N THR A 22 " --> pdb=" O ARG A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 44 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 Processing helix chain 'A' and resid 86 through 90 Processing helix chain 'A' and resid 100 through 119 removed outlier: 3.547A pdb=" N ARG A 104 " --> pdb=" O SER A 100 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLN A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS A 118 " --> pdb=" O LEU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 133 Processing helix chain 'A' and resid 252 through 273 removed outlier: 4.061A pdb=" N GLU A 256 " --> pdb=" O LYS A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 289 removed outlier: 3.784A pdb=" N GLN A 283 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR A 289 " --> pdb=" O VAL A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 309 removed outlier: 4.013A pdb=" N TYR A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 364 Processing helix chain 'A' and resid 371 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: 4.466A pdb=" N PHE A 409 " --> pdb=" O LEU A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 429 removed outlier: 3.729A 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: 4.085A pdb=" N ASP A 441 " --> pdb=" O ARG A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 453 removed outlier: 3.861A pdb=" N PHE A 448 " --> pdb=" O ASP A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 467 Processing helix chain 'A' and resid 483 through 503 removed outlier: 3.686A pdb=" N ALA A 487 " --> pdb=" O THR A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 529 Processing helix chain 'A' and resid 586 through 591 Processing helix chain 'A' and resid 592 through 610 Processing helix chain 'A' and resid 630 through 639 Processing helix chain 'A' and resid 639 through 665 removed outlier: 4.371A pdb=" N PHE A 643 " --> pdb=" O SER A 639 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ALA A 647 " --> pdb=" O PHE A 643 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N TRP A 648 " --> pdb=" O MET A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 674 Processing helix chain 'A' and resid 677 through 707 removed outlier: 3.649A 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 737 removed outlier: 3.799A pdb=" N VAL A 718 " --> pdb=" O ASP A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 740 No H-bonds generated for 'chain 'A' and resid 738 through 740' Processing helix chain 'A' and resid 742 through 767 removed outlier: 4.349A pdb=" N GLY A 751 " --> pdb=" O ALA A 747 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE A 752 " --> pdb=" O ALA A 748 " (cutoff:3.500A) Proline residue: A 760 - end of helix removed outlier: 3.608A pdb=" N ALA A 766 " --> pdb=" O VAL A 762 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N TRP A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 771 removed outlier: 3.840A 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 800 removed outlier: 3.649A pdb=" N ALA A 786 " --> pdb=" O LEU A 782 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLN A 800 " --> pdb=" O LEU A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 846 removed outlier: 3.627A pdb=" N ALA A 844 " --> pdb=" O TRP A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 948 Processing helix chain 'A' and resid 968 through 973 removed outlier: 3.584A pdb=" N GLN A 973 " --> pdb=" O SER A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1002 Processing helix chain 'A' and resid 1004 through 1020 removed outlier: 3.868A 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 1045 Processing helix chain 'A' and resid 1046 through 1051 removed outlier: 6.705A pdb=" N GLY A1049 " --> pdb=" O ALA A1046 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY A1050 " --> pdb=" O PHE A1047 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER A1051 " --> pdb=" O VAL A1048 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1046 through 1051' Processing helix chain 'A' and resid 1064 through 1078 Processing helix chain 'A' and resid 1090 through 1098 removed outlier: 3.658A pdb=" N ALA A1094 " --> pdb=" O HIS A1090 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1122 removed outlier: 3.862A pdb=" N LEU A1122 " --> pdb=" O LEU A1118 " (cutoff:3.500A) Processing helix chain 'A' and resid 1180 through 1191 removed outlier: 3.511A pdb=" N SER A1184 " --> pdb=" O VAL A1180 " (cutoff:3.500A) Processing helix chain 'A' and resid 1216 through 1228 removed outlier: 3.673A pdb=" N GLU A1220 " --> pdb=" O GLY A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1243 through 1252 removed outlier: 3.735A pdb=" N ILE A1247 " --> pdb=" O THR A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1321 through 1342 removed outlier: 4.125A pdb=" N THR A1325 " --> pdb=" O GLY A1321 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLN A1326 " --> pdb=" O TRP A1322 " (cutoff:3.500A) Processing helix chain 'A' and resid 1348 through 1365 removed outlier: 4.098A 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: 3.551A pdb=" N MET A1383 " --> pdb=" O GLN A1380 " (cutoff:3.500A) removed outlier: 4.083A 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 1398 through 1409 Processing helix chain 'A' and resid 1442 through 1451 Processing helix chain 'A' and resid 1504 through 1522 Processing helix chain 'A' and resid 1550 through 1562 Processing helix chain 'A' and resid 1568 through 1583 Processing helix chain 'A' and resid 1600 through 1617 removed outlier: 3.753A pdb=" N SER A1604 " --> pdb=" O HIS A1600 " (cutoff:3.500A) Processing helix chain 'A' and resid 1623 through 1627 Processing helix chain 'A' and resid 1639 through 1649 Processing helix chain 'A' and resid 1650 through 1666 removed outlier: 4.696A pdb=" N LEU A1656 " --> pdb=" O SER A1652 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A1657 " --> pdb=" O VAL A1653 " (cutoff:3.500A) Processing helix chain 'A' and resid 1667 through 1681 removed outlier: 4.104A pdb=" N SER A1671 " --> pdb=" O PHE A1667 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE A1672 " --> pdb=" O VAL A1668 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL A1681 " --> pdb=" O ILE A1677 " (cutoff:3.500A) Processing helix chain 'A' and resid 1684 through 1691 removed outlier: 4.226A pdb=" N SER A1691 " --> pdb=" O LEU A1687 " (cutoff:3.500A) Processing helix chain 'A' and resid 1694 through 1724 removed outlier: 3.563A pdb=" N VAL A1712 " --> pdb=" O CYS A1708 " (cutoff:3.500A) Proline residue: A1713 - end of helix removed outlier: 3.896A pdb=" N PHE A1724 " --> pdb=" O ILE A1720 " (cutoff:3.500A) Processing helix chain 'A' and resid 1726 through 1731 removed outlier: 3.724A pdb=" N SER A1731 " --> pdb=" O LYS A1727 " (cutoff:3.500A) Processing helix chain 'A' and resid 1734 through 1753 Proline residue: A1751 - end of helix Processing helix chain 'A' and resid 1754 through 1758 Processing helix chain 'A' and resid 1765 through 1787 removed outlier: 3.945A pdb=" N VAL A1769 " --> pdb=" O THR A1765 " (cutoff:3.500A) Processing helix chain 'A' and resid 1801 through 1807 Processing helix chain 'A' and resid 1810 through 1836 Processing helix chain 'A' and resid 1850 through 1873 removed outlier: 3.710A pdb=" N GLN A1871 " --> pdb=" O THR A1867 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR A1872 " --> pdb=" O VAL A1868 " (cutoff:3.500A) Processing helix chain 'A' and resid 2002 through 2014 removed outlier: 3.540A pdb=" N HIS A2006 " --> pdb=" O THR A2002 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL A2007 " --> pdb=" O GLY A2003 " (cutoff:3.500A) Processing helix chain 'A' and resid 2020 through 2032 Processing helix chain 'A' and resid 2034 through 2038 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 2092 removed outlier: 3.504A pdb=" N LEU A2083 " --> pdb=" O ALA A2079 " (cutoff:3.500A) Processing helix chain 'A' and resid 2103 through 2111 removed outlier: 3.559A pdb=" N CYS A2107 " --> pdb=" O SER A2103 " (cutoff:3.500A) Processing helix chain 'A' and resid 2128 through 2135 Processing helix chain 'A' and resid 2152 through 2163 removed outlier: 3.779A pdb=" N GLN A2156 " --> pdb=" O LEU A2152 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE A2163 " --> pdb=" O PHE A2159 " (cutoff:3.500A) Processing helix chain 'A' and resid 2186 through 2201 removed outlier: 4.388A pdb=" N LYS A2199 " --> pdb=" O SER A2195 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ARG A2200 " --> pdb=" O GLN A2196 " (cutoff:3.500A) Processing helix chain 'A' and resid 2212 through 2223 removed outlier: 3.660A pdb=" N VAL A2216 " --> pdb=" O THR A2212 " (cutoff:3.500A) removed outlier: 4.130A 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: 6.552A pdb=" N GLY A 616 " --> pdb=" O VAL A1590 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N VAL A1592 " --> pdb=" O GLY A 616 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TYR A 618 " --> pdb=" O VAL A1592 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N PHE A1594 " --> pdb=" O TYR A 618 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLN A 620 " --> pdb=" O PHE A1594 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N TYR A1388 " --> pdb=" O GLY A1533 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N PHE A1535 " --> pdb=" O TYR A1388 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N PHE A1390 " --> pdb=" O PHE A1535 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N LEU A1537 " --> pdb=" O PHE A1390 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N SER A1392 " --> pdb=" O LEU A1537 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N VAL A1539 " --> pdb=" O SER A1392 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 511 through 512 removed outlier: 6.485A pdb=" N LEU A 384 " --> pdb=" O ILE A 536 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N PHE A 538 " --> pdb=" O LEU A 384 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N THR A 386 " --> pdb=" O PHE A 538 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LYS A 553 " --> pdb=" O THR A 539 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL A 552 " --> pdb=" O THR A1630 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N PHE A1632 " --> pdb=" O VAL A 552 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N TYR A 554 " --> pdb=" O PHE A1632 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 920 through 924 removed outlier: 3.504A pdb=" N VAL A 899 " --> pdb=" O PHE A 923 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 975 through 978 Processing sheet with id=AA6, first strand: chain 'A' and resid 1101 through 1105 removed outlier: 6.035A pdb=" N SER A1105 " --> pdb=" O LEU A1109 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LEU A1109 " --> pdb=" O SER A1105 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1195 through 1200 removed outlier: 5.945A pdb=" N LEU A1196 " --> pdb=" O VAL A1207 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL A1207 " --> pdb=" O LEU A1196 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1942 through 1943 removed outlier: 6.537A pdb=" N ARG A2113 " --> pdb=" O GLY A1943 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 1988 through 1991 removed outlier: 6.260A pdb=" N GLY A1989 " --> pdb=" O PHE A2067 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ASP A2069 " --> pdb=" O GLY A1989 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N CYS A1991 " --> pdb=" O ASP A2069 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VAL A2066 " --> pdb=" O VAL A2098 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N THR A2100 " --> pdb=" O VAL A2066 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU A2068 " --> pdb=" O THR A2100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 2167 through 2172 removed outlier: 6.314A pdb=" N LEU A2168 " --> pdb=" O GLN A2179 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N GLN A2179 " --> pdb=" O LEU A2168 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU A2170 " --> pdb=" O GLN A2177 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET A2175 " --> pdb=" O HIS A2172 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP A2205 " --> pdb=" O ARG A2144 " (cutoff:3.500A) 750 hydrogen bonds defined for protein. 2187 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.95 Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4331 1.34 - 1.46: 3159 1.46 - 1.58: 6503 1.58 - 1.70: 0 1.70 - 1.82: 136 Bond restraints: 14129 Sorted by residual: bond pdb=" C VAL A1737 " pdb=" N LEU A1738 " ideal model delta sigma weight residual 1.335 1.555 -0.221 1.27e-02 6.20e+03 3.02e+02 bond pdb=" C LEU A1738 " pdb=" N ALA A1739 " ideal model delta sigma weight residual 1.334 1.413 -0.079 1.33e-02 5.65e+03 3.52e+01 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.487 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.57e+01 bond pdb=" C VAL A1712 " pdb=" N PRO A1713 " ideal model delta sigma weight residual 1.335 1.358 -0.023 1.36e-02 5.41e+03 2.82e+00 ... (remaining 14124 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.30: 19122 3.30 - 6.59: 86 6.59 - 9.89: 9 9.89 - 13.18: 1 13.18 - 16.48: 1 Bond angle restraints: 19219 Sorted by residual: angle pdb=" CA PRO A1713 " pdb=" N PRO A1713 " pdb=" CD PRO A1713 " ideal model delta sigma weight residual 112.00 102.02 9.98 1.40e+00 5.10e-01 5.08e+01 angle pdb=" C SER A2127 " pdb=" CA SER A2127 " pdb=" CB SER A2127 " ideal model delta sigma weight residual 116.63 108.52 8.11 1.16e+00 7.43e-01 4.89e+01 angle pdb=" C VAL A1712 " pdb=" N PRO A1713 " pdb=" CA PRO A1713 " ideal model delta sigma weight residual 119.05 111.77 7.28 1.11e+00 8.12e-01 4.30e+01 angle pdb=" C VAL A1737 " pdb=" N LEU A1738 " pdb=" CA LEU A1738 " ideal model delta sigma weight residual 120.82 129.27 -8.45 1.50e+00 4.44e-01 3.18e+01 angle pdb=" CA VAL A1712 " pdb=" C VAL A1712 " pdb=" N PRO A1713 " ideal model delta sigma weight residual 120.83 117.41 3.42 6.10e-01 2.69e+00 3.15e+01 ... (remaining 19214 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.45: 8047 23.45 - 46.90: 412 46.90 - 70.35: 64 70.35 - 93.80: 30 93.80 - 117.25: 18 Dihedral angle restraints: 8571 sinusoidal: 3421 harmonic: 5150 Sorted by residual: dihedral pdb=" CB CYS A1418 " pdb=" SG CYS A1418 " pdb=" SG CYS A1429 " pdb=" CB CYS A1429 " ideal model delta sinusoidal sigma weight residual -86.00 0.95 -86.95 1 1.00e+01 1.00e-02 9.09e+01 dihedral pdb=" CB CYS A1463 " pdb=" SG CYS A1463 " pdb=" SG CYS A1477 " pdb=" CB CYS A1477 " ideal model delta sinusoidal sigma weight residual -86.00 -8.54 -77.46 1 1.00e+01 1.00e-02 7.52e+01 dihedral pdb=" C PRO A1713 " pdb=" N PRO A1713 " pdb=" CA PRO A1713 " pdb=" CB PRO A1713 " ideal model delta harmonic sigma weight residual -120.70 -131.27 10.57 0 2.50e+00 1.60e-01 1.79e+01 ... (remaining 8568 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 2191 0.106 - 0.212: 40 0.212 - 0.318: 8 0.318 - 0.423: 2 0.423 - 0.529: 1 Chirality restraints: 2242 Sorted by residual: chirality pdb=" CA PRO A1713 " pdb=" N PRO A1713 " pdb=" C PRO A1713 " pdb=" CB PRO A1713 " both_signs ideal model delta sigma weight residual False 2.72 2.19 0.53 2.00e-01 2.50e+01 7.00e+00 chirality pdb=" C14 CLR A2504 " pdb=" C13 CLR A2504 " pdb=" C15 CLR A2504 " pdb=" C8 CLR A2504 " both_signs ideal model delta sigma weight residual False -2.32 -2.66 0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" C14 CLR A2501 " pdb=" C13 CLR A2501 " pdb=" C15 CLR A2501 " pdb=" C8 CLR A2501 " both_signs ideal model delta sigma weight residual False -2.32 -2.66 0.34 2.00e-01 2.50e+01 2.91e+00 ... (remaining 2239 not shown) Planarity restraints: 2404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A1712 " 0.149 5.00e-02 4.00e+02 2.25e-01 8.09e+01 pdb=" N PRO A1713 " -0.389 5.00e-02 4.00e+02 pdb=" CA PRO A1713 " 0.124 5.00e-02 4.00e+02 pdb=" CD PRO A1713 " 0.117 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1738 " 0.013 2.00e-02 2.50e+03 2.49e-02 6.19e+00 pdb=" C LEU A1738 " -0.043 2.00e-02 2.50e+03 pdb=" O LEU A1738 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA A1739 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A1710 " 0.012 2.00e-02 2.50e+03 2.38e-02 5.66e+00 pdb=" C TYR A1710 " -0.041 2.00e-02 2.50e+03 pdb=" O TYR A1710 " 0.015 2.00e-02 2.50e+03 pdb=" N VAL A1711 " 0.014 2.00e-02 2.50e+03 ... (remaining 2401 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 228 2.69 - 3.24: 13391 3.24 - 3.80: 21349 3.80 - 4.35: 26626 4.35 - 4.90: 44873 Nonbonded interactions: 106467 Sorted by model distance: nonbonded pdb=" OE2 GLU A2070 " pdb=" ND1 HIS A2102 " model vdw 2.141 3.120 nonbonded pdb=" OD2 ASP A1706 " pdb=" OH TYR A1754 " model vdw 2.231 3.040 nonbonded pdb=" OG1 THR A1124 " pdb=" OE2 GLU A1246 " model vdw 2.252 3.040 nonbonded pdb=" OE1 GLU A 925 " pdb=" OG1 THR A1083 " model vdw 2.278 3.040 nonbonded pdb=" O SER A2182 " pdb=" OG SER A2182 " model vdw 2.299 3.040 ... (remaining 106462 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.180 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: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.580 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 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 : 0.005 0.387 14146 Z= 0.386 Angle : 0.596 16.477 19258 Z= 0.335 Chirality : 0.044 0.529 2242 Planarity : 0.006 0.225 2400 Dihedral : 15.733 117.246 5227 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.49 % Allowed : 9.87 % Favored : 87.64 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.19), residues: 1753 helix: 0.11 (0.16), residues: 966 sheet: -1.33 (0.39), residues: 174 loop : -3.26 (0.21), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A2173 TYR 0.007 0.000 TYR A1698 PHE 0.006 0.000 PHE A1449 TRP 0.009 0.000 TRP A1705 HIS 0.001 0.000 HIS A 894 Details of bonding type rmsd covalent geometry : bond 0.00317 (14129) covalent geometry : angle 0.59361 (19219) SS BOND : bond 0.00256 ( 6) SS BOND : angle 1.47110 ( 12) hydrogen bonds : bond 0.12551 ( 750) hydrogen bonds : angle 4.89643 ( 2187) Misc. bond : bond 0.27347 ( 2) link_BETA1-3 : bond 0.00320 ( 1) link_BETA1-3 : angle 1.31723 ( 3) link_BETA1-4 : bond 0.00422 ( 3) link_BETA1-4 : angle 1.17031 ( 9) link_BETA1-6 : bond 0.00408 ( 1) link_BETA1-6 : angle 1.21739 ( 3) link_NAG-ASN : bond 0.00212 ( 4) link_NAG-ASN : angle 1.14318 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 273 time to evaluate : 0.485 Fit side-chains revert: symmetry clash REVERT: A 17 PHE cc_start: 0.8219 (m-80) cc_final: 0.7997 (t80) REVERT: A 99 LYS cc_start: 0.7189 (mmtt) cc_final: 0.6198 (tmmt) REVERT: A 662 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7616 (tm-30) REVERT: A 982 ASN cc_start: 0.7514 (p0) cc_final: 0.7311 (p0) REVERT: A 1128 LEU cc_start: 0.8084 (pt) cc_final: 0.7794 (pt) REVERT: A 1180 VAL cc_start: 0.9163 (m) cc_final: 0.8934 (t) REVERT: A 1245 GLU cc_start: 0.8416 (tm-30) cc_final: 0.8209 (tt0) REVERT: A 1363 VAL cc_start: 0.8689 (OUTLIER) cc_final: 0.8481 (m) REVERT: A 1656 LEU cc_start: 0.8922 (tt) cc_final: 0.8570 (mm) outliers start: 35 outliers final: 22 residues processed: 302 average time/residue: 0.1283 time to fit residues: 55.7275 Evaluate side-chains 212 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 189 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1363 VAL Chi-restraints excluded: chain A residue 1427 THR Chi-restraints excluded: chain A residue 1537 LEU Chi-restraints excluded: chain A residue 1551 VAL Chi-restraints excluded: chain A residue 1602 ILE Chi-restraints excluded: chain A residue 1713 PRO Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1841 VAL Chi-restraints excluded: chain A residue 2065 VAL Chi-restraints excluded: chain A residue 2073 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 6.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 283 GLN A 302 GLN A 361 ASN A 452 GLN A 470 HIS A 820 ASN A 894 HIS A1600 HIS ** A1634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1688 GLN A2179 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.107018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.074247 restraints weight = 26680.587| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.69 r_work: 0.2906 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 14146 Z= 0.233 Angle : 0.728 10.258 19258 Z= 0.360 Chirality : 0.048 0.222 2242 Planarity : 0.005 0.055 2400 Dihedral : 9.236 79.441 2238 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 4.12 % Allowed : 13.21 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.20), residues: 1753 helix: 1.02 (0.17), residues: 979 sheet: -0.59 (0.42), residues: 163 loop : -2.69 (0.22), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 276 TYR 0.023 0.002 TYR A1210 PHE 0.029 0.002 PHE A 725 TRP 0.016 0.002 TRP A1747 HIS 0.011 0.002 HIS A 470 Details of bonding type rmsd covalent geometry : bond 0.00556 (14129) covalent geometry : angle 0.71780 (19219) SS BOND : bond 0.00345 ( 6) SS BOND : angle 2.60331 ( 12) hydrogen bonds : bond 0.05282 ( 750) hydrogen bonds : angle 3.92458 ( 2187) Misc. bond : bond 0.00257 ( 2) link_BETA1-3 : bond 0.00152 ( 1) link_BETA1-3 : angle 2.07381 ( 3) link_BETA1-4 : bond 0.00638 ( 3) link_BETA1-4 : angle 3.56446 ( 9) link_BETA1-6 : bond 0.00627 ( 1) link_BETA1-6 : angle 3.74136 ( 3) link_NAG-ASN : bond 0.00328 ( 4) link_NAG-ASN : angle 2.34163 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 199 time to evaluate : 0.555 Fit side-chains revert: symmetry clash REVERT: A 99 LYS cc_start: 0.8317 (mmtt) cc_final: 0.8114 (mmmm) REVERT: A 601 GLU cc_start: 0.8652 (mm-30) cc_final: 0.7773 (mt-10) REVERT: A 662 GLU cc_start: 0.8833 (tm-30) cc_final: 0.8535 (tt0) REVERT: A 1180 VAL cc_start: 0.9132 (m) cc_final: 0.8874 (t) REVERT: A 1245 GLU cc_start: 0.8672 (tm-30) cc_final: 0.8232 (tt0) REVERT: A 1357 PHE cc_start: 0.7463 (OUTLIER) cc_final: 0.5958 (t80) REVERT: A 1380 GLN cc_start: 0.9010 (OUTLIER) cc_final: 0.8548 (pt0) REVERT: A 1786 PHE cc_start: 0.6852 (t80) cc_final: 0.6551 (t80) REVERT: A 2059 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8245 (pp) REVERT: A 2135 PHE cc_start: 0.9432 (m-80) cc_final: 0.9221 (m-80) outliers start: 58 outliers final: 36 residues processed: 246 average time/residue: 0.1040 time to fit residues: 39.1221 Evaluate side-chains 215 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 176 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 712 TYR Chi-restraints excluded: chain A residue 754 TYR Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1357 PHE Chi-restraints excluded: chain A residue 1363 VAL Chi-restraints excluded: chain A residue 1380 GLN Chi-restraints excluded: chain A residue 1414 PHE Chi-restraints excluded: chain A residue 1427 THR Chi-restraints excluded: chain A residue 1463 CYS Chi-restraints excluded: chain A residue 1551 VAL Chi-restraints excluded: chain A residue 1720 ILE Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1841 VAL Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 2029 ILE Chi-restraints excluded: chain A residue 2032 LEU Chi-restraints excluded: chain A residue 2059 LEU Chi-restraints excluded: chain A residue 2065 VAL Chi-restraints excluded: chain A residue 2066 VAL Chi-restraints excluded: chain A residue 2073 THR Chi-restraints excluded: chain A residue 2097 VAL Chi-restraints excluded: chain A residue 2099 LEU Chi-restraints excluded: chain A residue 2170 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 18 optimal weight: 0.7980 chunk 165 optimal weight: 8.9990 chunk 92 optimal weight: 7.9990 chunk 154 optimal weight: 0.7980 chunk 133 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 175 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 27 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 470 HIS ** A1634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2174 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.108970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.076802 restraints weight = 26781.248| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.61 r_work: 0.2968 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14146 Z= 0.117 Angle : 0.570 10.707 19258 Z= 0.279 Chirality : 0.042 0.164 2242 Planarity : 0.004 0.056 2400 Dihedral : 7.371 61.635 2222 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.05 % Allowed : 15.55 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.21), residues: 1753 helix: 1.51 (0.17), residues: 978 sheet: -0.43 (0.42), residues: 163 loop : -2.34 (0.23), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2200 TYR 0.017 0.001 TYR A1210 PHE 0.023 0.001 PHE A2158 TRP 0.016 0.001 TRP A1705 HIS 0.004 0.001 HIS A 551 Details of bonding type rmsd covalent geometry : bond 0.00256 (14129) covalent geometry : angle 0.56073 (19219) SS BOND : bond 0.00297 ( 6) SS BOND : angle 1.54044 ( 12) hydrogen bonds : bond 0.03818 ( 750) hydrogen bonds : angle 3.65653 ( 2187) Misc. bond : bond 0.00151 ( 2) link_BETA1-3 : bond 0.00527 ( 1) link_BETA1-3 : angle 1.88790 ( 3) link_BETA1-4 : bond 0.00261 ( 3) link_BETA1-4 : angle 3.08789 ( 9) link_BETA1-6 : bond 0.00959 ( 1) link_BETA1-6 : angle 2.71858 ( 3) link_NAG-ASN : bond 0.00229 ( 4) link_NAG-ASN : angle 2.19608 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 183 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 378 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9166 (tt) REVERT: A 631 ILE cc_start: 0.8440 (tt) cc_final: 0.8230 (tp) REVERT: A 662 GLU cc_start: 0.8836 (tm-30) cc_final: 0.8150 (tm-30) REVERT: A 1128 LEU cc_start: 0.8233 (pt) cc_final: 0.7936 (tt) REVERT: A 1180 VAL cc_start: 0.9037 (m) cc_final: 0.8782 (t) REVERT: A 1245 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8325 (tt0) REVERT: A 1357 PHE cc_start: 0.7556 (OUTLIER) cc_final: 0.6077 (t80) REVERT: A 1363 VAL cc_start: 0.8834 (p) cc_final: 0.8617 (m) REVERT: A 1552 ASN cc_start: 0.8626 (t0) cc_final: 0.8313 (m-40) REVERT: A 1721 PHE cc_start: 0.7630 (OUTLIER) cc_final: 0.5766 (t80) REVERT: A 1786 PHE cc_start: 0.6930 (t80) cc_final: 0.6579 (t80) REVERT: A 2059 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8217 (pp) outliers start: 43 outliers final: 29 residues processed: 218 average time/residue: 0.1037 time to fit residues: 35.2883 Evaluate side-chains 202 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 169 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 754 TYR Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain A residue 1357 PHE Chi-restraints excluded: chain A residue 1427 THR Chi-restraints excluded: chain A residue 1463 CYS Chi-restraints excluded: chain A residue 1551 VAL Chi-restraints excluded: chain A residue 1693 VAL Chi-restraints excluded: chain A residue 1721 PHE Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1841 VAL Chi-restraints excluded: chain A residue 1988 MET Chi-restraints excluded: chain A residue 2029 ILE Chi-restraints excluded: chain A residue 2032 LEU Chi-restraints excluded: chain A residue 2059 LEU Chi-restraints excluded: chain A residue 2065 VAL Chi-restraints excluded: chain A residue 2066 VAL Chi-restraints excluded: chain A residue 2073 THR Chi-restraints excluded: chain A residue 2099 LEU Chi-restraints excluded: chain A residue 2174 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 125 optimal weight: 4.9990 chunk 118 optimal weight: 0.6980 chunk 136 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 173 optimal weight: 3.9990 chunk 169 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 167 optimal weight: 20.0000 chunk 87 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 ASN ** A1634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2174 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.105126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.072556 restraints weight = 26801.619| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.66 r_work: 0.2874 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14146 Z= 0.202 Angle : 0.633 9.167 19258 Z= 0.316 Chirality : 0.045 0.212 2242 Planarity : 0.005 0.055 2400 Dihedral : 6.516 57.280 2220 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 4.26 % Allowed : 16.26 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.21), residues: 1753 helix: 1.64 (0.17), residues: 979 sheet: -0.48 (0.39), residues: 181 loop : -2.26 (0.24), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A2200 TYR 0.013 0.001 TYR A 924 PHE 0.022 0.002 PHE A1605 TRP 0.015 0.001 TRP A1705 HIS 0.006 0.001 HIS A 550 Details of bonding type rmsd covalent geometry : bond 0.00486 (14129) covalent geometry : angle 0.62282 (19219) SS BOND : bond 0.00809 ( 6) SS BOND : angle 2.21447 ( 12) hydrogen bonds : bond 0.04766 ( 750) hydrogen bonds : angle 3.76809 ( 2187) Misc. bond : bond 0.00141 ( 2) link_BETA1-3 : bond 0.00694 ( 1) link_BETA1-3 : angle 2.00079 ( 3) link_BETA1-4 : bond 0.00534 ( 3) link_BETA1-4 : angle 3.11073 ( 9) link_BETA1-6 : bond 0.00805 ( 1) link_BETA1-6 : angle 2.49681 ( 3) link_NAG-ASN : bond 0.00309 ( 4) link_NAG-ASN : angle 2.50802 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 179 time to evaluate : 0.531 Fit side-chains revert: symmetry clash REVERT: A 378 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.8722 (mp) REVERT: A 662 GLU cc_start: 0.8748 (tm-30) cc_final: 0.8527 (tt0) REVERT: A 1128 LEU cc_start: 0.8410 (pt) cc_final: 0.7952 (tt) REVERT: A 1180 VAL cc_start: 0.9099 (m) cc_final: 0.8863 (t) REVERT: A 1245 GLU cc_start: 0.8749 (tm-30) cc_final: 0.8300 (tt0) REVERT: A 1552 ASN cc_start: 0.8662 (t0) cc_final: 0.8433 (m-40) REVERT: A 1693 VAL cc_start: 0.6862 (OUTLIER) cc_final: 0.6583 (t) REVERT: A 1721 PHE cc_start: 0.7876 (OUTLIER) cc_final: 0.5832 (t80) REVERT: A 1786 PHE cc_start: 0.6842 (t80) cc_final: 0.6605 (t80) REVERT: A 2059 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8239 (pp) outliers start: 60 outliers final: 38 residues processed: 225 average time/residue: 0.1068 time to fit residues: 36.8791 Evaluate side-chains 211 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 169 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 754 TYR Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain A residue 1352 VAL Chi-restraints excluded: chain A residue 1357 PHE Chi-restraints excluded: chain A residue 1363 VAL Chi-restraints excluded: chain A residue 1414 PHE Chi-restraints excluded: chain A residue 1427 THR Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1551 VAL Chi-restraints excluded: chain A residue 1693 VAL Chi-restraints excluded: chain A residue 1721 PHE Chi-restraints excluded: chain A residue 1762 ILE Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1841 VAL Chi-restraints excluded: chain A residue 2029 ILE Chi-restraints excluded: chain A residue 2032 LEU Chi-restraints excluded: chain A residue 2059 LEU Chi-restraints excluded: chain A residue 2065 VAL Chi-restraints excluded: chain A residue 2066 VAL Chi-restraints excluded: chain A residue 2097 VAL Chi-restraints excluded: chain A residue 2099 LEU Chi-restraints excluded: chain A residue 2100 THR Chi-restraints excluded: chain A residue 2108 GLU Chi-restraints excluded: chain A residue 2174 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 142 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 164 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 114 optimal weight: 0.3980 chunk 116 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 chunk 150 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 ASN ** A1634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2174 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.106358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.074465 restraints weight = 26535.461| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.60 r_work: 0.2912 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14146 Z= 0.124 Angle : 0.575 11.120 19258 Z= 0.285 Chirality : 0.042 0.169 2242 Planarity : 0.005 0.117 2400 Dihedral : 6.158 56.109 2219 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.55 % Allowed : 17.90 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.21), residues: 1753 helix: 1.80 (0.17), residues: 980 sheet: -0.40 (0.39), residues: 181 loop : -2.28 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A2200 TYR 0.013 0.001 TYR A1206 PHE 0.021 0.001 PHE A1218 TRP 0.018 0.001 TRP A1705 HIS 0.005 0.001 HIS A 470 Details of bonding type rmsd covalent geometry : bond 0.00274 (14129) covalent geometry : angle 0.56643 (19219) SS BOND : bond 0.00494 ( 6) SS BOND : angle 2.09446 ( 12) hydrogen bonds : bond 0.04094 ( 750) hydrogen bonds : angle 3.65669 ( 2187) Misc. bond : bond 0.00066 ( 2) link_BETA1-3 : bond 0.00565 ( 1) link_BETA1-3 : angle 1.97070 ( 3) link_BETA1-4 : bond 0.00297 ( 3) link_BETA1-4 : angle 2.50642 ( 9) link_BETA1-6 : bond 0.00847 ( 1) link_BETA1-6 : angle 2.05832 ( 3) link_NAG-ASN : bond 0.00160 ( 4) link_NAG-ASN : angle 2.37402 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 180 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.8397 (ttm170) cc_final: 0.8175 (ttp-170) REVERT: A 378 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.8803 (mp) REVERT: A 662 GLU cc_start: 0.8829 (tm-30) cc_final: 0.8581 (tt0) REVERT: A 742 ARG cc_start: 0.8499 (mmt90) cc_final: 0.7965 (mtm180) REVERT: A 1128 LEU cc_start: 0.8473 (pt) cc_final: 0.8125 (tt) REVERT: A 1180 VAL cc_start: 0.9048 (m) cc_final: 0.8798 (t) REVERT: A 1245 GLU cc_start: 0.8878 (tm-30) cc_final: 0.8448 (tt0) REVERT: A 1380 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8556 (pt0) REVERT: A 1552 ASN cc_start: 0.8746 (t0) cc_final: 0.8528 (m-40) REVERT: A 1693 VAL cc_start: 0.6959 (OUTLIER) cc_final: 0.6637 (t) REVERT: A 1721 PHE cc_start: 0.7939 (OUTLIER) cc_final: 0.5967 (t80) REVERT: A 1786 PHE cc_start: 0.6912 (t80) cc_final: 0.6569 (t80) REVERT: A 2059 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8306 (pp) REVERT: A 2131 LEU cc_start: 0.8831 (mt) cc_final: 0.8602 (mt) REVERT: A 2156 GLN cc_start: 0.8317 (tt0) cc_final: 0.7267 (mp10) REVERT: A 2204 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8413 (mt-10) outliers start: 50 outliers final: 35 residues processed: 219 average time/residue: 0.1070 time to fit residues: 35.6316 Evaluate side-chains 212 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 172 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 754 TYR Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 935 ASN Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1357 PHE Chi-restraints excluded: chain A residue 1380 GLN Chi-restraints excluded: chain A residue 1414 PHE Chi-restraints excluded: chain A residue 1427 THR Chi-restraints excluded: chain A residue 1463 CYS Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1551 VAL Chi-restraints excluded: chain A residue 1693 VAL Chi-restraints excluded: chain A residue 1721 PHE Chi-restraints excluded: chain A residue 1762 ILE Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1841 VAL Chi-restraints excluded: chain A residue 2029 ILE Chi-restraints excluded: chain A residue 2059 LEU Chi-restraints excluded: chain A residue 2065 VAL Chi-restraints excluded: chain A residue 2066 VAL Chi-restraints excluded: chain A residue 2097 VAL Chi-restraints excluded: chain A residue 2099 LEU Chi-restraints excluded: chain A residue 2174 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 162 optimal weight: 5.9990 chunk 105 optimal weight: 0.0870 chunk 113 optimal weight: 0.6980 chunk 136 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 10 optimal weight: 7.9990 chunk 6 optimal weight: 0.4980 chunk 160 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 49 optimal weight: 4.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2174 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.107462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.075730 restraints weight = 26375.906| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.59 r_work: 0.2939 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14146 Z= 0.108 Angle : 0.550 10.002 19258 Z= 0.272 Chirality : 0.040 0.162 2242 Planarity : 0.005 0.126 2400 Dihedral : 5.925 59.317 2219 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.55 % Allowed : 18.11 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.21), residues: 1753 helix: 1.90 (0.17), residues: 989 sheet: -0.25 (0.40), residues: 172 loop : -2.24 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A2200 TYR 0.014 0.001 TYR A1206 PHE 0.024 0.001 PHE A 287 TRP 0.018 0.001 TRP A1705 HIS 0.004 0.001 HIS A 470 Details of bonding type rmsd covalent geometry : bond 0.00227 (14129) covalent geometry : angle 0.54228 (19219) SS BOND : bond 0.00347 ( 6) SS BOND : angle 1.72636 ( 12) hydrogen bonds : bond 0.03675 ( 750) hydrogen bonds : angle 3.58539 ( 2187) Misc. bond : bond 0.00428 ( 2) link_BETA1-3 : bond 0.00601 ( 1) link_BETA1-3 : angle 1.97806 ( 3) link_BETA1-4 : bond 0.00252 ( 3) link_BETA1-4 : angle 2.28060 ( 9) link_BETA1-6 : bond 0.00860 ( 1) link_BETA1-6 : angle 1.68961 ( 3) link_NAG-ASN : bond 0.00155 ( 4) link_NAG-ASN : angle 2.24460 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 181 time to evaluate : 0.519 Fit side-chains revert: symmetry clash REVERT: A 19 ARG cc_start: 0.8392 (ttm170) cc_final: 0.8185 (ttp-170) REVERT: A 378 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.8814 (mp) REVERT: A 662 GLU cc_start: 0.8786 (tm-30) cc_final: 0.8510 (tt0) REVERT: A 742 ARG cc_start: 0.8462 (mmt90) cc_final: 0.7941 (mtm180) REVERT: A 1015 MET cc_start: 0.7672 (ttm) cc_final: 0.7389 (mtt) REVERT: A 1128 LEU cc_start: 0.8438 (pt) cc_final: 0.8101 (tt) REVERT: A 1180 VAL cc_start: 0.9048 (m) cc_final: 0.8804 (t) REVERT: A 1245 GLU cc_start: 0.8898 (tm-30) cc_final: 0.8465 (tt0) REVERT: A 1552 ASN cc_start: 0.8745 (t0) cc_final: 0.8528 (m-40) REVERT: A 1693 VAL cc_start: 0.6854 (OUTLIER) cc_final: 0.6525 (t) REVERT: A 1721 PHE cc_start: 0.7929 (OUTLIER) cc_final: 0.6001 (t80) REVERT: A 1786 PHE cc_start: 0.6894 (t80) cc_final: 0.6546 (t80) REVERT: A 2059 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8321 (pp) REVERT: A 2131 LEU cc_start: 0.8829 (mt) cc_final: 0.8591 (mt) REVERT: A 2204 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8439 (mt-10) outliers start: 50 outliers final: 33 residues processed: 220 average time/residue: 0.1086 time to fit residues: 36.3573 Evaluate side-chains 209 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 172 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 754 TYR Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1357 PHE Chi-restraints excluded: chain A residue 1363 VAL Chi-restraints excluded: chain A residue 1414 PHE Chi-restraints excluded: chain A residue 1427 THR Chi-restraints excluded: chain A residue 1463 CYS Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1551 VAL Chi-restraints excluded: chain A residue 1693 VAL Chi-restraints excluded: chain A residue 1721 PHE Chi-restraints excluded: chain A residue 1762 ILE Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1841 VAL Chi-restraints excluded: chain A residue 2059 LEU Chi-restraints excluded: chain A residue 2065 VAL Chi-restraints excluded: chain A residue 2066 VAL Chi-restraints excluded: chain A residue 2097 VAL Chi-restraints excluded: chain A residue 2099 LEU Chi-restraints excluded: chain A residue 2108 GLU Chi-restraints excluded: chain A residue 2174 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 76 optimal weight: 0.8980 chunk 6 optimal weight: 0.0000 chunk 41 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 HIS A 935 ASN ** A1634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1774 ASN A2174 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.105855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.073591 restraints weight = 26547.779| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.63 r_work: 0.2897 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14146 Z= 0.149 Angle : 0.588 10.528 19258 Z= 0.292 Chirality : 0.042 0.182 2242 Planarity : 0.005 0.120 2400 Dihedral : 5.931 58.123 2219 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.41 % Allowed : 18.54 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.21), residues: 1753 helix: 1.95 (0.17), residues: 980 sheet: -0.29 (0.39), residues: 181 loop : -2.16 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A2200 TYR 0.012 0.001 TYR A1206 PHE 0.025 0.002 PHE A2158 TRP 0.016 0.001 TRP A1705 HIS 0.005 0.001 HIS A1634 Details of bonding type rmsd covalent geometry : bond 0.00348 (14129) covalent geometry : angle 0.58010 (19219) SS BOND : bond 0.00408 ( 6) SS BOND : angle 2.07043 ( 12) hydrogen bonds : bond 0.04172 ( 750) hydrogen bonds : angle 3.62858 ( 2187) Misc. bond : bond 0.00432 ( 2) link_BETA1-3 : bond 0.00625 ( 1) link_BETA1-3 : angle 1.94657 ( 3) link_BETA1-4 : bond 0.00345 ( 3) link_BETA1-4 : angle 2.48830 ( 9) link_BETA1-6 : bond 0.00711 ( 1) link_BETA1-6 : angle 1.52670 ( 3) link_NAG-ASN : bond 0.00170 ( 4) link_NAG-ASN : angle 2.38255 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 170 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: A 19 ARG cc_start: 0.8324 (ttm170) cc_final: 0.8123 (ttp-170) REVERT: A 378 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8750 (mp) REVERT: A 662 GLU cc_start: 0.8660 (tm-30) cc_final: 0.8432 (tt0) REVERT: A 742 ARG cc_start: 0.8393 (mmt90) cc_final: 0.7935 (mtm180) REVERT: A 1128 LEU cc_start: 0.8377 (pt) cc_final: 0.8017 (tt) REVERT: A 1180 VAL cc_start: 0.9079 (m) cc_final: 0.8843 (t) REVERT: A 1245 GLU cc_start: 0.8756 (tm-30) cc_final: 0.8308 (tt0) REVERT: A 1380 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.8448 (pt0) REVERT: A 1693 VAL cc_start: 0.6848 (OUTLIER) cc_final: 0.6576 (t) REVERT: A 1721 PHE cc_start: 0.7951 (OUTLIER) cc_final: 0.6075 (t80) REVERT: A 1786 PHE cc_start: 0.6831 (t80) cc_final: 0.6601 (t80) REVERT: A 2059 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8312 (pp) REVERT: A 2131 LEU cc_start: 0.8790 (mt) cc_final: 0.8545 (mt) REVERT: A 2204 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8346 (mt-10) outliers start: 48 outliers final: 35 residues processed: 209 average time/residue: 0.1068 time to fit residues: 34.0054 Evaluate side-chains 204 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 164 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 754 TYR Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1352 VAL Chi-restraints excluded: chain A residue 1357 PHE Chi-restraints excluded: chain A residue 1363 VAL Chi-restraints excluded: chain A residue 1380 GLN Chi-restraints excluded: chain A residue 1414 PHE Chi-restraints excluded: chain A residue 1427 THR Chi-restraints excluded: chain A residue 1463 CYS Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1551 VAL Chi-restraints excluded: chain A residue 1693 VAL Chi-restraints excluded: chain A residue 1721 PHE Chi-restraints excluded: chain A residue 1762 ILE Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1841 VAL Chi-restraints excluded: chain A residue 2059 LEU Chi-restraints excluded: chain A residue 2065 VAL Chi-restraints excluded: chain A residue 2066 VAL Chi-restraints excluded: chain A residue 2097 VAL Chi-restraints excluded: chain A residue 2099 LEU Chi-restraints excluded: chain A residue 2108 GLU Chi-restraints excluded: chain A residue 2174 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 110 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 148 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 176 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 131 optimal weight: 5.9990 chunk 56 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 ASN A1552 ASN ** A1634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2174 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.106531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.074804 restraints weight = 26184.428| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.58 r_work: 0.2921 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14146 Z= 0.118 Angle : 0.573 11.399 19258 Z= 0.281 Chirality : 0.041 0.174 2242 Planarity : 0.004 0.075 2400 Dihedral : 5.794 57.811 2219 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.12 % Allowed : 19.18 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.21), residues: 1753 helix: 1.99 (0.17), residues: 984 sheet: -0.19 (0.40), residues: 181 loop : -2.09 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A2189 TYR 0.013 0.001 TYR A1206 PHE 0.018 0.001 PHE A 846 TRP 0.018 0.001 TRP A1705 HIS 0.005 0.001 HIS A 470 Details of bonding type rmsd covalent geometry : bond 0.00260 (14129) covalent geometry : angle 0.56572 (19219) SS BOND : bond 0.00433 ( 6) SS BOND : angle 1.87119 ( 12) hydrogen bonds : bond 0.03874 ( 750) hydrogen bonds : angle 3.58572 ( 2187) Misc. bond : bond 0.00174 ( 2) link_BETA1-3 : bond 0.00600 ( 1) link_BETA1-3 : angle 1.83552 ( 3) link_BETA1-4 : bond 0.00270 ( 3) link_BETA1-4 : angle 2.23752 ( 9) link_BETA1-6 : bond 0.00788 ( 1) link_BETA1-6 : angle 1.41754 ( 3) link_NAG-ASN : bond 0.00162 ( 4) link_NAG-ASN : angle 2.29915 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 166 time to evaluate : 0.505 Fit side-chains revert: symmetry clash REVERT: A 378 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.8833 (mp) REVERT: A 662 GLU cc_start: 0.8789 (tm-30) cc_final: 0.8534 (tt0) REVERT: A 742 ARG cc_start: 0.8485 (mmt90) cc_final: 0.7961 (mtm180) REVERT: A 1015 MET cc_start: 0.7681 (ttm) cc_final: 0.7395 (mtt) REVERT: A 1128 LEU cc_start: 0.8480 (pt) cc_final: 0.8156 (tt) REVERT: A 1180 VAL cc_start: 0.9033 (m) cc_final: 0.8816 (t) REVERT: A 1245 GLU cc_start: 0.8877 (tm-30) cc_final: 0.8444 (tt0) REVERT: A 1380 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8504 (pt0) REVERT: A 1693 VAL cc_start: 0.7017 (OUTLIER) cc_final: 0.6693 (t) REVERT: A 1721 PHE cc_start: 0.8036 (OUTLIER) cc_final: 0.6227 (t80) REVERT: A 1786 PHE cc_start: 0.6941 (t80) cc_final: 0.6618 (t80) REVERT: A 1999 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8387 (mt-10) REVERT: A 2059 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8354 (pp) REVERT: A 2187 LEU cc_start: 0.6969 (pt) cc_final: 0.6707 (tt) REVERT: A 2204 GLU cc_start: 0.8853 (mt-10) cc_final: 0.8475 (mt-10) outliers start: 44 outliers final: 36 residues processed: 203 average time/residue: 0.1008 time to fit residues: 31.1371 Evaluate side-chains 204 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 163 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 754 TYR Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1352 VAL Chi-restraints excluded: chain A residue 1357 PHE Chi-restraints excluded: chain A residue 1363 VAL Chi-restraints excluded: chain A residue 1380 GLN Chi-restraints excluded: chain A residue 1414 PHE Chi-restraints excluded: chain A residue 1427 THR Chi-restraints excluded: chain A residue 1463 CYS Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1551 VAL Chi-restraints excluded: chain A residue 1693 VAL Chi-restraints excluded: chain A residue 1721 PHE Chi-restraints excluded: chain A residue 1762 ILE Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1841 VAL Chi-restraints excluded: chain A residue 2059 LEU Chi-restraints excluded: chain A residue 2065 VAL Chi-restraints excluded: chain A residue 2066 VAL Chi-restraints excluded: chain A residue 2097 VAL Chi-restraints excluded: chain A residue 2099 LEU Chi-restraints excluded: chain A residue 2108 GLU Chi-restraints excluded: chain A residue 2174 ASN Chi-restraints excluded: chain A residue 2190 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 145 optimal weight: 6.9990 chunk 114 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 chunk 88 optimal weight: 0.4980 chunk 163 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 146 optimal weight: 0.7980 chunk 158 optimal weight: 6.9990 chunk 62 optimal weight: 0.7980 chunk 169 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 ASN ** A1634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2174 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.106657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.074964 restraints weight = 26526.953| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.59 r_work: 0.2920 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14146 Z= 0.118 Angle : 0.574 11.742 19258 Z= 0.280 Chirality : 0.041 0.177 2242 Planarity : 0.004 0.058 2400 Dihedral : 5.721 56.591 2219 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.20 % Allowed : 19.03 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.21), residues: 1753 helix: 2.02 (0.17), residues: 984 sheet: -0.14 (0.40), residues: 181 loop : -2.05 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2189 TYR 0.011 0.001 TYR A1206 PHE 0.017 0.001 PHE A 846 TRP 0.017 0.001 TRP A1705 HIS 0.005 0.001 HIS A 470 Details of bonding type rmsd covalent geometry : bond 0.00262 (14129) covalent geometry : angle 0.56703 (19219) SS BOND : bond 0.00385 ( 6) SS BOND : angle 1.85602 ( 12) hydrogen bonds : bond 0.03815 ( 750) hydrogen bonds : angle 3.56851 ( 2187) Misc. bond : bond 0.00133 ( 2) link_BETA1-3 : bond 0.00576 ( 1) link_BETA1-3 : angle 1.76904 ( 3) link_BETA1-4 : bond 0.00259 ( 3) link_BETA1-4 : angle 2.21633 ( 9) link_BETA1-6 : bond 0.00735 ( 1) link_BETA1-6 : angle 1.39852 ( 3) link_NAG-ASN : bond 0.00157 ( 4) link_NAG-ASN : angle 2.29095 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 167 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 378 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.8937 (mm) REVERT: A 662 GLU cc_start: 0.8799 (tm-30) cc_final: 0.8542 (tt0) REVERT: A 742 ARG cc_start: 0.8487 (mmt90) cc_final: 0.7985 (mtm180) REVERT: A 1015 MET cc_start: 0.7678 (ttm) cc_final: 0.7394 (mtt) REVERT: A 1128 LEU cc_start: 0.8480 (pt) cc_final: 0.8205 (tt) REVERT: A 1180 VAL cc_start: 0.9036 (m) cc_final: 0.8816 (t) REVERT: A 1245 GLU cc_start: 0.8896 (tm-30) cc_final: 0.8475 (tt0) REVERT: A 1380 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8534 (pt0) REVERT: A 1693 VAL cc_start: 0.7015 (OUTLIER) cc_final: 0.6695 (t) REVERT: A 1721 PHE cc_start: 0.8040 (OUTLIER) cc_final: 0.6306 (t80) REVERT: A 1786 PHE cc_start: 0.6946 (t80) cc_final: 0.6625 (t80) REVERT: A 1999 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8382 (mt-10) REVERT: A 2059 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8350 (pp) REVERT: A 2131 LEU cc_start: 0.8831 (mt) cc_final: 0.8583 (mp) REVERT: A 2204 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8480 (mt-10) outliers start: 45 outliers final: 37 residues processed: 203 average time/residue: 0.1049 time to fit residues: 32.6348 Evaluate side-chains 207 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 165 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 754 TYR Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1352 VAL Chi-restraints excluded: chain A residue 1357 PHE Chi-restraints excluded: chain A residue 1363 VAL Chi-restraints excluded: chain A residue 1380 GLN Chi-restraints excluded: chain A residue 1414 PHE Chi-restraints excluded: chain A residue 1427 THR Chi-restraints excluded: chain A residue 1463 CYS Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1477 CYS Chi-restraints excluded: chain A residue 1551 VAL Chi-restraints excluded: chain A residue 1693 VAL Chi-restraints excluded: chain A residue 1721 PHE Chi-restraints excluded: chain A residue 1753 MET Chi-restraints excluded: chain A residue 1762 ILE Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1841 VAL Chi-restraints excluded: chain A residue 2059 LEU Chi-restraints excluded: chain A residue 2065 VAL Chi-restraints excluded: chain A residue 2066 VAL Chi-restraints excluded: chain A residue 2097 VAL Chi-restraints excluded: chain A residue 2099 LEU Chi-restraints excluded: chain A residue 2108 GLU Chi-restraints excluded: chain A residue 2190 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 124 optimal weight: 4.9990 chunk 166 optimal weight: 0.8980 chunk 134 optimal weight: 0.8980 chunk 40 optimal weight: 0.4980 chunk 156 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 154 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 112 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.107381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.075359 restraints weight = 26433.986| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.64 r_work: 0.2933 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14146 Z= 0.112 Angle : 0.569 11.859 19258 Z= 0.279 Chirality : 0.040 0.180 2242 Planarity : 0.004 0.053 2400 Dihedral : 5.590 55.522 2219 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.12 % Allowed : 19.53 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.21), residues: 1753 helix: 2.08 (0.17), residues: 984 sheet: 0.14 (0.41), residues: 173 loop : -2.02 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2189 TYR 0.011 0.001 TYR A1206 PHE 0.016 0.001 PHE A 846 TRP 0.018 0.001 TRP A1705 HIS 0.005 0.001 HIS A 470 Details of bonding type rmsd covalent geometry : bond 0.00244 (14129) covalent geometry : angle 0.56331 (19219) SS BOND : bond 0.00332 ( 6) SS BOND : angle 1.72124 ( 12) hydrogen bonds : bond 0.03622 ( 750) hydrogen bonds : angle 3.50547 ( 2187) Misc. bond : bond 0.00101 ( 2) link_BETA1-3 : bond 0.00603 ( 1) link_BETA1-3 : angle 1.66116 ( 3) link_BETA1-4 : bond 0.00234 ( 3) link_BETA1-4 : angle 2.09205 ( 9) link_BETA1-6 : bond 0.00783 ( 1) link_BETA1-6 : angle 1.32596 ( 3) link_NAG-ASN : bond 0.00162 ( 4) link_NAG-ASN : angle 2.21306 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 169 time to evaluate : 0.483 Fit side-chains revert: symmetry clash REVERT: A 378 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8871 (mm) REVERT: A 662 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8387 (tt0) REVERT: A 742 ARG cc_start: 0.8293 (mmt90) cc_final: 0.7883 (mtm180) REVERT: A 1015 MET cc_start: 0.7562 (ttm) cc_final: 0.7281 (mtt) REVERT: A 1128 LEU cc_start: 0.8332 (pt) cc_final: 0.8105 (tt) REVERT: A 1180 VAL cc_start: 0.9068 (m) cc_final: 0.8862 (t) REVERT: A 1245 GLU cc_start: 0.8710 (tm-30) cc_final: 0.8282 (tt0) REVERT: A 1380 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8376 (pt0) REVERT: A 1693 VAL cc_start: 0.6756 (OUTLIER) cc_final: 0.6488 (t) REVERT: A 1721 PHE cc_start: 0.7920 (OUTLIER) cc_final: 0.6198 (t80) REVERT: A 1753 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.8615 (mtt) REVERT: A 1786 PHE cc_start: 0.6947 (t80) cc_final: 0.6686 (t80) REVERT: A 1999 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8164 (mt-10) REVERT: A 2059 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8298 (pp) REVERT: A 2131 LEU cc_start: 0.8751 (mt) cc_final: 0.8498 (mp) REVERT: A 2204 GLU cc_start: 0.8714 (mt-10) cc_final: 0.8420 (mt-10) outliers start: 44 outliers final: 36 residues processed: 205 average time/residue: 0.1056 time to fit residues: 33.4485 Evaluate side-chains 207 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 165 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 754 TYR Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1357 PHE Chi-restraints excluded: chain A residue 1363 VAL Chi-restraints excluded: chain A residue 1380 GLN Chi-restraints excluded: chain A residue 1427 THR Chi-restraints excluded: chain A residue 1463 CYS Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1477 CYS Chi-restraints excluded: chain A residue 1551 VAL Chi-restraints excluded: chain A residue 1693 VAL Chi-restraints excluded: chain A residue 1721 PHE Chi-restraints excluded: chain A residue 1753 MET Chi-restraints excluded: chain A residue 1762 ILE Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1841 VAL Chi-restraints excluded: chain A residue 2000 LEU Chi-restraints excluded: chain A residue 2059 LEU Chi-restraints excluded: chain A residue 2065 VAL Chi-restraints excluded: chain A residue 2066 VAL Chi-restraints excluded: chain A residue 2097 VAL Chi-restraints excluded: chain A residue 2099 LEU Chi-restraints excluded: chain A residue 2108 GLU Chi-restraints excluded: chain A residue 2190 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 67 optimal weight: 0.0040 chunk 100 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 72 optimal weight: 0.0870 chunk 66 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 overall best weight: 0.5370 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN ** A1634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.107860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.075967 restraints weight = 26674.198| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.65 r_work: 0.2944 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14146 Z= 0.107 Angle : 0.571 11.809 19258 Z= 0.278 Chirality : 0.040 0.181 2242 Planarity : 0.004 0.053 2400 Dihedral : 5.490 55.036 2219 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.05 % Allowed : 19.60 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.21), residues: 1753 helix: 2.10 (0.17), residues: 985 sheet: 0.26 (0.41), residues: 172 loop : -1.96 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2200 TYR 0.011 0.001 TYR A 650 PHE 0.018 0.001 PHE A1835 TRP 0.018 0.001 TRP A1705 HIS 0.005 0.001 HIS A 470 Details of bonding type rmsd covalent geometry : bond 0.00230 (14129) covalent geometry : angle 0.56580 (19219) SS BOND : bond 0.00316 ( 6) SS BOND : angle 1.61221 ( 12) hydrogen bonds : bond 0.03564 ( 750) hydrogen bonds : angle 3.46165 ( 2187) Misc. bond : bond 0.00093 ( 2) link_BETA1-3 : bond 0.00592 ( 1) link_BETA1-3 : angle 1.61297 ( 3) link_BETA1-4 : bond 0.00224 ( 3) link_BETA1-4 : angle 2.05482 ( 9) link_BETA1-6 : bond 0.00786 ( 1) link_BETA1-6 : angle 1.34014 ( 3) link_NAG-ASN : bond 0.00172 ( 4) link_NAG-ASN : angle 2.05607 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4144.69 seconds wall clock time: 71 minutes 20.94 seconds (4280.94 seconds total)