Starting phenix.real_space_refine on Mon Jun 23 06:15:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oq3_17103/06_2025/8oq3_17103.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oq3_17103/06_2025/8oq3_17103.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8oq3_17103/06_2025/8oq3_17103.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oq3_17103/06_2025/8oq3_17103.map" model { file = "/net/cci-nas-00/data/ceres_data/8oq3_17103/06_2025/8oq3_17103.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oq3_17103/06_2025/8oq3_17103.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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 118 5.16 5 C 16850 2.51 5 N 4492 2.21 5 O 5136 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 26596 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 12307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1556, 12307 Classifications: {'peptide': 1556} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 77, 'TRANS': 1477} Chain breaks: 1 Chain: "C" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 938 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "D" Number of atoms: 12307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1556, 12307 Classifications: {'peptide': 1556} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 77, 'TRANS': 1477} Chain breaks: 1 Chain: "F" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 938 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 17.62, per 1000 atoms: 0.66 Number of scatterers: 26596 At special positions: 0 Unit cell: (104.167, 199.923, 199.276, 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 118 16.00 O 5136 8.00 N 4492 7.00 C 16850 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=23, symmetry=0 Simple disulfide: pdb=" SG CYS A 559 " - pdb=" SG CYS A 816 " distance=2.03 Simple disulfide: pdb=" SG CYS A 627 " - pdb=" SG CYS A 662 " distance=2.03 Simple disulfide: pdb=" SG CYS A 873 " - pdb=" SG CYS A1513 " distance=2.03 Simple disulfide: pdb=" SG CYS A1101 " - pdb=" SG CYS A1158 " distance=2.03 Simple disulfide: pdb=" SG CYS A1358 " - pdb=" SG CYS A1489 " distance=2.03 Simple disulfide: pdb=" SG CYS A1389 " - pdb=" SG CYS A1458 " distance=2.03 Simple disulfide: pdb=" SG CYS A1506 " - pdb=" SG CYS A1511 " distance=2.03 Simple disulfide: pdb=" SG CYS A1518 " - pdb=" SG CYS A1590 " distance=2.03 Simple disulfide: pdb=" SG CYS A1537 " - pdb=" SG CYS A1661 " distance=2.03 Simple disulfide: pdb=" SG CYS A1637 " - pdb=" SG CYS A1646 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.02 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS F 108 " distance=2.02 Simple disulfide: pdb=" SG CYS D 559 " - pdb=" SG CYS D 816 " distance=2.03 Simple disulfide: pdb=" SG CYS D 627 " - pdb=" SG CYS D 662 " distance=2.03 Simple disulfide: pdb=" SG CYS D 873 " - pdb=" SG CYS D1513 " distance=2.03 Simple disulfide: pdb=" SG CYS D1101 " - pdb=" SG CYS D1158 " distance=2.03 Simple disulfide: pdb=" SG CYS D1358 " - pdb=" SG CYS D1489 " distance=2.03 Simple disulfide: pdb=" SG CYS D1389 " - pdb=" SG CYS D1458 " distance=2.03 Simple disulfide: pdb=" SG CYS D1506 " - pdb=" SG CYS D1511 " distance=2.03 Simple disulfide: pdb=" SG CYS D1518 " - pdb=" SG CYS D1590 " distance=2.03 Simple disulfide: pdb=" SG CYS D1537 " - pdb=" SG CYS D1661 " distance=2.03 Simple disulfide: pdb=" SG CYS D1637 " - pdb=" SG CYS D1646 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " NAG-ASN " NAG A1701 " - " ASN A 939 " " NAG D1701 " - " ASN D 939 " " NAG G 1 " - " ASN D 85 " " NAG H 1 " - " ASN A 85 " Time building additional restraints: 6.36 Conformation dependent library (CDL) restraints added in 3.6 seconds 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6288 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 51 sheets defined 19.7% alpha, 35.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.47 Creating SS restraints... Processing helix chain 'A' and resid 77 through 81 removed outlier: 3.521A pdb=" N THR A 80 " --> pdb=" O THR A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 311 removed outlier: 3.505A pdb=" N LEU A 307 " --> pdb=" O SER A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 320 removed outlier: 3.500A pdb=" N VAL A 320 " --> pdb=" O GLU A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 removed outlier: 3.779A pdb=" N ASN A 451 " --> pdb=" O THR A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 526 removed outlier: 3.975A pdb=" N ILE A 526 " --> pdb=" O THR A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 606 Processing helix chain 'A' and resid 612 through 622 Processing helix chain 'A' and resid 634 through 643 Processing helix chain 'A' and resid 754 through 759 removed outlier: 3.644A pdb=" N GLU A 759 " --> pdb=" O ILE A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1004 removed outlier: 3.886A pdb=" N LEU A1003 " --> pdb=" O LEU A1000 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE A1004 " --> pdb=" O LYS A1001 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1000 through 1004' Processing helix chain 'A' and resid 1012 through 1032 Proline residue: A1020 - end of helix Processing helix chain 'A' and resid 1039 through 1057 removed outlier: 3.937A pdb=" N GLN A1043 " --> pdb=" O LEU A1039 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LYS A1050 " --> pdb=" O LEU A1046 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLN A1055 " --> pdb=" O LYS A1051 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU A1057 " --> pdb=" O TYR A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1090 removed outlier: 3.701A pdb=" N LEU A1088 " --> pdb=" O LYS A1084 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1112 removed outlier: 3.829A pdb=" N GLN A1112 " --> pdb=" O ILE A1108 " (cutoff:3.500A) Processing helix chain 'A' and resid 1130 through 1134 removed outlier: 3.734A pdb=" N LEU A1133 " --> pdb=" O ILE A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1153 removed outlier: 3.607A pdb=" N ALA A1142 " --> pdb=" O GLU A1138 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1177 Processing helix chain 'A' and resid 1185 through 1198 Processing helix chain 'A' and resid 1203 through 1213 Processing helix chain 'A' and resid 1214 through 1218 removed outlier: 3.524A pdb=" N ASN A1218 " --> pdb=" O LYS A1215 " (cutoff:3.500A) Processing helix chain 'A' and resid 1225 through 1243 removed outlier: 3.776A pdb=" N ASN A1229 " --> pdb=" O LYS A1225 " (cutoff:3.500A) Processing helix chain 'A' and resid 1248 through 1260 removed outlier: 4.023A pdb=" N VAL A1252 " --> pdb=" O PHE A1248 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARG A1260 " --> pdb=" O LEU A1256 " (cutoff:3.500A) Processing helix chain 'A' and resid 1268 through 1286 removed outlier: 3.717A pdb=" N PHE A1276 " --> pdb=" O THR A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1414 through 1423 Processing helix chain 'A' and resid 1497 through 1501 Processing helix chain 'A' and resid 1528 through 1537 removed outlier: 3.578A pdb=" N CYS A1537 " --> pdb=" O LEU A1533 " (cutoff:3.500A) Processing helix chain 'A' and resid 1590 through 1595 removed outlier: 3.840A pdb=" N LYS A1595 " --> pdb=" O ARG A1591 " (cutoff:3.500A) Processing helix chain 'A' and resid 1609 through 1611 No H-bonds generated for 'chain 'A' and resid 1609 through 1611' Processing helix chain 'A' and resid 1635 through 1639 removed outlier: 3.763A pdb=" N ASP A1639 " --> pdb=" O GLU A1636 " (cutoff:3.500A) Processing helix chain 'A' and resid 1642 through 1657 Processing helix chain 'C' and resid 62 through 65 removed outlier: 4.080A pdb=" N LYS C 65 " --> pdb=" O ASP C 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 62 through 65' Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.967A pdb=" N THR C 91 " --> pdb=" O PRO C 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 81 Processing helix chain 'D' and resid 303 through 309 removed outlier: 3.848A pdb=" N ASP D 309 " --> pdb=" O LYS D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 320 removed outlier: 3.512A pdb=" N VAL D 320 " --> pdb=" O GLU D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 436 removed outlier: 4.026A pdb=" N GLN D 436 " --> pdb=" O GLU D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 452 removed outlier: 3.633A pdb=" N ASN D 451 " --> pdb=" O THR D 448 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER D 452 " --> pdb=" O VAL D 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 448 through 452' Processing helix chain 'D' and resid 522 through 526 removed outlier: 3.568A pdb=" N PHE D 525 " --> pdb=" O THR D 522 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE D 526 " --> pdb=" O THR D 523 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 522 through 526' Processing helix chain 'D' and resid 600 through 606 Processing helix chain 'D' and resid 612 through 623 Processing helix chain 'D' and resid 634 through 643 Processing helix chain 'D' and resid 754 through 760 Processing helix chain 'D' and resid 996 through 1004 removed outlier: 3.636A pdb=" N ARG D 999 " --> pdb=" O ASP D 996 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS D1001 " --> pdb=" O GLU D 998 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N HIS D1002 " --> pdb=" O ARG D 999 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE D1004 " --> pdb=" O LYS D1001 " (cutoff:3.500A) Processing helix chain 'D' and resid 1012 through 1032 Proline residue: D1020 - end of helix Processing helix chain 'D' and resid 1033 through 1038 Processing helix chain 'D' and resid 1040 through 1055 removed outlier: 4.435A pdb=" N GLY D1044 " --> pdb=" O GLU D1040 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU D1046 " --> pdb=" O ARG D1042 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN D1055 " --> pdb=" O LYS D1051 " (cutoff:3.500A) Processing helix chain 'D' and resid 1075 through 1089 removed outlier: 3.505A pdb=" N THR D1079 " --> pdb=" O SER D1075 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU D1088 " --> pdb=" O LYS D1084 " (cutoff:3.500A) Processing helix chain 'D' and resid 1097 through 1111 removed outlier: 3.619A pdb=" N LYS D1111 " --> pdb=" O LEU D1107 " (cutoff:3.500A) Processing helix chain 'D' and resid 1130 through 1134 removed outlier: 4.598A pdb=" N LEU D1133 " --> pdb=" O ILE D1130 " (cutoff:3.500A) Processing helix chain 'D' and resid 1138 through 1154 removed outlier: 3.548A pdb=" N ALA D1142 " --> pdb=" O GLU D1138 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA D1154 " --> pdb=" O SER D1150 " (cutoff:3.500A) Processing helix chain 'D' and resid 1164 through 1179 removed outlier: 3.701A pdb=" N ALA D1178 " --> pdb=" O ASP D1174 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASN D1179 " --> pdb=" O PHE D1175 " (cutoff:3.500A) Processing helix chain 'D' and resid 1185 through 1198 removed outlier: 3.541A pdb=" N VAL D1189 " --> pdb=" O ARG D1185 " (cutoff:3.500A) Processing helix chain 'D' and resid 1203 through 1213 Processing helix chain 'D' and resid 1214 through 1218 removed outlier: 3.634A pdb=" N LYS D1217 " --> pdb=" O ALA D1214 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN D1218 " --> pdb=" O LYS D1215 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1214 through 1218' Processing helix chain 'D' and resid 1225 through 1243 removed outlier: 3.748A pdb=" N ASN D1229 " --> pdb=" O LYS D1225 " (cutoff:3.500A) Processing helix chain 'D' and resid 1248 through 1259 removed outlier: 3.915A pdb=" N VAL D1252 " --> pdb=" O PHE D1248 " (cutoff:3.500A) Processing helix chain 'D' and resid 1268 through 1285 removed outlier: 4.191A pdb=" N PHE D1276 " --> pdb=" O THR D1272 " (cutoff:3.500A) Processing helix chain 'D' and resid 1414 through 1423 Processing helix chain 'D' and resid 1430 through 1436 removed outlier: 3.512A pdb=" N LEU D1434 " --> pdb=" O SER D1430 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS D1436 " --> pdb=" O TYR D1432 " (cutoff:3.500A) Processing helix chain 'D' and resid 1497 through 1501 removed outlier: 3.579A pdb=" N GLY D1500 " --> pdb=" O LYS D1497 " (cutoff:3.500A) Processing helix chain 'D' and resid 1528 through 1537 Processing helix chain 'D' and resid 1587 through 1589 No H-bonds generated for 'chain 'D' and resid 1587 through 1589' Processing helix chain 'D' and resid 1590 through 1595 removed outlier: 3.918A pdb=" N LYS D1595 " --> pdb=" O ARG D1591 " (cutoff:3.500A) Processing helix chain 'D' and resid 1609 through 1611 No H-bonds generated for 'chain 'D' and resid 1609 through 1611' Processing helix chain 'D' and resid 1635 through 1639 removed outlier: 3.664A pdb=" N ASP D1639 " --> pdb=" O GLU D1636 " (cutoff:3.500A) Processing helix chain 'D' and resid 1642 through 1657 Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.545A pdb=" N ASP F 90 " --> pdb=" O LYS F 87 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR F 91 " --> pdb=" O PRO F 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 87 through 91' Processing helix chain 'F' and resid 106 through 110 removed outlier: 4.217A pdb=" N GLU F 109 " --> pdb=" O THR F 106 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 89 removed outlier: 8.451A pdb=" N THR A 41 " --> pdb=" O PRO A 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 35 removed outlier: 6.402A pdb=" N LEU A 34 " --> pdb=" O SER A 124 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N LYS A 104 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ASP A 61 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N VAL A 68 " --> pdb=" O ASP A 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 129 through 134 Processing sheet with id=AA4, first strand: chain 'A' and resid 138 through 139 Processing sheet with id=AA5, first strand: chain 'A' and resid 232 through 238 Processing sheet with id=AA6, first strand: chain 'A' and resid 243 through 244 removed outlier: 5.602A pdb=" N TYR A 243 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N MET A 338 " --> pdb=" O LEU A 332 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LEU A 332 " --> pdb=" O MET A 338 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N GLN A 340 " --> pdb=" O VAL A 330 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VAL A 330 " --> pdb=" O GLN A 340 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N GLU A 342 " --> pdb=" O ALA A 328 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ALA A 328 " --> pdb=" O GLU A 342 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N SER A 344 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL A 326 " --> pdb=" O SER A 344 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N PHE A 273 " --> pdb=" O SER A 287 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N SER A 287 " --> pdb=" O PHE A 273 " (cutoff:3.500A) removed outlier: 11.903A pdb=" N ILE A 275 " --> pdb=" O PRO A 285 " (cutoff:3.500A) removed outlier: 10.325A pdb=" N ASP A 277 " --> pdb=" O SER A 283 " (cutoff:3.500A) removed outlier: 10.654A pdb=" N SER A 283 " --> pdb=" O ASP A 277 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 356 Processing sheet with id=AA8, first strand: chain 'A' and resid 363 through 364 Processing sheet with id=AA9, first strand: chain 'A' and resid 455 through 460 Processing sheet with id=AB1, first strand: chain 'A' and resid 499 through 507 removed outlier: 5.095A pdb=" N LEU A 500 " --> pdb=" O ASN A 496 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ASN A 496 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS A 502 " --> pdb=" O ILE A 494 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N TYR A 489 " --> pdb=" O THR A 536 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N THR A 536 " --> pdb=" O TYR A 489 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 564 through 567 Processing sheet with id=AB3, first strand: chain 'A' and resid 770 through 771 Processing sheet with id=AB4, first strand: chain 'A' and resid 775 through 777 Processing sheet with id=AB5, first strand: chain 'A' and resid 829 through 834 removed outlier: 4.040A pdb=" N ARG A 848 " --> pdb=" O ARG A 834 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 838 through 840 removed outlier: 5.967A pdb=" N VAL A 839 " --> pdb=" O VAL A 932 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 936 through 947 removed outlier: 3.997A pdb=" N TYR A1348 " --> pdb=" O MET A 938 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL A1344 " --> pdb=" O VAL A 942 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL A 944 " --> pdb=" O LEU A1342 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU A1342 " --> pdb=" O VAL A 944 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N THR A 946 " --> pdb=" O GLY A1340 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLY A1340 " --> pdb=" O THR A 946 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 957 through 962 removed outlier: 3.965A pdb=" N GLU A1335 " --> pdb=" O ASP A1295 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1060 through 1061 removed outlier: 3.627A pdb=" N ALA A1065 " --> pdb=" O GLN A1061 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1361 through 1369 Processing sheet with id=AC2, first strand: chain 'A' and resid 1427 through 1428 Processing sheet with id=AC3, first strand: chain 'A' and resid 1504 through 1507 Processing sheet with id=AC4, first strand: chain 'A' and resid 1619 through 1621 removed outlier: 6.715A pdb=" N GLU A1560 " --> pdb=" O VAL A1552 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N VAL A1552 " --> pdb=" O GLU A1560 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE A1562 " --> pdb=" O VAL A1550 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR A1543 " --> pdb=" O GLY A1606 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N HIS A1601 " --> pdb=" O TRP A1631 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AC6, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AC7, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.068A pdb=" N GLY C 10 " --> pdb=" O THR C 120 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N SER C 122 " --> pdb=" O GLY C 10 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL C 12 " --> pdb=" O SER C 122 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N ARG C 38 " --> pdb=" O PHE C 47 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N PHE C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.068A pdb=" N GLY C 10 " --> pdb=" O THR C 120 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N SER C 122 " --> pdb=" O GLY C 10 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL C 12 " --> pdb=" O SER C 122 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 83 through 89 removed outlier: 8.444A pdb=" N THR D 41 " --> pdb=" O PRO D 31 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 33 through 35 removed outlier: 4.171A pdb=" N GLN D 115 " --> pdb=" O PHE D 112 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LYS D 104 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ASP D 61 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N VAL D 68 " --> pdb=" O ASP D 61 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 129 through 134 Processing sheet with id=AD3, first strand: chain 'D' and resid 138 through 139 Processing sheet with id=AD4, first strand: chain 'D' and resid 232 through 238 Processing sheet with id=AD5, first strand: chain 'D' and resid 243 through 244 removed outlier: 5.576A pdb=" N TYR D 243 " --> pdb=" O VAL D 349 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N MET D 338 " --> pdb=" O LEU D 332 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N LEU D 332 " --> pdb=" O MET D 338 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N GLN D 340 " --> pdb=" O VAL D 330 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N VAL D 330 " --> pdb=" O GLN D 340 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLU D 342 " --> pdb=" O ALA D 328 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ALA D 328 " --> pdb=" O GLU D 342 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N SER D 344 " --> pdb=" O VAL D 326 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL D 326 " --> pdb=" O SER D 344 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N PHE D 273 " --> pdb=" O SER D 287 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N SER D 287 " --> pdb=" O PHE D 273 " (cutoff:3.500A) removed outlier: 11.809A pdb=" N ILE D 275 " --> pdb=" O PRO D 285 " (cutoff:3.500A) removed outlier: 10.607A pdb=" N ASP D 277 " --> pdb=" O SER D 283 " (cutoff:3.500A) removed outlier: 10.389A pdb=" N SER D 283 " --> pdb=" O ASP D 277 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 354 through 356 Processing sheet with id=AD7, first strand: chain 'D' and resid 363 through 364 Processing sheet with id=AD8, first strand: chain 'D' and resid 455 through 459 Processing sheet with id=AD9, first strand: chain 'D' and resid 499 through 507 removed outlier: 5.097A pdb=" N LEU D 500 " --> pdb=" O ASN D 496 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ASN D 496 " --> pdb=" O LEU D 500 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS D 502 " --> pdb=" O ILE D 494 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N TYR D 489 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N THR D 536 " --> pdb=" O TYR D 489 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 564 through 567 Processing sheet with id=AE2, first strand: chain 'D' and resid 770 through 771 Processing sheet with id=AE3, first strand: chain 'D' and resid 775 through 777 Processing sheet with id=AE4, first strand: chain 'D' and resid 829 through 834 removed outlier: 4.056A pdb=" N ARG D 848 " --> pdb=" O ARG D 834 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 838 through 840 removed outlier: 3.831A pdb=" N HIS D 882 " --> pdb=" O LEU D 866 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 936 through 947 removed outlier: 5.538A pdb=" N ARG D 937 " --> pdb=" O ALA D1350 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ALA D1350 " --> pdb=" O ARG D 937 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ASN D 939 " --> pdb=" O TYR D1348 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N TYR D1348 " --> pdb=" O ASN D 939 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N THR D 941 " --> pdb=" O THR D1346 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N THR D1346 " --> pdb=" O THR D 941 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N GLN D1339 " --> pdb=" O THR D 985 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 957 through 961 removed outlier: 3.594A pdb=" N GLU D1335 " --> pdb=" O ASP D1295 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1361 through 1369 Processing sheet with id=AE9, first strand: chain 'D' and resid 1398 through 1399 removed outlier: 3.698A pdb=" N VAL D1451 " --> pdb=" O ALA D1398 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 1428 through 1429 Processing sheet with id=AF2, first strand: chain 'D' and resid 1504 through 1507 Processing sheet with id=AF3, first strand: chain 'D' and resid 1619 through 1621 removed outlier: 6.479A pdb=" N GLU D1560 " --> pdb=" O VAL D1552 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL D1552 " --> pdb=" O GLU D1560 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE D1562 " --> pdb=" O VAL D1550 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LYS D1546 " --> pdb=" O GLU D1566 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N THR D1568 " --> pdb=" O VAL D1544 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N VAL D1544 " --> pdb=" O THR D1568 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LYS D1570 " --> pdb=" O ASP D1542 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASP D1542 " --> pdb=" O LYS D1570 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR D1543 " --> pdb=" O GLY D1606 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N HIS D1601 " --> pdb=" O TRP D1631 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AF5, first strand: chain 'F' and resid 10 through 13 removed outlier: 5.635A pdb=" N ARG F 38 " --> pdb=" O PHE F 47 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N PHE F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 10 through 13 1113 hydrogen bonds defined for protein. 3012 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: 15.13 Time building geometry restraints manager: 7.65 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: 8459 1.34 - 1.46: 5976 1.46 - 1.58: 12502 1.58 - 1.71: 7 1.71 - 1.83: 188 Bond restraints: 27132 Sorted by residual: bond pdb=" C1 NAG A1701 " pdb=" O5 NAG A1701 " ideal model delta sigma weight residual 1.406 1.487 -0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" CG1 ILE D 921 " pdb=" CD1 ILE D 921 " ideal model delta sigma weight residual 1.513 1.396 0.117 3.90e-02 6.57e+02 9.02e+00 bond pdb=" CG1 ILE A 921 " pdb=" CD1 ILE A 921 " ideal model delta sigma weight residual 1.513 1.396 0.117 3.90e-02 6.57e+02 8.93e+00 bond pdb=" C VAL A1249 " pdb=" N PRO A1250 " ideal model delta sigma weight residual 1.329 1.363 -0.034 1.18e-02 7.18e+03 8.34e+00 bond pdb=" CB LYS D1375 " pdb=" CG LYS D1375 " ideal model delta sigma weight residual 1.520 1.606 -0.086 3.00e-02 1.11e+03 8.26e+00 ... (remaining 27127 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.23: 36305 4.23 - 8.46: 392 8.46 - 12.68: 69 12.68 - 16.91: 17 16.91 - 21.14: 5 Bond angle restraints: 36788 Sorted by residual: angle pdb=" C ASN D 939 " pdb=" CA ASN D 939 " pdb=" CB ASN D 939 " ideal model delta sigma weight residual 110.79 120.71 -9.92 1.39e+00 5.18e-01 5.09e+01 angle pdb=" CB ARG A 979 " pdb=" CG ARG A 979 " pdb=" CD ARG A 979 " ideal model delta sigma weight residual 111.30 127.25 -15.95 2.30e+00 1.89e-01 4.81e+01 angle pdb=" CB MET A1015 " pdb=" CG MET A1015 " pdb=" SD MET A1015 " ideal model delta sigma weight residual 112.70 131.85 -19.15 3.00e+00 1.11e-01 4.07e+01 angle pdb=" CB LYS A1353 " pdb=" CG LYS A1353 " pdb=" CD LYS A1353 " ideal model delta sigma weight residual 111.30 125.66 -14.36 2.30e+00 1.89e-01 3.90e+01 angle pdb=" CA MET D1199 " pdb=" CB MET D1199 " pdb=" CG MET D1199 " ideal model delta sigma weight residual 114.10 125.95 -11.85 2.00e+00 2.50e-01 3.51e+01 ... (remaining 36783 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.47: 14978 21.47 - 42.93: 1318 42.93 - 64.40: 254 64.40 - 85.87: 77 85.87 - 107.33: 18 Dihedral angle restraints: 16645 sinusoidal: 6881 harmonic: 9764 Sorted by residual: dihedral pdb=" CA MET D1018 " pdb=" C MET D1018 " pdb=" N THR D1019 " pdb=" CA THR D1019 " ideal model delta harmonic sigma weight residual -180.00 -143.18 -36.82 0 5.00e+00 4.00e-02 5.42e+01 dihedral pdb=" CB CYS C 108 " pdb=" SG CYS C 108 " pdb=" SG CYS F 108 " pdb=" CB CYS F 108 " ideal model delta sinusoidal sigma weight residual -86.00 -146.49 60.49 1 1.00e+01 1.00e-02 4.87e+01 dihedral pdb=" CA CYS D 662 " pdb=" C CYS D 662 " pdb=" N PRO D 663 " pdb=" CA PRO D 663 " ideal model delta harmonic sigma weight residual -180.00 -149.98 -30.02 0 5.00e+00 4.00e-02 3.60e+01 ... (remaining 16642 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 3610 0.093 - 0.186: 513 0.186 - 0.279: 36 0.279 - 0.372: 11 0.372 - 0.465: 2 Chirality restraints: 4172 Sorted by residual: chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN D 85 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.41e+00 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A 85 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.89e+00 chirality pdb=" C1 NAG A1701 " pdb=" ND2 ASN A 939 " pdb=" C2 NAG A1701 " pdb=" O5 NAG A1701 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.34e+00 ... (remaining 4169 not shown) Planarity restraints: 4756 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A1037 " 0.024 2.00e-02 2.50e+03 3.65e-02 2.33e+01 pdb=" CG PHE A1037 " -0.082 2.00e-02 2.50e+03 pdb=" CD1 PHE A1037 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 PHE A1037 " 0.033 2.00e-02 2.50e+03 pdb=" CE1 PHE A1037 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A1037 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A1037 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1282 " -0.024 2.00e-02 2.50e+03 2.49e-02 1.24e+01 pdb=" CG TYR A1282 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 TYR A1282 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR A1282 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A1282 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A1282 " -0.022 2.00e-02 2.50e+03 pdb=" CZ TYR A1282 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A1282 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP D1499 " 0.017 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C ASP D1499 " -0.060 2.00e-02 2.50e+03 pdb=" O ASP D1499 " 0.023 2.00e-02 2.50e+03 pdb=" N GLY D1500 " 0.020 2.00e-02 2.50e+03 ... (remaining 4753 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 7705 2.83 - 3.35: 20989 3.35 - 3.87: 45747 3.87 - 4.38: 50131 4.38 - 4.90: 88902 Nonbonded interactions: 213474 Sorted by model distance: nonbonded pdb=" OE1 GLU A 45 " pdb=" OH TYR A 534 " model vdw 2.313 3.040 nonbonded pdb=" OG1 THR D 522 " pdb=" OD1 ASP D 524 " model vdw 2.321 3.040 nonbonded pdb=" OD1 ASP D 135 " pdb=" OH TYR D 139 " model vdw 2.327 3.040 nonbonded pdb=" OH TYR A 227 " pdb=" OE1 GLU A 769 " model vdw 2.331 3.040 nonbonded pdb=" OD1 ASP A 135 " pdb=" OH TYR A 139 " model vdw 2.338 3.040 ... (remaining 213469 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: 0.13 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } 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=0.00 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: 8.190 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: 0.020 Extract box with map and model: 1.260 Check model and map are aligned: 0.220 Set scattering table: 0.220 Process input model: 68.400 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.140 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: 0.020 Load rotamer database and sin/cos tables:12.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 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 : 0.007 0.117 27163 Z= 0.303 Angle : 1.163 21.140 36858 Z= 0.595 Chirality : 0.064 0.465 4172 Planarity : 0.008 0.106 4752 Dihedral : 17.278 107.335 10288 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.14 % Allowed : 21.26 % Favored : 76.60 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.13), residues: 3346 helix: -3.10 (0.14), residues: 542 sheet: -0.17 (0.14), residues: 1310 loop : -1.32 (0.14), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A1605 HIS 0.007 0.001 HIS A 457 PHE 0.082 0.003 PHE A1037 TYR 0.058 0.003 TYR A1282 ARG 0.019 0.001 ARG F 19 Details of bonding type rmsd link_NAG-ASN : bond 0.01748 ( 4) link_NAG-ASN : angle 5.47713 ( 12) link_BETA1-4 : bond 0.01185 ( 4) link_BETA1-4 : angle 4.02808 ( 12) hydrogen bonds : bond 0.12627 ( 1079) hydrogen bonds : angle 6.91790 ( 3012) SS BOND : bond 0.00356 ( 23) SS BOND : angle 1.15701 ( 46) covalent geometry : bond 0.00674 (27132) covalent geometry : angle 1.15736 (36788) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 191 time to evaluate : 3.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 938 MET cc_start: 0.8518 (ttp) cc_final: 0.8250 (tmt) REVERT: A 1298 LEU cc_start: 0.9584 (pt) cc_final: 0.9050 (tp) REVERT: D 1015 MET cc_start: 0.7407 (mmm) cc_final: 0.5303 (ttm) REVERT: D 1018 MET cc_start: 0.3021 (mmp) cc_final: 0.1728 (ptm) REVERT: D 1199 MET cc_start: 0.6736 (pmm) cc_final: 0.6392 (pmm) outliers start: 63 outliers final: 47 residues processed: 244 average time/residue: 1.1516 time to fit residues: 337.9459 Evaluate side-chains 229 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 182 time to evaluate : 3.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1030 GLU Chi-restraints excluded: chain A residue 1390 THR Chi-restraints excluded: chain A residue 1459 LEU Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 305 LYS Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 371 ASP Chi-restraints excluded: chain D residue 410 SER Chi-restraints excluded: chain D residue 487 ILE Chi-restraints excluded: chain D residue 514 LEU Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 598 VAL Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 648 SER Chi-restraints excluded: chain D residue 881 ARG Chi-restraints excluded: chain D residue 974 THR Chi-restraints excluded: chain D residue 1090 VAL Chi-restraints excluded: chain D residue 1341 THR Chi-restraints excluded: chain D residue 1390 THR Chi-restraints excluded: chain D residue 1395 ASP Chi-restraints excluded: chain D residue 1404 ASP Chi-restraints excluded: chain D residue 1469 VAL Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 67 ARG Chi-restraints excluded: chain F residue 122 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 282 optimal weight: 20.0000 chunk 253 optimal weight: 0.0070 chunk 140 optimal weight: 2.9990 chunk 86 optimal weight: 0.3980 chunk 170 optimal weight: 6.9990 chunk 135 optimal weight: 6.9990 chunk 261 optimal weight: 7.9990 chunk 101 optimal weight: 8.9990 chunk 159 optimal weight: 0.5980 chunk 194 optimal weight: 0.9980 chunk 303 optimal weight: 1.9990 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 103 ASN A 154 HIS A 313 ASN A 333 HIS A 354 GLN A 398 GLN ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 574 GLN A 827 GLN A 858 GLN A1043 GLN A1056 GLN A1136 ASN A1182 ASN A1229 ASN A1309 HIS ** A1473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1643 GLN D 474 ASN D1229 ASN D1289 HIS D1290 GLN ** D1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1473 GLN F 13 GLN F 77 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.138196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.084931 restraints weight = 56228.350| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 3.39 r_work: 0.3145 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27163 Z= 0.122 Angle : 0.587 14.168 36858 Z= 0.297 Chirality : 0.045 0.241 4172 Planarity : 0.004 0.058 4752 Dihedral : 7.796 78.437 3865 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.23 % Allowed : 18.31 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.14), residues: 3346 helix: -1.09 (0.20), residues: 560 sheet: 0.00 (0.14), residues: 1320 loop : -0.87 (0.15), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1605 HIS 0.004 0.001 HIS A 60 PHE 0.016 0.001 PHE A1652 TYR 0.026 0.001 TYR F 80 ARG 0.005 0.000 ARG A 979 Details of bonding type rmsd link_NAG-ASN : bond 0.00752 ( 4) link_NAG-ASN : angle 2.80999 ( 12) link_BETA1-4 : bond 0.00420 ( 4) link_BETA1-4 : angle 3.17523 ( 12) hydrogen bonds : bond 0.03436 ( 1079) hydrogen bonds : angle 5.50394 ( 3012) SS BOND : bond 0.00194 ( 23) SS BOND : angle 0.60932 ( 46) covalent geometry : bond 0.00266 (27132) covalent geometry : angle 0.58258 (36788) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 192 time to evaluate : 2.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 513 ASP cc_start: 0.8625 (m-30) cc_final: 0.8162 (m-30) REVERT: A 879 LYS cc_start: -0.1489 (OUTLIER) cc_final: -0.2051 (ptmm) REVERT: A 938 MET cc_start: 0.8850 (ttp) cc_final: 0.8432 (tmt) REVERT: A 966 ASP cc_start: 0.7897 (OUTLIER) cc_final: 0.7207 (m-30) REVERT: D 581 MET cc_start: 0.9210 (OUTLIER) cc_final: 0.8698 (ttt) REVERT: D 1015 MET cc_start: 0.7366 (mmm) cc_final: 0.6270 (ttm) REVERT: D 1347 MET cc_start: 0.7984 (mtm) cc_final: 0.7575 (mtt) REVERT: F 65 LYS cc_start: 0.8605 (tptp) cc_final: 0.8082 (ttpp) REVERT: F 73 ASP cc_start: 0.8070 (t0) cc_final: 0.7596 (t0) REVERT: F 115 GLN cc_start: 0.9262 (mm-40) cc_final: 0.9010 (mm-40) outliers start: 95 outliers final: 39 residues processed: 264 average time/residue: 1.1363 time to fit residues: 362.0321 Evaluate side-chains 217 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 175 time to evaluate : 3.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 879 LYS Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1030 GLU Chi-restraints excluded: chain A residue 1129 MET Chi-restraints excluded: chain A residue 1246 PHE Chi-restraints excluded: chain A residue 1288 ASP Chi-restraints excluded: chain A residue 1390 THR Chi-restraints excluded: chain A residue 1479 VAL Chi-restraints excluded: chain A residue 1656 MET Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 487 ILE Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 514 LEU Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 598 VAL Chi-restraints excluded: chain D residue 850 VAL Chi-restraints excluded: chain D residue 1390 THR Chi-restraints excluded: chain D residue 1395 ASP Chi-restraints excluded: chain D residue 1469 VAL Chi-restraints excluded: chain D residue 1485 LEU Chi-restraints excluded: chain F residue 67 ARG Chi-restraints excluded: chain F residue 120 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 13 optimal weight: 4.9990 chunk 104 optimal weight: 7.9990 chunk 257 optimal weight: 30.0000 chunk 117 optimal weight: 9.9990 chunk 190 optimal weight: 0.9980 chunk 281 optimal weight: 20.0000 chunk 119 optimal weight: 4.9990 chunk 169 optimal weight: 5.9990 chunk 120 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 HIS A 154 HIS A 378 ASN A 858 GLN A 882 HIS A 883 GLN A1127 GLN ** A1473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 453 ASN D 784 ASN D 882 HIS ** D1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.134539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.080515 restraints weight = 56666.630| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 3.45 r_work: 0.2981 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.104 27163 Z= 0.373 Angle : 0.710 12.810 36858 Z= 0.359 Chirality : 0.049 0.189 4172 Planarity : 0.005 0.061 4752 Dihedral : 6.739 79.857 3823 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.77 % Allowed : 18.48 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.14), residues: 3346 helix: 0.00 (0.22), residues: 546 sheet: 0.09 (0.14), residues: 1284 loop : -0.67 (0.15), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1605 HIS 0.007 0.001 HIS D 918 PHE 0.016 0.002 PHE D 475 TYR 0.016 0.002 TYR D 147 ARG 0.010 0.001 ARG D 979 Details of bonding type rmsd link_NAG-ASN : bond 0.00454 ( 4) link_NAG-ASN : angle 2.17441 ( 12) link_BETA1-4 : bond 0.00299 ( 4) link_BETA1-4 : angle 2.90328 ( 12) hydrogen bonds : bond 0.03756 ( 1079) hydrogen bonds : angle 5.47879 ( 3012) SS BOND : bond 0.00407 ( 23) SS BOND : angle 1.33125 ( 46) covalent geometry : bond 0.00863 (27132) covalent geometry : angle 0.70588 (36788) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 184 time to evaluate : 3.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 879 LYS cc_start: -0.2540 (OUTLIER) cc_final: -0.3491 (pttt) REVERT: A 921 ILE cc_start: 0.8872 (OUTLIER) cc_final: 0.8511 (pp) REVERT: A 938 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8536 (tmt) REVERT: A 966 ASP cc_start: 0.7956 (OUTLIER) cc_final: 0.7421 (m-30) REVERT: A 1255 TRP cc_start: 0.8751 (t60) cc_final: 0.8412 (t60) REVERT: D 305 LYS cc_start: 0.9402 (OUTLIER) cc_final: 0.8944 (tptp) REVERT: D 1274 MET cc_start: 0.4051 (OUTLIER) cc_final: 0.3740 (tpt) REVERT: D 1439 SER cc_start: 0.9479 (m) cc_final: 0.9242 (t) REVERT: F 3 GLN cc_start: 0.8860 (mm-40) cc_final: 0.8049 (mp10) REVERT: F 62 ASP cc_start: 0.9031 (t0) cc_final: 0.8740 (t0) REVERT: F 65 LYS cc_start: 0.8782 (tptp) cc_final: 0.8314 (ttpp) REVERT: F 73 ASP cc_start: 0.8247 (t0) cc_final: 0.7375 (t0) REVERT: F 76 LYS cc_start: 0.8863 (pttm) cc_final: 0.8529 (pmtt) REVERT: F 115 GLN cc_start: 0.9337 (mm-40) cc_final: 0.9118 (mm-40) outliers start: 111 outliers final: 56 residues processed: 268 average time/residue: 1.1740 time to fit residues: 379.5346 Evaluate side-chains 231 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 169 time to evaluate : 2.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 154 HIS Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 879 LYS Chi-restraints excluded: chain A residue 921 ILE Chi-restraints excluded: chain A residue 938 MET Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1030 GLU Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1129 MET Chi-restraints excluded: chain A residue 1246 PHE Chi-restraints excluded: chain A residue 1284 LYS Chi-restraints excluded: chain A residue 1288 ASP Chi-restraints excluded: chain A residue 1390 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 76 LYS Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 305 LYS Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 487 ILE Chi-restraints excluded: chain D residue 514 LEU Chi-restraints excluded: chain D residue 598 VAL Chi-restraints excluded: chain D residue 850 VAL Chi-restraints excluded: chain D residue 1269 THR Chi-restraints excluded: chain D residue 1274 MET Chi-restraints excluded: chain D residue 1390 THR Chi-restraints excluded: chain D residue 1395 ASP Chi-restraints excluded: chain D residue 1469 VAL Chi-restraints excluded: chain F residue 67 ARG Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 120 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 304 optimal weight: 0.7980 chunk 323 optimal weight: 6.9990 chunk 268 optimal weight: 20.0000 chunk 154 optimal weight: 50.0000 chunk 252 optimal weight: 8.9990 chunk 164 optimal weight: 7.9990 chunk 278 optimal weight: 30.0000 chunk 41 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 317 optimal weight: 3.9990 chunk 258 optimal weight: 30.0000 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 HIS A 858 GLN A1179 ASN A1270 GLN A1277 GLN ** A1473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1473 GLN F 13 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.142851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.088649 restraints weight = 57571.316| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 3.43 r_work: 0.3017 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 27163 Z= 0.261 Angle : 0.631 11.765 36858 Z= 0.318 Chirality : 0.047 0.189 4172 Planarity : 0.004 0.060 4752 Dihedral : 6.140 80.654 3822 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.63 % Allowed : 19.16 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.14), residues: 3346 helix: 0.43 (0.22), residues: 546 sheet: 0.15 (0.14), residues: 1290 loop : -0.53 (0.16), residues: 1510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1605 HIS 0.006 0.001 HIS A 154 PHE 0.023 0.001 PHE A1273 TYR 0.019 0.001 TYR F 80 ARG 0.007 0.000 ARG D 979 Details of bonding type rmsd link_NAG-ASN : bond 0.00406 ( 4) link_NAG-ASN : angle 2.04071 ( 12) link_BETA1-4 : bond 0.00300 ( 4) link_BETA1-4 : angle 2.71116 ( 12) hydrogen bonds : bond 0.03337 ( 1079) hydrogen bonds : angle 5.28417 ( 3012) SS BOND : bond 0.00327 ( 23) SS BOND : angle 1.09490 ( 46) covalent geometry : bond 0.00600 (27132) covalent geometry : angle 0.62716 (36788) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 178 time to evaluate : 2.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 VAL cc_start: 0.8734 (OUTLIER) cc_final: 0.8498 (m) REVERT: A 755 ILE cc_start: 0.9205 (OUTLIER) cc_final: 0.8965 (tp) REVERT: A 879 LYS cc_start: -0.2257 (OUTLIER) cc_final: -0.3140 (pttt) REVERT: A 921 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8397 (pp) REVERT: A 938 MET cc_start: 0.8886 (ttp) cc_final: 0.8435 (tmt) REVERT: A 966 ASP cc_start: 0.7876 (OUTLIER) cc_final: 0.7295 (m-30) REVERT: A 1255 TRP cc_start: 0.8749 (t60) cc_final: 0.8337 (t60) REVERT: A 1416 ASP cc_start: 0.9378 (m-30) cc_final: 0.8764 (t0) REVERT: A 1620 TYR cc_start: 0.6901 (m-80) cc_final: 0.6233 (m-80) REVERT: D 973 ASP cc_start: 0.8122 (t0) cc_final: 0.7804 (m-30) REVERT: D 1274 MET cc_start: 0.4233 (OUTLIER) cc_final: 0.3945 (tpt) REVERT: D 1347 MET cc_start: 0.7702 (mtt) cc_final: 0.7400 (mtm) REVERT: F 3 GLN cc_start: 0.8778 (mm-40) cc_final: 0.8007 (mp10) REVERT: F 18 LEU cc_start: 0.8789 (tp) cc_final: 0.8552 (tt) REVERT: F 34 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.8389 (mmm) REVERT: F 62 ASP cc_start: 0.8979 (t0) cc_final: 0.8708 (t0) REVERT: F 65 LYS cc_start: 0.8736 (tptp) cc_final: 0.8273 (ttpp) REVERT: F 73 ASP cc_start: 0.8357 (t0) cc_final: 0.7684 (t0) REVERT: F 78 MET cc_start: 0.8020 (pp-130) cc_final: 0.7422 (pp-130) outliers start: 107 outliers final: 61 residues processed: 255 average time/residue: 1.1293 time to fit residues: 347.9470 Evaluate side-chains 236 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 168 time to evaluate : 2.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 879 LYS Chi-restraints excluded: chain A residue 921 ILE Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1030 GLU Chi-restraints excluded: chain A residue 1084 LYS Chi-restraints excluded: chain A residue 1129 MET Chi-restraints excluded: chain A residue 1188 THR Chi-restraints excluded: chain A residue 1246 PHE Chi-restraints excluded: chain A residue 1288 ASP Chi-restraints excluded: chain A residue 1331 THR Chi-restraints excluded: chain A residue 1390 THR Chi-restraints excluded: chain A residue 1408 MET Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 487 ILE Chi-restraints excluded: chain D residue 514 LEU Chi-restraints excluded: chain D residue 598 VAL Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 762 VAL Chi-restraints excluded: chain D residue 850 VAL Chi-restraints excluded: chain D residue 1112 GLN Chi-restraints excluded: chain D residue 1269 THR Chi-restraints excluded: chain D residue 1274 MET Chi-restraints excluded: chain D residue 1323 GLU Chi-restraints excluded: chain D residue 1390 THR Chi-restraints excluded: chain D residue 1395 ASP Chi-restraints excluded: chain F residue 34 MET Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 122 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 274 optimal weight: 50.0000 chunk 138 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 139 optimal weight: 0.7980 chunk 231 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 114 optimal weight: 20.0000 chunk 190 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 146 optimal weight: 20.0000 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 154 HIS A 858 GLN A1473 GLN D1601 HIS F 13 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.143476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.087052 restraints weight = 53432.885| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 3.95 r_work: 0.3044 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 27163 Z= 0.153 Angle : 0.587 15.264 36858 Z= 0.294 Chirality : 0.045 0.190 4172 Planarity : 0.004 0.055 4752 Dihedral : 5.687 81.223 3817 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.23 % Allowed : 19.70 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.15), residues: 3346 helix: 0.76 (0.23), residues: 546 sheet: 0.21 (0.14), residues: 1294 loop : -0.41 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D1605 HIS 0.005 0.001 HIS A 333 PHE 0.021 0.001 PHE A1273 TYR 0.018 0.001 TYR F 80 ARG 0.004 0.000 ARG D 979 Details of bonding type rmsd link_NAG-ASN : bond 0.00458 ( 4) link_NAG-ASN : angle 2.01939 ( 12) link_BETA1-4 : bond 0.00362 ( 4) link_BETA1-4 : angle 2.47541 ( 12) hydrogen bonds : bond 0.03036 ( 1079) hydrogen bonds : angle 5.05169 ( 3012) SS BOND : bond 0.00230 ( 23) SS BOND : angle 0.79991 ( 46) covalent geometry : bond 0.00349 (27132) covalent geometry : angle 0.58421 (36788) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 185 time to evaluate : 3.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 VAL cc_start: 0.8732 (OUTLIER) cc_final: 0.8526 (m) REVERT: A 755 ILE cc_start: 0.9266 (OUTLIER) cc_final: 0.9032 (tp) REVERT: A 879 LYS cc_start: -0.2134 (OUTLIER) cc_final: -0.2984 (pttt) REVERT: A 921 ILE cc_start: 0.8642 (OUTLIER) cc_final: 0.8304 (pp) REVERT: A 938 MET cc_start: 0.8840 (OUTLIER) cc_final: 0.8456 (tmt) REVERT: A 966 ASP cc_start: 0.7844 (OUTLIER) cc_final: 0.7356 (m-30) REVERT: A 973 ASP cc_start: 0.8378 (t0) cc_final: 0.8088 (t0) REVERT: A 1255 TRP cc_start: 0.8775 (t60) cc_final: 0.8366 (t60) REVERT: A 1416 ASP cc_start: 0.9341 (m-30) cc_final: 0.8781 (t0) REVERT: A 1620 TYR cc_start: 0.7126 (m-80) cc_final: 0.6350 (m-80) REVERT: C 43 LYS cc_start: 0.9116 (tppt) cc_final: 0.8657 (mmmt) REVERT: D 299 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8295 (mm-30) REVERT: D 305 LYS cc_start: 0.9434 (OUTLIER) cc_final: 0.8894 (tptp) REVERT: D 973 ASP cc_start: 0.8173 (t0) cc_final: 0.7842 (m-30) REVERT: D 1015 MET cc_start: 0.7313 (mmt) cc_final: 0.6954 (pmm) REVERT: D 1274 MET cc_start: 0.4337 (OUTLIER) cc_final: 0.4093 (tpt) REVERT: D 1347 MET cc_start: 0.7597 (mtt) cc_final: 0.7373 (mtm) REVERT: F 3 GLN cc_start: 0.8729 (mm-40) cc_final: 0.7938 (mp10) REVERT: F 18 LEU cc_start: 0.8786 (tp) cc_final: 0.8517 (tt) REVERT: F 34 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.8392 (mmm) REVERT: F 65 LYS cc_start: 0.8667 (tptp) cc_final: 0.8202 (ttpp) REVERT: F 73 ASP cc_start: 0.8594 (t0) cc_final: 0.7985 (t0) REVERT: F 78 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.7554 (pp-130) outliers start: 95 outliers final: 53 residues processed: 256 average time/residue: 1.6099 time to fit residues: 499.6017 Evaluate side-chains 234 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 171 time to evaluate : 2.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 879 LYS Chi-restraints excluded: chain A residue 921 ILE Chi-restraints excluded: chain A residue 938 MET Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1030 GLU Chi-restraints excluded: chain A residue 1084 LYS Chi-restraints excluded: chain A residue 1129 MET Chi-restraints excluded: chain A residue 1246 PHE Chi-restraints excluded: chain A residue 1288 ASP Chi-restraints excluded: chain A residue 1331 THR Chi-restraints excluded: chain A residue 1390 THR Chi-restraints excluded: chain A residue 1407 MET Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 305 LYS Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 487 ILE Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 514 LEU Chi-restraints excluded: chain D residue 598 VAL Chi-restraints excluded: chain D residue 627 CYS Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 850 VAL Chi-restraints excluded: chain D residue 978 THR Chi-restraints excluded: chain D residue 1112 GLN Chi-restraints excluded: chain D residue 1269 THR Chi-restraints excluded: chain D residue 1274 MET Chi-restraints excluded: chain D residue 1390 THR Chi-restraints excluded: chain D residue 1395 ASP Chi-restraints excluded: chain D residue 1407 MET Chi-restraints excluded: chain D residue 1469 VAL Chi-restraints excluded: chain F residue 34 MET Chi-restraints excluded: chain F residue 78 MET Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 120 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 312 optimal weight: 50.0000 chunk 264 optimal weight: 20.0000 chunk 8 optimal weight: 2.9990 chunk 181 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 168 optimal weight: 1.9990 chunk 198 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 292 optimal weight: 2.9990 chunk 224 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 HIS ** A 483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 858 GLN A1277 GLN A1473 GLN A1601 HIS C 115 GLN D 574 GLN F 13 GLN F 77 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.140608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.085844 restraints weight = 54893.406| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 3.74 r_work: 0.3051 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 27163 Z= 0.165 Angle : 0.589 12.991 36858 Z= 0.294 Chirality : 0.045 0.197 4172 Planarity : 0.004 0.049 4752 Dihedral : 5.528 81.462 3817 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.12 % Allowed : 19.74 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.15), residues: 3346 helix: 0.94 (0.23), residues: 546 sheet: 0.28 (0.14), residues: 1286 loop : -0.33 (0.16), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D1605 HIS 0.005 0.001 HIS A 483 PHE 0.023 0.001 PHE A1273 TYR 0.023 0.001 TYR A1282 ARG 0.009 0.000 ARG D 979 Details of bonding type rmsd link_NAG-ASN : bond 0.00424 ( 4) link_NAG-ASN : angle 1.95904 ( 12) link_BETA1-4 : bond 0.00358 ( 4) link_BETA1-4 : angle 2.28119 ( 12) hydrogen bonds : bond 0.03002 ( 1079) hydrogen bonds : angle 4.96250 ( 3012) SS BOND : bond 0.00233 ( 23) SS BOND : angle 0.80444 ( 46) covalent geometry : bond 0.00380 (27132) covalent geometry : angle 0.58613 (36788) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 188 time to evaluate : 2.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 513 ASP cc_start: 0.8674 (m-30) cc_final: 0.8285 (m-30) REVERT: A 879 LYS cc_start: -0.2291 (OUTLIER) cc_final: -0.3118 (pttt) REVERT: A 921 ILE cc_start: 0.8650 (OUTLIER) cc_final: 0.8283 (pp) REVERT: A 938 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.8475 (tmt) REVERT: A 966 ASP cc_start: 0.7795 (OUTLIER) cc_final: 0.7308 (m-30) REVERT: A 973 ASP cc_start: 0.8443 (t0) cc_final: 0.8121 (t0) REVERT: A 1255 TRP cc_start: 0.8802 (t60) cc_final: 0.8379 (t60) REVERT: A 1416 ASP cc_start: 0.9360 (m-30) cc_final: 0.8803 (t0) REVERT: A 1620 TYR cc_start: 0.7104 (m-80) cc_final: 0.6263 (m-80) REVERT: C 7 THR cc_start: 0.8921 (m) cc_final: 0.8633 (p) REVERT: C 53 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.8053 (ttp80) REVERT: D 973 ASP cc_start: 0.8136 (t0) cc_final: 0.7824 (m-30) REVERT: D 1274 MET cc_start: 0.4151 (OUTLIER) cc_final: 0.3869 (tpt) REVERT: D 1347 MET cc_start: 0.7607 (mtt) cc_final: 0.7327 (mtm) REVERT: F 18 LEU cc_start: 0.8851 (tp) cc_final: 0.8586 (tp) REVERT: F 28 ILE cc_start: 0.8350 (OUTLIER) cc_final: 0.8035 (tt) REVERT: F 34 MET cc_start: 0.8768 (OUTLIER) cc_final: 0.8307 (mmm) REVERT: F 65 LYS cc_start: 0.8642 (tptp) cc_final: 0.8199 (ttpp) REVERT: F 73 ASP cc_start: 0.8592 (t0) cc_final: 0.8231 (t0) REVERT: F 78 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7599 (pp-130) outliers start: 92 outliers final: 52 residues processed: 253 average time/residue: 1.2273 time to fit residues: 371.8166 Evaluate side-chains 237 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 176 time to evaluate : 2.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 879 LYS Chi-restraints excluded: chain A residue 921 ILE Chi-restraints excluded: chain A residue 938 MET Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1030 GLU Chi-restraints excluded: chain A residue 1084 LYS Chi-restraints excluded: chain A residue 1129 MET Chi-restraints excluded: chain A residue 1246 PHE Chi-restraints excluded: chain A residue 1288 ASP Chi-restraints excluded: chain A residue 1331 THR Chi-restraints excluded: chain A residue 1390 THR Chi-restraints excluded: chain C residue 53 ARG Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 338 MET Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 487 ILE Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 514 LEU Chi-restraints excluded: chain D residue 598 VAL Chi-restraints excluded: chain D residue 627 CYS Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 850 VAL Chi-restraints excluded: chain D residue 881 ARG Chi-restraints excluded: chain D residue 978 THR Chi-restraints excluded: chain D residue 1112 GLN Chi-restraints excluded: chain D residue 1269 THR Chi-restraints excluded: chain D residue 1274 MET Chi-restraints excluded: chain D residue 1395 ASP Chi-restraints excluded: chain D residue 1415 THR Chi-restraints excluded: chain D residue 1469 VAL Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 34 MET Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain F residue 78 MET Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 122 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 76 optimal weight: 0.6980 chunk 320 optimal weight: 50.0000 chunk 206 optimal weight: 4.9990 chunk 102 optimal weight: 40.0000 chunk 197 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 173 optimal weight: 4.9990 chunk 303 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 HIS A 656 GLN A 858 GLN ** A1229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1270 GLN D1643 GLN F 13 GLN F 77 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.142760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.089065 restraints weight = 57173.712| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 3.36 r_work: 0.3012 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.102 27163 Z= 0.289 Angle : 0.657 11.981 36858 Z= 0.330 Chirality : 0.047 0.198 4172 Planarity : 0.004 0.052 4752 Dihedral : 5.635 81.662 3812 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.26 % Allowed : 20.31 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.15), residues: 3346 helix: 0.96 (0.23), residues: 546 sheet: 0.22 (0.14), residues: 1284 loop : -0.35 (0.16), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D1605 HIS 0.005 0.001 HIS A 483 PHE 0.032 0.002 PHE A1037 TYR 0.019 0.001 TYR C 80 ARG 0.008 0.000 ARG D 979 Details of bonding type rmsd link_NAG-ASN : bond 0.00324 ( 4) link_NAG-ASN : angle 1.82055 ( 12) link_BETA1-4 : bond 0.00329 ( 4) link_BETA1-4 : angle 2.18074 ( 12) hydrogen bonds : bond 0.03302 ( 1079) hydrogen bonds : angle 5.11037 ( 3012) SS BOND : bond 0.00336 ( 23) SS BOND : angle 1.08485 ( 46) covalent geometry : bond 0.00670 (27132) covalent geometry : angle 0.65451 (36788) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 180 time to evaluate : 2.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 751 LEU cc_start: -0.2149 (OUTLIER) cc_final: -0.3512 (mt) REVERT: A 755 ILE cc_start: 0.9214 (OUTLIER) cc_final: 0.8996 (tp) REVERT: A 879 LYS cc_start: -0.2482 (OUTLIER) cc_final: -0.3583 (pttt) REVERT: A 921 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8431 (pp) REVERT: A 938 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.8476 (tmt) REVERT: A 966 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.7422 (m-30) REVERT: A 1255 TRP cc_start: 0.8764 (t60) cc_final: 0.8307 (t60) REVERT: A 1416 ASP cc_start: 0.9379 (m-30) cc_final: 0.8801 (t0) REVERT: A 1620 TYR cc_start: 0.7059 (m-80) cc_final: 0.6173 (m-80) REVERT: A 1622 ILE cc_start: 0.9246 (mt) cc_final: 0.8947 (pp) REVERT: C 7 THR cc_start: 0.8922 (m) cc_final: 0.8612 (p) REVERT: C 53 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.8067 (ttp80) REVERT: D 305 LYS cc_start: 0.9441 (OUTLIER) cc_final: 0.8897 (tptp) REVERT: D 394 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7570 (mm-30) REVERT: D 973 ASP cc_start: 0.8187 (t0) cc_final: 0.7869 (m-30) REVERT: D 1274 MET cc_start: 0.4298 (OUTLIER) cc_final: 0.4077 (tpt) REVERT: F 28 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.8158 (tt) REVERT: F 34 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8499 (mmm) REVERT: F 62 ASP cc_start: 0.9011 (t0) cc_final: 0.8734 (t0) REVERT: F 65 LYS cc_start: 0.8720 (tptp) cc_final: 0.8293 (ttpp) REVERT: F 73 ASP cc_start: 0.8596 (t0) cc_final: 0.8331 (t0) outliers start: 96 outliers final: 63 residues processed: 252 average time/residue: 1.2153 time to fit residues: 370.9886 Evaluate side-chains 247 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 173 time to evaluate : 3.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 879 LYS Chi-restraints excluded: chain A residue 921 ILE Chi-restraints excluded: chain A residue 938 MET Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1030 GLU Chi-restraints excluded: chain A residue 1084 LYS Chi-restraints excluded: chain A residue 1129 MET Chi-restraints excluded: chain A residue 1246 PHE Chi-restraints excluded: chain A residue 1288 ASP Chi-restraints excluded: chain A residue 1331 THR Chi-restraints excluded: chain A residue 1390 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 53 ARG Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 305 LYS Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 487 ILE Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 514 LEU Chi-restraints excluded: chain D residue 598 VAL Chi-restraints excluded: chain D residue 627 CYS Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 850 VAL Chi-restraints excluded: chain D residue 881 ARG Chi-restraints excluded: chain D residue 978 THR Chi-restraints excluded: chain D residue 1112 GLN Chi-restraints excluded: chain D residue 1269 THR Chi-restraints excluded: chain D residue 1274 MET Chi-restraints excluded: chain D residue 1390 THR Chi-restraints excluded: chain D residue 1395 ASP Chi-restraints excluded: chain D residue 1415 THR Chi-restraints excluded: chain D residue 1454 SER Chi-restraints excluded: chain D residue 1469 VAL Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 34 MET Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 122 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 253 optimal weight: 7.9990 chunk 188 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 282 optimal weight: 20.0000 chunk 307 optimal weight: 10.0000 chunk 291 optimal weight: 10.0000 chunk 301 optimal weight: 4.9990 chunk 36 optimal weight: 0.0870 chunk 270 optimal weight: 9.9990 chunk 220 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 HIS A 858 GLN ** A1473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN D1198 GLN F 13 GLN F 77 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.134345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.080521 restraints weight = 56511.896| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 3.40 r_work: 0.3043 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 27163 Z= 0.171 Angle : 0.615 11.721 36858 Z= 0.307 Chirality : 0.046 0.206 4172 Planarity : 0.004 0.048 4752 Dihedral : 5.482 81.885 3812 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.40 % Allowed : 20.48 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.15), residues: 3346 helix: 1.08 (0.23), residues: 546 sheet: 0.30 (0.14), residues: 1280 loop : -0.29 (0.16), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D1605 HIS 0.003 0.001 HIS A 333 PHE 0.029 0.001 PHE A1037 TYR 0.029 0.001 TYR A1282 ARG 0.009 0.000 ARG D 979 Details of bonding type rmsd link_NAG-ASN : bond 0.00357 ( 4) link_NAG-ASN : angle 1.79759 ( 12) link_BETA1-4 : bond 0.00327 ( 4) link_BETA1-4 : angle 2.09189 ( 12) hydrogen bonds : bond 0.03038 ( 1079) hydrogen bonds : angle 4.98432 ( 3012) SS BOND : bond 0.00233 ( 23) SS BOND : angle 0.82123 ( 46) covalent geometry : bond 0.00394 (27132) covalent geometry : angle 0.61251 (36788) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 183 time to evaluate : 4.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 513 ASP cc_start: 0.8705 (m-30) cc_final: 0.8339 (m-30) REVERT: A 751 LEU cc_start: -0.2319 (OUTLIER) cc_final: -0.4663 (mm) REVERT: A 755 ILE cc_start: 0.9248 (OUTLIER) cc_final: 0.9012 (tp) REVERT: A 879 LYS cc_start: -0.2550 (OUTLIER) cc_final: -0.3469 (pttt) REVERT: A 938 MET cc_start: 0.8830 (OUTLIER) cc_final: 0.8449 (tmt) REVERT: A 966 ASP cc_start: 0.7968 (OUTLIER) cc_final: 0.7496 (m-30) REVERT: A 1030 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7615 (mp0) REVERT: A 1255 TRP cc_start: 0.8769 (t60) cc_final: 0.8311 (t60) REVERT: A 1298 LEU cc_start: 0.9715 (pt) cc_final: 0.9209 (OUTLIER) REVERT: A 1416 ASP cc_start: 0.9363 (m-30) cc_final: 0.8798 (t0) REVERT: A 1620 TYR cc_start: 0.7082 (m-80) cc_final: 0.6148 (m-80) REVERT: C 7 THR cc_start: 0.8918 (m) cc_final: 0.8626 (p) REVERT: C 53 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.8050 (ttp80) REVERT: D 305 LYS cc_start: 0.9435 (OUTLIER) cc_final: 0.8886 (tptp) REVERT: D 394 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7515 (mm-30) REVERT: D 973 ASP cc_start: 0.8191 (t0) cc_final: 0.7871 (m-30) REVERT: D 1274 MET cc_start: 0.4287 (ttt) cc_final: 0.4017 (tpt) REVERT: F 18 LEU cc_start: 0.8495 (tp) cc_final: 0.8295 (tt) REVERT: F 28 ILE cc_start: 0.8424 (OUTLIER) cc_final: 0.8091 (tt) REVERT: F 34 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8462 (mmm) REVERT: F 62 ASP cc_start: 0.9027 (t0) cc_final: 0.8743 (t0) REVERT: F 65 LYS cc_start: 0.8655 (tptp) cc_final: 0.8227 (ttpp) REVERT: F 77 ASN cc_start: 0.7477 (OUTLIER) cc_final: 0.7243 (m-40) REVERT: F 78 MET cc_start: 0.8055 (pp-130) cc_final: 0.7578 (pp-130) outliers start: 100 outliers final: 62 residues processed: 259 average time/residue: 1.7025 time to fit residues: 542.6389 Evaluate side-chains 245 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 173 time to evaluate : 2.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 879 LYS Chi-restraints excluded: chain A residue 938 MET Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 1030 GLU Chi-restraints excluded: chain A residue 1084 LYS Chi-restraints excluded: chain A residue 1129 MET Chi-restraints excluded: chain A residue 1246 PHE Chi-restraints excluded: chain A residue 1248 PHE Chi-restraints excluded: chain A residue 1288 ASP Chi-restraints excluded: chain A residue 1331 THR Chi-restraints excluded: chain A residue 1390 THR Chi-restraints excluded: chain A residue 1479 VAL Chi-restraints excluded: chain A residue 1485 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 53 ARG Chi-restraints excluded: chain C residue 76 LYS Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 305 LYS Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 410 SER Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 487 ILE Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 598 VAL Chi-restraints excluded: chain D residue 627 CYS Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 850 VAL Chi-restraints excluded: chain D residue 881 ARG Chi-restraints excluded: chain D residue 978 THR Chi-restraints excluded: chain D residue 1112 GLN Chi-restraints excluded: chain D residue 1269 THR Chi-restraints excluded: chain D residue 1390 THR Chi-restraints excluded: chain D residue 1395 ASP Chi-restraints excluded: chain D residue 1415 THR Chi-restraints excluded: chain D residue 1425 VAL Chi-restraints excluded: chain D residue 1454 SER Chi-restraints excluded: chain D residue 1469 VAL Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 34 MET Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 122 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 70 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 148 optimal weight: 10.0000 chunk 187 optimal weight: 3.9990 chunk 314 optimal weight: 40.0000 chunk 127 optimal weight: 0.0270 chunk 54 optimal weight: 0.0270 chunk 182 optimal weight: 2.9990 chunk 236 optimal weight: 1.9990 chunk 230 optimal weight: 3.9990 chunk 147 optimal weight: 7.9990 overall best weight: 1.8102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 858 GLN ** A1229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1270 GLN A1277 GLN A1473 GLN F 13 GLN F 77 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.134266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.080169 restraints weight = 57062.402| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 3.43 r_work: 0.3036 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 27163 Z= 0.183 Angle : 0.622 11.384 36858 Z= 0.309 Chirality : 0.046 0.199 4172 Planarity : 0.004 0.049 4752 Dihedral : 5.391 82.105 3810 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.82 % Allowed : 21.23 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.15), residues: 3346 helix: 1.15 (0.23), residues: 546 sheet: 0.32 (0.14), residues: 1286 loop : -0.24 (0.17), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D1605 HIS 0.003 0.001 HIS A 333 PHE 0.037 0.001 PHE A1037 TYR 0.023 0.001 TYR F 80 ARG 0.005 0.000 ARG D 979 Details of bonding type rmsd link_NAG-ASN : bond 0.00352 ( 4) link_NAG-ASN : angle 1.78509 ( 12) link_BETA1-4 : bond 0.00419 ( 4) link_BETA1-4 : angle 2.06864 ( 12) hydrogen bonds : bond 0.03021 ( 1079) hydrogen bonds : angle 4.96768 ( 3012) SS BOND : bond 0.00230 ( 23) SS BOND : angle 0.80612 ( 46) covalent geometry : bond 0.00425 (27132) covalent geometry : angle 0.61999 (36788) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 176 time to evaluate : 3.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 HIS cc_start: 0.8591 (OUTLIER) cc_final: 0.8259 (t70) REVERT: A 513 ASP cc_start: 0.8734 (m-30) cc_final: 0.8372 (m-30) REVERT: A 751 LEU cc_start: -0.2129 (OUTLIER) cc_final: -0.4674 (mm) REVERT: A 755 ILE cc_start: 0.9252 (OUTLIER) cc_final: 0.9010 (tp) REVERT: A 879 LYS cc_start: -0.2577 (OUTLIER) cc_final: -0.3576 (pttt) REVERT: A 938 MET cc_start: 0.8858 (OUTLIER) cc_final: 0.8450 (tmt) REVERT: A 966 ASP cc_start: 0.8025 (OUTLIER) cc_final: 0.7536 (m-30) REVERT: A 1030 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7563 (mp0) REVERT: A 1255 TRP cc_start: 0.8762 (t60) cc_final: 0.8285 (t60) REVERT: A 1298 LEU cc_start: 0.9737 (pt) cc_final: 0.9250 (OUTLIER) REVERT: A 1416 ASP cc_start: 0.9388 (m-30) cc_final: 0.8803 (t0) REVERT: A 1620 TYR cc_start: 0.6976 (m-80) cc_final: 0.6074 (m-80) REVERT: C 7 THR cc_start: 0.8908 (m) cc_final: 0.8626 (p) REVERT: C 53 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.8071 (ttp80) REVERT: D 305 LYS cc_start: 0.9431 (OUTLIER) cc_final: 0.8889 (tptp) REVERT: D 394 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7530 (mm-30) REVERT: D 973 ASP cc_start: 0.8278 (t0) cc_final: 0.7921 (m-30) REVERT: D 1274 MET cc_start: 0.4236 (OUTLIER) cc_final: 0.3969 (tpt) REVERT: F 28 ILE cc_start: 0.8465 (OUTLIER) cc_final: 0.8196 (tt) REVERT: F 34 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8424 (mmm) REVERT: F 62 ASP cc_start: 0.8962 (t0) cc_final: 0.8671 (t0) REVERT: F 65 LYS cc_start: 0.8663 (tptp) cc_final: 0.8245 (ttpp) REVERT: F 78 MET cc_start: 0.7961 (pp-130) cc_final: 0.7545 (pp-130) outliers start: 83 outliers final: 59 residues processed: 238 average time/residue: 1.2257 time to fit residues: 354.0782 Evaluate side-chains 243 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 173 time to evaluate : 3.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 154 HIS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 879 LYS Chi-restraints excluded: chain A residue 938 MET Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 1030 GLU Chi-restraints excluded: chain A residue 1084 LYS Chi-restraints excluded: chain A residue 1129 MET Chi-restraints excluded: chain A residue 1246 PHE Chi-restraints excluded: chain A residue 1288 ASP Chi-restraints excluded: chain A residue 1331 THR Chi-restraints excluded: chain A residue 1390 THR Chi-restraints excluded: chain A residue 1407 MET Chi-restraints excluded: chain A residue 1479 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 53 ARG Chi-restraints excluded: chain C residue 76 LYS Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 305 LYS Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 487 ILE Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 598 VAL Chi-restraints excluded: chain D residue 627 CYS Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 850 VAL Chi-restraints excluded: chain D residue 881 ARG Chi-restraints excluded: chain D residue 978 THR Chi-restraints excluded: chain D residue 1112 GLN Chi-restraints excluded: chain D residue 1269 THR Chi-restraints excluded: chain D residue 1274 MET Chi-restraints excluded: chain D residue 1390 THR Chi-restraints excluded: chain D residue 1395 ASP Chi-restraints excluded: chain D residue 1415 THR Chi-restraints excluded: chain D residue 1425 VAL Chi-restraints excluded: chain D residue 1454 SER Chi-restraints excluded: chain D residue 1469 VAL Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 34 MET Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 122 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 214 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 109 optimal weight: 20.0000 chunk 10 optimal weight: 5.9990 chunk 227 optimal weight: 0.9980 chunk 306 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 221 optimal weight: 7.9990 chunk 263 optimal weight: 30.0000 chunk 273 optimal weight: 8.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 858 GLN ** A1229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN F 13 GLN F 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.142602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.089530 restraints weight = 56799.535| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 3.32 r_work: 0.3016 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.117 27163 Z= 0.264 Angle : 0.661 11.141 36858 Z= 0.330 Chirality : 0.047 0.238 4172 Planarity : 0.004 0.051 4752 Dihedral : 5.470 82.392 3809 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.82 % Allowed : 21.30 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.15), residues: 3346 helix: 1.12 (0.23), residues: 546 sheet: 0.26 (0.14), residues: 1284 loop : -0.27 (0.17), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D1605 HIS 0.004 0.001 HIS D 868 PHE 0.038 0.001 PHE A1037 TYR 0.035 0.001 TYR A1282 ARG 0.005 0.000 ARG D 979 Details of bonding type rmsd link_NAG-ASN : bond 0.00300 ( 4) link_NAG-ASN : angle 1.71746 ( 12) link_BETA1-4 : bond 0.00321 ( 4) link_BETA1-4 : angle 2.03039 ( 12) hydrogen bonds : bond 0.03202 ( 1079) hydrogen bonds : angle 5.07355 ( 3012) SS BOND : bond 0.00295 ( 23) SS BOND : angle 0.99905 ( 46) covalent geometry : bond 0.00612 (27132) covalent geometry : angle 0.65899 (36788) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 176 time to evaluate : 3.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 HIS cc_start: 0.8674 (OUTLIER) cc_final: 0.8366 (t70) REVERT: A 751 LEU cc_start: -0.2150 (OUTLIER) cc_final: -0.3505 (mt) REVERT: A 755 ILE cc_start: 0.9263 (OUTLIER) cc_final: 0.9017 (tp) REVERT: A 879 LYS cc_start: -0.2672 (OUTLIER) cc_final: -0.3743 (pttt) REVERT: A 938 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8406 (tmt) REVERT: A 966 ASP cc_start: 0.7852 (OUTLIER) cc_final: 0.7399 (m-30) REVERT: A 1255 TRP cc_start: 0.8783 (t60) cc_final: 0.8298 (t60) REVERT: A 1298 LEU cc_start: 0.9651 (pt) cc_final: 0.9137 (OUTLIER) REVERT: A 1416 ASP cc_start: 0.9388 (m-30) cc_final: 0.8821 (t0) REVERT: A 1584 PHE cc_start: 0.7756 (m-10) cc_final: 0.7548 (m-10) REVERT: A 1620 TYR cc_start: 0.6989 (m-80) cc_final: 0.6023 (m-80) REVERT: C 7 THR cc_start: 0.8932 (m) cc_final: 0.8633 (p) REVERT: C 53 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.8085 (ttp80) REVERT: D 305 LYS cc_start: 0.9436 (OUTLIER) cc_final: 0.8897 (tptp) REVERT: D 394 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7558 (mm-30) REVERT: D 973 ASP cc_start: 0.8198 (t0) cc_final: 0.7888 (m-30) REVERT: D 1274 MET cc_start: 0.4274 (OUTLIER) cc_final: 0.3992 (tpt) REVERT: F 28 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.8240 (tt) REVERT: F 34 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.8349 (mmm) REVERT: F 62 ASP cc_start: 0.8977 (t0) cc_final: 0.8698 (t0) REVERT: F 65 LYS cc_start: 0.8693 (tptp) cc_final: 0.8279 (ttpp) REVERT: F 78 MET cc_start: 0.8082 (pp-130) cc_final: 0.7598 (pp-130) outliers start: 83 outliers final: 62 residues processed: 241 average time/residue: 1.4560 time to fit residues: 429.4511 Evaluate side-chains 245 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 173 time to evaluate : 3.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 154 HIS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 879 LYS Chi-restraints excluded: chain A residue 938 MET Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 1030 GLU Chi-restraints excluded: chain A residue 1084 LYS Chi-restraints excluded: chain A residue 1129 MET Chi-restraints excluded: chain A residue 1246 PHE Chi-restraints excluded: chain A residue 1288 ASP Chi-restraints excluded: chain A residue 1331 THR Chi-restraints excluded: chain A residue 1390 THR Chi-restraints excluded: chain A residue 1407 MET Chi-restraints excluded: chain A residue 1479 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 53 ARG Chi-restraints excluded: chain C residue 76 LYS Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 305 LYS Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 487 ILE Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 598 VAL Chi-restraints excluded: chain D residue 627 CYS Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 850 VAL Chi-restraints excluded: chain D residue 881 ARG Chi-restraints excluded: chain D residue 978 THR Chi-restraints excluded: chain D residue 1112 GLN Chi-restraints excluded: chain D residue 1269 THR Chi-restraints excluded: chain D residue 1274 MET Chi-restraints excluded: chain D residue 1390 THR Chi-restraints excluded: chain D residue 1395 ASP Chi-restraints excluded: chain D residue 1415 THR Chi-restraints excluded: chain D residue 1425 VAL Chi-restraints excluded: chain D residue 1454 SER Chi-restraints excluded: chain D residue 1469 VAL Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 34 MET Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 122 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 183 optimal weight: 0.4980 chunk 2 optimal weight: 0.9990 chunk 109 optimal weight: 30.0000 chunk 129 optimal weight: 0.3980 chunk 30 optimal weight: 0.7980 chunk 191 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 268 optimal weight: 20.0000 chunk 6 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 858 GLN ** A1473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 GLN F 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.135170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.081744 restraints weight = 56737.471| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 3.41 r_work: 0.3074 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 27163 Z= 0.122 Angle : 0.612 12.122 36858 Z= 0.304 Chirality : 0.046 0.259 4172 Planarity : 0.004 0.046 4752 Dihedral : 5.239 82.589 3809 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.55 % Allowed : 21.57 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.15), residues: 3346 helix: 1.17 (0.23), residues: 550 sheet: 0.34 (0.14), residues: 1280 loop : -0.11 (0.17), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D1605 HIS 0.003 0.001 HIS A1026 PHE 0.038 0.001 PHE A1037 TYR 0.013 0.001 TYR A1282 ARG 0.006 0.000 ARG D 979 Details of bonding type rmsd link_NAG-ASN : bond 0.00393 ( 4) link_NAG-ASN : angle 1.77998 ( 12) link_BETA1-4 : bond 0.00372 ( 4) link_BETA1-4 : angle 2.00156 ( 12) hydrogen bonds : bond 0.02908 ( 1079) hydrogen bonds : angle 4.88197 ( 3012) SS BOND : bond 0.00164 ( 23) SS BOND : angle 0.67867 ( 46) covalent geometry : bond 0.00279 (27132) covalent geometry : angle 0.61049 (36788) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24649.84 seconds wall clock time: 430 minutes 3.55 seconds (25803.55 seconds total)