Starting phenix.real_space_refine on Sun May 3 12:03:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xmn_38483/05_2026/8xmn_38483.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xmn_38483/05_2026/8xmn_38483.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xmn_38483/05_2026/8xmn_38483.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xmn_38483/05_2026/8xmn_38483.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xmn_38483/05_2026/8xmn_38483.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xmn_38483/05_2026/8xmn_38483.map" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.015 sd= 0.050 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: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 98 5.16 5 C 8627 2.51 5 N 2040 2.21 5 O 2337 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 163 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13110 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 10299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1277, 10299 Classifications: {'peptide': 1277} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 1234} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1416 Classifications: {'peptide': 173} Link IDs: {'TRANS': 172} Chain: "C" Number of atoms: 980 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 119, 971 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 112} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Conformer: "B" Number of residues, atoms: 119, 971 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 112} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 bond proxies already assigned to first conformer: 981 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 303 Unusual residues: {'LPE': 5, 'NAG': 2, 'PCW': 3} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 3.07, per 1000 atoms: 0.23 Number of scatterers: 13110 At special positions: 0 Unit cell: (113.886, 136.496, 136.496, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 98 16.00 P 8 15.00 O 2337 8.00 N 2040 7.00 C 8627 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 275 " - pdb=" SG CYS A 324 " distance=2.08 Simple disulfide: pdb=" SG CYS A 315 " - pdb=" SG CYS A 330 " distance=2.02 Simple disulfide: pdb=" SG CYS A 895 " - pdb=" SG CYS C 55 " distance=2.04 Simple disulfide: pdb=" SG CYS A 897 " - pdb=" SG CYS A 903 " distance=2.05 Simple disulfide: pdb=" SG CYS A 935 " - pdb=" SG CYS A 944 " distance=2.02 Simple disulfide: pdb=" SG CYS A1350 " - pdb=" SG CYS A1370 " distance=2.04 Simple disulfide: pdb=" SG CYS A1715 " - pdb=" SG CYS A1730 " distance=2.03 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 43 " distance=2.03 Simple disulfide: pdb=" SG CYS B 40 " - pdb=" SG CYS B 121 " distance=2.04 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 127 " distance=2.03 Simple disulfide: pdb=" SG CYS C 72 " - pdb=" SG CYS C 75 " 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 D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A2001 " - " ASN A1375 " " NAG A2002 " - " ASN A 283 " " NAG B 301 " - " ASN B 93 " " NAG B 302 " - " ASN B 110 " " NAG B 303 " - " ASN B 114 " " NAG B 304 " - " ASN B 135 " " NAG D 1 " - " ASN A1366 " " NAG E 1 " - " ASN A1352 " Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 689.6 milliseconds 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2984 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 9 sheets defined 64.8% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 16 through 31 removed outlier: 4.304A pdb=" N GLU A 24 " --> pdb=" O LEU A 20 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLN A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG A 26 " --> pdb=" O LEU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 64 removed outlier: 3.868A pdb=" N TYR A 63 " --> pdb=" O PRO A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'A' and resid 79 through 85 removed outlier: 3.969A pdb=" N ASP A 84 " --> pdb=" O PRO A 80 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LYS A 85 " --> pdb=" O TYR A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 113 through 124 Processing helix chain 'A' and resid 125 through 144 removed outlier: 3.855A pdb=" N SER A 129 " --> pdb=" O HIS A 125 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR A 138 " --> pdb=" O CYS A 134 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 175 removed outlier: 4.318A pdb=" N VAL A 155 " --> pdb=" O TRP A 151 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS A 170 " --> pdb=" O GLU A 166 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA A 173 " --> pdb=" O VAL A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 186 Processing helix chain 'A' and resid 187 through 206 removed outlier: 4.060A pdb=" N LEU A 191 " --> pdb=" O PRO A 187 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASP A 192 " --> pdb=" O TRP A 188 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE A 193 " --> pdb=" O ASN A 189 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN A 206 " --> pdb=" O THR A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 219 removed outlier: 3.637A pdb=" N PHE A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG A 217 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A 219 " --> pdb=" O THR A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 228 removed outlier: 4.051A pdb=" N SER A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 243 Processing helix chain 'A' and resid 246 through 268 Processing helix chain 'A' and resid 269 through 271 No H-bonds generated for 'chain 'A' and resid 269 through 271' Processing helix chain 'A' and resid 285 through 292 removed outlier: 3.986A pdb=" N THR A 292 " --> pdb=" O SER A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 301 Processing helix chain 'A' and resid 346 through 359 Processing helix chain 'A' and resid 362 through 375 removed outlier: 4.280A pdb=" N LEU A 366 " --> pdb=" O TYR A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 422 removed outlier: 3.915A pdb=" N PHE A 382 " --> pdb=" O TYR A 378 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER A 390 " --> pdb=" O ILE A 386 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N PHE A 391 " --> pdb=" O PHE A 387 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A 393 " --> pdb=" O GLY A 389 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N ILE A 394 " --> pdb=" O SER A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 740 Processing helix chain 'A' and resid 745 through 762 Processing helix chain 'A' and resid 769 through 798 Processing helix chain 'A' and resid 799 through 804 Processing helix chain 'A' and resid 806 through 825 removed outlier: 3.580A pdb=" N PHE A 811 " --> pdb=" O GLY A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 838 removed outlier: 3.656A pdb=" N PHE A 837 " --> pdb=" O LEU A 834 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ARG A 838 " --> pdb=" O ARG A 835 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 848 removed outlier: 3.537A pdb=" N LYS A 847 " --> pdb=" O LYS A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 862 Processing helix chain 'A' and resid 866 through 889 removed outlier: 3.947A pdb=" N THR A 870 " --> pdb=" O PHE A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 895 Processing helix chain 'A' and resid 895 through 900 removed outlier: 4.171A pdb=" N ILE A 899 " --> pdb=" O CYS A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 926 Processing helix chain 'A' and resid 928 through 940 removed outlier: 3.524A pdb=" N MET A 932 " --> pdb=" O TRP A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 972 removed outlier: 3.530A pdb=" N SER A 972 " --> pdb=" O LEU A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 1014 removed outlier: 3.538A pdb=" N ARG A 994 " --> pdb=" O ILE A 990 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR A1001 " --> pdb=" O LYS A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1176 through 1191 Processing helix chain 'A' and resid 1191 through 1210 removed outlier: 3.805A pdb=" N ALA A1210 " --> pdb=" O SER A1206 " (cutoff:3.500A) Processing helix chain 'A' and resid 1211 through 1212 No H-bonds generated for 'chain 'A' and resid 1211 through 1212' Processing helix chain 'A' and resid 1213 through 1218 removed outlier: 4.459A pdb=" N GLU A1217 " --> pdb=" O ILE A1214 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1249 Processing helix chain 'A' and resid 1249 through 1255 Processing helix chain 'A' and resid 1256 through 1278 Processing helix chain 'A' and resid 1283 through 1285 No H-bonds generated for 'chain 'A' and resid 1283 through 1285' Processing helix chain 'A' and resid 1286 through 1291 removed outlier: 3.681A pdb=" N ARG A1290 " --> pdb=" O ILE A1286 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR A1291 " --> pdb=" O LYS A1287 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1286 through 1291' Processing helix chain 'A' and resid 1292 through 1303 Proline residue: A1297 - end of helix removed outlier: 4.122A pdb=" N LEU A1301 " --> pdb=" O LEU A1298 " (cutoff:3.500A) Processing helix chain 'A' and resid 1304 through 1316 Processing helix chain 'A' and resid 1317 through 1343 removed outlier: 3.684A pdb=" N ASN A1323 " --> pdb=" O PRO A1319 " (cutoff:3.500A) Processing helix chain 'A' and resid 1366 through 1375 Processing helix chain 'A' and resid 1391 through 1403 Processing helix chain 'A' and resid 1407 through 1416 removed outlier: 4.352A pdb=" N ILE A1411 " --> pdb=" O GLY A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1430 through 1432 No H-bonds generated for 'chain 'A' and resid 1430 through 1432' Processing helix chain 'A' and resid 1433 through 1466 removed outlier: 3.599A pdb=" N PHE A1437 " --> pdb=" O MET A1433 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N THR A1448 " --> pdb=" O GLY A1444 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU A1449 " --> pdb=" O SER A1445 " (cutoff:3.500A) Processing helix chain 'A' and resid 1475 through 1489 removed outlier: 3.551A pdb=" N LEU A1488 " --> pdb=" O ALA A1484 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY A1489 " --> pdb=" O MET A1485 " (cutoff:3.500A) Processing helix chain 'A' and resid 1502 through 1513 Processing helix chain 'A' and resid 1514 through 1534 removed outlier: 4.236A pdb=" N ASP A1518 " --> pdb=" O ASN A1514 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE A1519 " --> pdb=" O GLN A1515 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR A1531 " --> pdb=" O LEU A1527 " (cutoff:3.500A) Processing helix chain 'A' and resid 1540 through 1569 Processing helix chain 'A' and resid 1572 through 1575 Processing helix chain 'A' and resid 1576 through 1603 Processing helix chain 'A' and resid 1605 through 1613 Processing helix chain 'A' and resid 1616 through 1621 removed outlier: 4.213A pdb=" N ILE A1620 " --> pdb=" O ARG A1616 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU A1621 " --> pdb=" O ILE A1617 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1616 through 1621' Processing helix chain 'A' and resid 1622 through 1627 removed outlier: 4.265A pdb=" N GLY A1626 " --> pdb=" O ARG A1622 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA A1627 " --> pdb=" O LEU A1623 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1622 through 1627' Processing helix chain 'A' and resid 1630 through 1666 Proline residue: A1642 - end of helix Processing helix chain 'A' and resid 1683 through 1696 removed outlier: 4.047A pdb=" N THR A1696 " --> pdb=" O PHE A1692 " (cutoff:3.500A) Processing helix chain 'A' and resid 1699 through 1705 removed outlier: 3.506A pdb=" N LEU A1703 " --> pdb=" O GLY A1699 " (cutoff:3.500A) Processing helix chain 'A' and resid 1732 through 1767 Processing helix chain 'B' and resid 112 through 115 removed outlier: 3.666A pdb=" N HIS B 115 " --> pdb=" O THR B 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 112 through 115' Processing helix chain 'B' and resid 153 through 192 Processing helix chain 'C' and resid 104 through 108 Processing sheet with id=AA1, first strand: chain 'A' and resid 74 through 75 removed outlier: 3.532A pdb=" N ILE A 89 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 273 through 277 Processing sheet with id=AA3, first strand: chain 'A' and resid 1349 through 1352 removed outlier: 3.508A pdb=" N ARG A1381 " --> pdb=" O ILE A1351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.176A pdb=" N ALA B 30 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ASN B 50 " --> pdb=" O PHE B 128 " (cutoff:3.500A) removed outlier: 9.148A pdb=" N THR B 53 " --> pdb=" O GLU B 74 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N GLU B 74 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N THR B 55 " --> pdb=" O ARG B 72 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ARG B 72 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N TRP B 57 " --> pdb=" O ILE B 70 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.176A pdb=" N ALA B 30 " --> pdb=" O VAL B 147 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 36 through 38 Processing sheet with id=AA7, first strand: chain 'C' and resid 31 through 33 removed outlier: 4.403A pdb=" N GLU C 31 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR C 51 " --> pdb=" O THR C 33 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 37 through 41 removed outlier: 6.125A pdb=" N LEU C 38 " --> pdb=" O GLN C 145 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N LEU C 147 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL C 40 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N TYR C 69 " --> pdb=" O MET C 79 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N MET C 79 " --> pdb=" O TYR C 69 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE C 88 " --> pdb=" O GLN C 82 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 46 through 48 removed outlier: 3.819A pdb=" N MET C 113 " --> pdb=" O GLU C 100 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLU C 100 " --> pdb=" O MET C 113 " (cutoff:3.500A) 776 hydrogen bonds defined for protein. 2208 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: 1.88 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 2008 1.29 - 1.42: 3563 1.42 - 1.56: 7658 1.56 - 1.70: 16 1.70 - 1.83: 158 Bond restraints: 13403 Sorted by residual: bond pdb=" C ILE A1588 " pdb=" O ILE A1588 " ideal model delta sigma weight residual 1.237 1.151 0.086 1.17e-02 7.31e+03 5.40e+01 bond pdb=" CA PHE A1440 " pdb=" C PHE A1440 " ideal model delta sigma weight residual 1.524 1.437 0.087 1.26e-02 6.30e+03 4.75e+01 bond pdb=" CA TYR A1436 " pdb=" C TYR A1436 " ideal model delta sigma weight residual 1.524 1.438 0.086 1.26e-02 6.30e+03 4.63e+01 bond pdb=" CA ARG A1367 " pdb=" C ARG A1367 " ideal model delta sigma weight residual 1.523 1.436 0.087 1.34e-02 5.57e+03 4.25e+01 bond pdb=" C11 PCW A2008 " pdb=" O3 PCW A2008 " ideal model delta sigma weight residual 1.326 1.451 -0.125 2.00e-02 2.50e+03 3.88e+01 ... (remaining 13398 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 16988 2.44 - 4.88: 899 4.88 - 7.32: 172 7.32 - 9.76: 41 9.76 - 12.19: 10 Bond angle restraints: 18110 Sorted by residual: angle pdb=" N ARG A 217 " pdb=" CA ARG A 217 " pdb=" C ARG A 217 " ideal model delta sigma weight residual 113.23 101.62 11.61 1.24e+00 6.50e-01 8.77e+01 angle pdb=" N ARG A 26 " pdb=" CA ARG A 26 " pdb=" C ARG A 26 " ideal model delta sigma weight residual 111.03 101.02 10.01 1.11e+00 8.12e-01 8.14e+01 angle pdb=" N TYR A1436 " pdb=" CA TYR A1436 " pdb=" C TYR A1436 " ideal model delta sigma weight residual 111.14 101.73 9.41 1.08e+00 8.57e-01 7.59e+01 angle pdb=" N SER C 76 " pdb=" CA SER C 76 " pdb=" C SER C 76 " ideal model delta sigma weight residual 110.50 122.69 -12.19 1.41e+00 5.03e-01 7.48e+01 angle pdb=" N LYS A1628 " pdb=" CA LYS A1628 " pdb=" C LYS A1628 " ideal model delta sigma weight residual 114.62 105.01 9.61 1.14e+00 7.69e-01 7.11e+01 ... (remaining 18105 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.12: 7724 31.12 - 62.24: 420 62.24 - 93.36: 29 93.36 - 124.48: 1 124.48 - 155.60: 3 Dihedral angle restraints: 8177 sinusoidal: 3560 harmonic: 4617 Sorted by residual: dihedral pdb=" CB CYS A1350 " pdb=" SG CYS A1350 " pdb=" SG CYS A1370 " pdb=" CB CYS A1370 " ideal model delta sinusoidal sigma weight residual -86.00 -171.40 85.40 1 1.00e+01 1.00e-02 8.83e+01 dihedral pdb=" CB CYS C 72 " pdb=" SG CYS C 72 " pdb=" SG CYS C 75 " pdb=" CB CYS C 75 " ideal model delta sinusoidal sigma weight residual 93.00 161.59 -68.59 1 1.00e+01 1.00e-02 6.09e+01 dihedral pdb=" CB CYS A1715 " pdb=" SG CYS A1715 " pdb=" SG CYS A1730 " pdb=" CB CYS A1730 " ideal model delta sinusoidal sigma weight residual 93.00 30.79 62.21 1 1.00e+01 1.00e-02 5.12e+01 ... (remaining 8174 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.145: 1935 0.145 - 0.291: 113 0.291 - 0.436: 19 0.436 - 0.582: 2 0.582 - 0.727: 1 Chirality restraints: 2070 Sorted by residual: chirality pdb=" CA CYS A 897 " pdb=" N CYS A 897 " pdb=" C CYS A 897 " pdb=" CB CYS A 897 " both_signs ideal model delta sigma weight residual False 2.51 1.78 0.73 2.00e-01 2.50e+01 1.32e+01 chirality pdb=" CA PHE A 824 " pdb=" N PHE A 824 " pdb=" C PHE A 824 " pdb=" CB PHE A 824 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.35e+00 chirality pdb=" CA PHE A1437 " pdb=" N PHE A1437 " pdb=" C PHE A1437 " pdb=" CB PHE A1437 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.87e+00 ... (remaining 2067 not shown) Planarity restraints: 2202 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 1 " -0.288 2.00e-02 2.50e+03 2.42e-01 7.33e+02 pdb=" C7 NAG E 1 " 0.076 2.00e-02 2.50e+03 pdb=" C8 NAG E 1 " -0.184 2.00e-02 2.50e+03 pdb=" N2 NAG E 1 " 0.412 2.00e-02 2.50e+03 pdb=" O7 NAG E 1 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A1443 " 0.025 2.00e-02 2.50e+03 5.01e-02 2.51e+01 pdb=" C PHE A1443 " -0.087 2.00e-02 2.50e+03 pdb=" O PHE A1443 " 0.032 2.00e-02 2.50e+03 pdb=" N GLY A1444 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1408 " 0.033 2.00e-02 2.50e+03 3.00e-02 2.25e+01 pdb=" CG TRP A1408 " -0.081 2.00e-02 2.50e+03 pdb=" CD1 TRP A1408 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP A1408 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A1408 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A1408 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A1408 " 0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1408 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1408 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A1408 " 0.003 2.00e-02 2.50e+03 ... (remaining 2199 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2124 2.74 - 3.28: 14081 3.28 - 3.82: 21231 3.82 - 4.36: 25396 4.36 - 4.90: 42258 Nonbonded interactions: 105090 Sorted by model distance: nonbonded pdb=" OD1 ASP C 45 " pdb=" NE ARG C 115 " model vdw 2.202 3.120 nonbonded pdb=" OG SER A 318 " pdb=" OD1 ASP A 320 " model vdw 2.208 3.040 nonbonded pdb=" OG1 THR C 68 " pdb=" ND2 ASN C 126 " model vdw 2.214 3.120 nonbonded pdb=" OE1 GLN B 61 " pdb=" NH1 ARG B 85 " model vdw 2.243 3.120 nonbonded pdb=" O LYS A 244 " pdb=" NZ LYS A 244 " model vdw 2.247 3.120 ... (remaining 105085 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' } 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=0.14 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: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.350 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 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 : 0.012 0.125 13424 Z= 0.690 Angle : 1.335 13.965 18162 Z= 0.790 Chirality : 0.081 0.727 2070 Planarity : 0.009 0.242 2194 Dihedral : 17.774 155.602 5160 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 20.28 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.63 % Favored : 93.17 % Rotamer: Outliers : 2.34 % Allowed : 3.26 % Favored : 94.40 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.21), residues: 1556 helix: 0.01 (0.17), residues: 899 sheet: -0.43 (0.41), residues: 142 loop : -2.07 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.002 ARG A 99 TYR 0.049 0.003 TYR A 362 PHE 0.030 0.003 PHE B 86 TRP 0.081 0.003 TRP A1408 HIS 0.007 0.002 HIS C 136 Details of bonding type rmsd covalent geometry : bond 0.01183 (13403) covalent geometry : angle 1.30771 (18110) SS BOND : bond 0.01827 ( 11) SS BOND : angle 5.51898 ( 22) hydrogen bonds : bond 0.15905 ( 768) hydrogen bonds : angle 7.58733 ( 2208) link_BETA1-4 : bond 0.00102 ( 2) link_BETA1-4 : angle 2.87631 ( 6) link_NAG-ASN : bond 0.00684 ( 8) link_NAG-ASN : angle 5.28364 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 246 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8570 (mmtp) REVERT: A 163 TYR cc_start: 0.7075 (m-80) cc_final: 0.6608 (m-80) REVERT: A 176 PHE cc_start: 0.8031 (t80) cc_final: 0.7524 (t80) REVERT: A 326 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6847 (mp0) REVERT: A 388 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7867 (tt) REVERT: A 742 MET cc_start: 0.8462 (ttt) cc_final: 0.8254 (ttt) REVERT: A 1452 PHE cc_start: 0.8359 (t80) cc_final: 0.7006 (m-10) REVERT: A 1762 ASN cc_start: 0.8817 (t0) cc_final: 0.8546 (t0) REVERT: B 162 MET cc_start: 0.7980 (mmt) cc_final: 0.7188 (mpp) REVERT: B 164 TYR cc_start: 0.8770 (m-80) cc_final: 0.8526 (m-80) REVERT: B 184 LYS cc_start: 0.9143 (tptp) cc_final: 0.8882 (tptp) REVERT: C 39 ASN cc_start: 0.5249 (m-40) cc_final: 0.5028 (p0) REVERT: C 79 MET cc_start: 0.7220 (tmm) cc_final: 0.7017 (tmm) REVERT: C 113 MET cc_start: 0.1885 (mmt) cc_final: 0.1134 (mtt) outliers start: 33 outliers final: 9 residues processed: 271 average time/residue: 0.1026 time to fit residues: 42.1703 Evaluate side-chains 214 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 202 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain A residue 952 MET Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1466 LYS Chi-restraints excluded: chain A residue 1569 LEU Chi-restraints excluded: chain A residue 1571 HIS Chi-restraints excluded: chain A residue 1628 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 8.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 ASN A 765 HIS A 989 GLN A1461 ASN A1463 GLN A1505 GLN A1539 GLN A1551 ASN A1665 ASN B 102 GLN C 42 ASN C 139 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.149533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.104762 restraints weight = 43414.540| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 3.93 r_work: 0.3296 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3302 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3302 r_free = 0.3302 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3302 r_free = 0.3302 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3302 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 13424 Z= 0.192 Angle : 0.745 9.718 18162 Z= 0.390 Chirality : 0.046 0.358 2070 Planarity : 0.005 0.065 2194 Dihedral : 12.604 151.969 2182 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.73 % Favored : 94.20 % Rotamer: Outliers : 2.06 % Allowed : 12.76 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.21), residues: 1556 helix: 0.49 (0.17), residues: 904 sheet: -0.82 (0.40), residues: 142 loop : -1.77 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 135 TYR 0.034 0.002 TYR A 362 PHE 0.029 0.002 PHE A 739 TRP 0.022 0.001 TRP A1408 HIS 0.007 0.001 HIS C 136 Details of bonding type rmsd covalent geometry : bond 0.00441 (13403) covalent geometry : angle 0.73038 (18110) SS BOND : bond 0.00635 ( 11) SS BOND : angle 1.96565 ( 22) hydrogen bonds : bond 0.05649 ( 768) hydrogen bonds : angle 5.44047 ( 2208) link_BETA1-4 : bond 0.00437 ( 2) link_BETA1-4 : angle 2.35527 ( 6) link_NAG-ASN : bond 0.00768 ( 8) link_NAG-ASN : angle 3.48622 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 234 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8414 (mttp) REVERT: A 163 TYR cc_start: 0.7233 (m-80) cc_final: 0.6722 (m-80) REVERT: A 326 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7349 (mp0) REVERT: A 367 TYR cc_start: 0.8713 (t80) cc_final: 0.7620 (t80) REVERT: A 1482 TYR cc_start: 0.8266 (t80) cc_final: 0.7914 (t80) REVERT: B 164 TYR cc_start: 0.8857 (m-80) cc_final: 0.8638 (m-80) REVERT: B 184 LYS cc_start: 0.9170 (tptp) cc_final: 0.8931 (tptp) REVERT: C 109 ASP cc_start: 0.7015 (OUTLIER) cc_final: 0.6768 (p0) REVERT: C 113 MET cc_start: 0.2467 (mmt) cc_final: 0.1389 (ttp) REVERT: C 125 TYR cc_start: 0.2572 (m-80) cc_final: 0.2314 (m-80) REVERT: C 129 ILE cc_start: 0.6847 (mp) cc_final: 0.6072 (tp) outliers start: 29 outliers final: 19 residues processed: 253 average time/residue: 0.0988 time to fit residues: 38.2746 Evaluate side-chains 228 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 206 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 810 ILE Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 952 MET Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 1327 VAL Chi-restraints excluded: chain A residue 1328 CYS Chi-restraints excluded: chain A residue 1366 ASN Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1571 HIS Chi-restraints excluded: chain A residue 1602 TYR Chi-restraints excluded: chain A residue 1628 LYS Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 109 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 50 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 128 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 136 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 139 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN A1762 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.150726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.106737 restraints weight = 43914.265| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 4.03 r_work: 0.3316 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3321 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3321 r_free = 0.3321 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3321 r_free = 0.3321 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3321 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13424 Z= 0.148 Angle : 0.651 9.701 18162 Z= 0.341 Chirality : 0.044 0.357 2070 Planarity : 0.004 0.046 2194 Dihedral : 11.936 153.095 2174 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.12 % Allowed : 15.66 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.21), residues: 1556 helix: 0.88 (0.17), residues: 896 sheet: -0.91 (0.40), residues: 142 loop : -1.53 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 135 TYR 0.027 0.002 TYR A 362 PHE 0.029 0.001 PHE A1509 TRP 0.014 0.001 TRP A1382 HIS 0.013 0.001 HIS A 765 Details of bonding type rmsd covalent geometry : bond 0.00322 (13403) covalent geometry : angle 0.63891 (18110) SS BOND : bond 0.00352 ( 11) SS BOND : angle 1.44106 ( 22) hydrogen bonds : bond 0.04941 ( 768) hydrogen bonds : angle 4.96169 ( 2208) link_BETA1-4 : bond 0.00152 ( 2) link_BETA1-4 : angle 2.48256 ( 6) link_NAG-ASN : bond 0.00692 ( 8) link_NAG-ASN : angle 2.97826 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 222 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 HIS cc_start: 0.8063 (OUTLIER) cc_final: 0.7761 (t70) REVERT: A 128 PHE cc_start: 0.8222 (t80) cc_final: 0.7675 (t80) REVERT: A 163 TYR cc_start: 0.7248 (m-80) cc_final: 0.6784 (m-80) REVERT: A 367 TYR cc_start: 0.8657 (t80) cc_final: 0.7447 (t80) REVERT: A 761 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.7695 (mtm) REVERT: A 798 MET cc_start: 0.6862 (tmm) cc_final: 0.6410 (tmm) REVERT: B 76 GLU cc_start: 0.8349 (tp30) cc_final: 0.8147 (tp30) REVERT: B 164 TYR cc_start: 0.8847 (m-80) cc_final: 0.8639 (m-80) REVERT: B 184 LYS cc_start: 0.9168 (tptp) cc_final: 0.8923 (tptp) REVERT: C 79 MET cc_start: 0.7686 (tmm) cc_final: 0.7447 (tmm) REVERT: C 87 ILE cc_start: 0.7784 (mt) cc_final: 0.7583 (mt) REVERT: C 113 MET cc_start: 0.2509 (mmt) cc_final: 0.1472 (ttp) REVERT: C 135 ARG cc_start: 0.7118 (mmm160) cc_final: 0.5973 (mpt-90) outliers start: 44 outliers final: 25 residues processed: 245 average time/residue: 0.0948 time to fit residues: 36.1317 Evaluate side-chains 232 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 205 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 810 ILE Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 890 LYS Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1328 CYS Chi-restraints excluded: chain A residue 1366 ASN Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1571 HIS Chi-restraints excluded: chain A residue 1576 VAL Chi-restraints excluded: chain A residue 1602 TYR Chi-restraints excluded: chain A residue 1628 LYS Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain C residue 58 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 17 optimal weight: 4.9990 chunk 136 optimal weight: 5.9990 chunk 8 optimal weight: 0.0670 chunk 54 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 79 optimal weight: 0.4980 chunk 147 optimal weight: 7.9990 chunk 53 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 overall best weight: 1.0922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1762 ASN B 102 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.151924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.109483 restraints weight = 43349.328| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 3.87 r_work: 0.3344 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3350 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3350 r_free = 0.3350 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3350 r_free = 0.3350 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3350 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13424 Z= 0.129 Angle : 0.628 13.015 18162 Z= 0.323 Chirality : 0.043 0.353 2070 Planarity : 0.004 0.044 2194 Dihedral : 11.212 155.494 2164 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.33 % Allowed : 17.43 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.21), residues: 1556 helix: 1.14 (0.17), residues: 886 sheet: -0.72 (0.40), residues: 136 loop : -1.29 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 135 TYR 0.023 0.001 TYR A 362 PHE 0.027 0.001 PHE A1509 TRP 0.014 0.001 TRP A1382 HIS 0.007 0.001 HIS A1571 Details of bonding type rmsd covalent geometry : bond 0.00276 (13403) covalent geometry : angle 0.61801 (18110) SS BOND : bond 0.00319 ( 11) SS BOND : angle 1.24496 ( 22) hydrogen bonds : bond 0.04495 ( 768) hydrogen bonds : angle 4.65875 ( 2208) link_BETA1-4 : bond 0.00399 ( 2) link_BETA1-4 : angle 2.26195 ( 6) link_NAG-ASN : bond 0.00631 ( 8) link_NAG-ASN : angle 2.78460 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 232 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 PHE cc_start: 0.8088 (t80) cc_final: 0.7644 (t80) REVERT: A 163 TYR cc_start: 0.7350 (m-80) cc_final: 0.7043 (m-80) REVERT: A 165 PHE cc_start: 0.8479 (OUTLIER) cc_final: 0.7646 (p90) REVERT: A 367 TYR cc_start: 0.8617 (t80) cc_final: 0.7433 (t80) REVERT: A 791 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.7267 (tpt) REVERT: A 798 MET cc_start: 0.7233 (tmm) cc_final: 0.6988 (ppp) REVERT: A 943 MET cc_start: 0.8615 (mmm) cc_final: 0.8337 (mmp) REVERT: A 952 MET cc_start: 0.8151 (mmm) cc_final: 0.7911 (tpt) REVERT: B 76 GLU cc_start: 0.8522 (tp30) cc_final: 0.8062 (tp30) REVERT: B 184 LYS cc_start: 0.9170 (tptp) cc_final: 0.8926 (tptp) REVERT: C 113 MET cc_start: 0.2852 (mmt) cc_final: 0.1693 (ttp) outliers start: 47 outliers final: 25 residues processed: 263 average time/residue: 0.0947 time to fit residues: 38.6313 Evaluate side-chains 239 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 212 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 278 ASN Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 791 MET Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 890 LYS Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1328 CYS Chi-restraints excluded: chain A residue 1349 GLU Chi-restraints excluded: chain A residue 1366 ASN Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1539 GLN Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1571 HIS Chi-restraints excluded: chain A residue 1602 TYR Chi-restraints excluded: chain A residue 1628 LYS Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain C residue 58 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 2 optimal weight: 7.9990 chunk 74 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 144 optimal weight: 0.2980 chunk 67 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 chunk 117 optimal weight: 0.7980 chunk 98 optimal weight: 6.9990 chunk 148 optimal weight: 50.0000 chunk 150 optimal weight: 0.1980 chunk 25 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 GLN A 956 ASN A1762 ASN B 102 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.152913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.108273 restraints weight = 45528.006| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 3.96 r_work: 0.3362 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3368 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3368 r_free = 0.3368 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3368 r_free = 0.3368 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3368 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13424 Z= 0.124 Angle : 0.620 10.439 18162 Z= 0.319 Chirality : 0.043 0.352 2070 Planarity : 0.004 0.043 2194 Dihedral : 10.698 155.381 2157 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.05 % Allowed : 19.63 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.22), residues: 1556 helix: 1.19 (0.17), residues: 890 sheet: -0.65 (0.41), residues: 138 loop : -1.18 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 152 TYR 0.020 0.001 TYR A 362 PHE 0.023 0.001 PHE A 733 TRP 0.012 0.001 TRP A1382 HIS 0.007 0.001 HIS A1571 Details of bonding type rmsd covalent geometry : bond 0.00265 (13403) covalent geometry : angle 0.61080 (18110) SS BOND : bond 0.00300 ( 11) SS BOND : angle 1.14840 ( 22) hydrogen bonds : bond 0.04271 ( 768) hydrogen bonds : angle 4.52901 ( 2208) link_BETA1-4 : bond 0.00405 ( 2) link_BETA1-4 : angle 2.18005 ( 6) link_NAG-ASN : bond 0.00650 ( 8) link_NAG-ASN : angle 2.69359 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 224 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 PHE cc_start: 0.8034 (t80) cc_final: 0.7595 (t80) REVERT: A 163 TYR cc_start: 0.7385 (m-80) cc_final: 0.7114 (m-80) REVERT: A 165 PHE cc_start: 0.8440 (OUTLIER) cc_final: 0.7493 (p90) REVERT: A 362 TYR cc_start: 0.8807 (t80) cc_final: 0.8384 (t80) REVERT: A 761 MET cc_start: 0.7919 (OUTLIER) cc_final: 0.7595 (mtm) REVERT: A 791 MET cc_start: 0.8292 (ttm) cc_final: 0.7155 (tpt) REVERT: A 798 MET cc_start: 0.7287 (tmm) cc_final: 0.6913 (ppp) REVERT: A 943 MET cc_start: 0.8634 (mmm) cc_final: 0.8368 (mmp) REVERT: A 952 MET cc_start: 0.8222 (mmm) cc_final: 0.7944 (tpt) REVERT: A 1482 TYR cc_start: 0.8395 (t80) cc_final: 0.8142 (t80) REVERT: A 1761 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7211 (mm-30) REVERT: B 76 GLU cc_start: 0.8434 (tp30) cc_final: 0.8048 (tp30) REVERT: B 184 LYS cc_start: 0.9158 (tptp) cc_final: 0.8915 (tptp) REVERT: C 113 MET cc_start: 0.2743 (mmt) cc_final: 0.1660 (ttp) outliers start: 43 outliers final: 26 residues processed: 250 average time/residue: 0.0905 time to fit residues: 35.2688 Evaluate side-chains 233 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 205 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 278 ASN Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 890 LYS Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1328 CYS Chi-restraints excluded: chain A residue 1349 GLU Chi-restraints excluded: chain A residue 1366 ASN Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1539 GLN Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1571 HIS Chi-restraints excluded: chain A residue 1602 TYR Chi-restraints excluded: chain A residue 1628 LYS Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain C residue 58 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 3 optimal weight: 9.9990 chunk 111 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 chunk 151 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 71 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 15 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 765 HIS A1539 GLN A1762 ASN B 102 GLN B 115 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.150155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.105117 restraints weight = 28627.739| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.87 r_work: 0.3375 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3378 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3378 r_free = 0.3378 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3378 r_free = 0.3378 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3378 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13424 Z= 0.184 Angle : 0.636 9.173 18162 Z= 0.329 Chirality : 0.044 0.354 2070 Planarity : 0.004 0.045 2194 Dihedral : 10.786 153.819 2157 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.96 % Favored : 94.98 % Rotamer: Outliers : 3.05 % Allowed : 20.98 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.22), residues: 1556 helix: 1.14 (0.17), residues: 894 sheet: -0.69 (0.41), residues: 148 loop : -1.21 (0.29), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 152 TYR 0.025 0.002 TYR B 32 PHE 0.024 0.002 PHE A 733 TRP 0.014 0.001 TRP A1382 HIS 0.007 0.001 HIS A1571 Details of bonding type rmsd covalent geometry : bond 0.00431 (13403) covalent geometry : angle 0.62559 (18110) SS BOND : bond 0.00380 ( 11) SS BOND : angle 1.38811 ( 22) hydrogen bonds : bond 0.04428 ( 768) hydrogen bonds : angle 4.58057 ( 2208) link_BETA1-4 : bond 0.00365 ( 2) link_BETA1-4 : angle 2.08854 ( 6) link_NAG-ASN : bond 0.00608 ( 8) link_NAG-ASN : angle 2.73882 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 213 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7910 (ttpt) REVERT: A 128 PHE cc_start: 0.8106 (t80) cc_final: 0.7727 (t80) REVERT: A 157 TYR cc_start: 0.7796 (m-80) cc_final: 0.6742 (t80) REVERT: A 163 TYR cc_start: 0.7300 (m-80) cc_final: 0.7009 (m-80) REVERT: A 165 PHE cc_start: 0.8455 (OUTLIER) cc_final: 0.7383 (p90) REVERT: A 791 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.7165 (tpt) REVERT: A 798 MET cc_start: 0.7350 (tmm) cc_final: 0.6974 (ppp) REVERT: A 943 MET cc_start: 0.8596 (mmm) cc_final: 0.8364 (mmp) REVERT: A 1761 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7245 (mm-30) REVERT: B 76 GLU cc_start: 0.8383 (tp30) cc_final: 0.8023 (tp30) REVERT: B 184 LYS cc_start: 0.9177 (tptp) cc_final: 0.8935 (tptp) REVERT: C 113 MET cc_start: 0.2730 (mmt) cc_final: 0.1710 (ttp) outliers start: 43 outliers final: 27 residues processed: 236 average time/residue: 0.0946 time to fit residues: 34.6867 Evaluate side-chains 232 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 202 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 791 MET Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1328 CYS Chi-restraints excluded: chain A residue 1366 ASN Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1571 HIS Chi-restraints excluded: chain A residue 1590 ILE Chi-restraints excluded: chain A residue 1602 TYR Chi-restraints excluded: chain A residue 1628 LYS Chi-restraints excluded: chain A residue 1762 ASN Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain C residue 58 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 52 optimal weight: 0.9990 chunk 136 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 146 optimal weight: 0.0050 chunk 54 optimal weight: 1.9990 chunk 144 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 119 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 GLN A 765 HIS ** A 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1762 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.152736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.108631 restraints weight = 52880.782| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 4.51 r_work: 0.3341 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3346 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3346 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 13424 Z= 0.124 Angle : 0.627 12.135 18162 Z= 0.321 Chirality : 0.043 0.345 2070 Planarity : 0.004 0.049 2194 Dihedral : 10.560 154.746 2157 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.62 % Allowed : 21.62 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.22), residues: 1556 helix: 1.28 (0.17), residues: 894 sheet: -0.65 (0.41), residues: 149 loop : -1.15 (0.30), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 135 TYR 0.026 0.001 TYR B 32 PHE 0.031 0.001 PHE A 183 TRP 0.013 0.001 TRP A1382 HIS 0.015 0.002 HIS A 765 Details of bonding type rmsd covalent geometry : bond 0.00267 (13403) covalent geometry : angle 0.61541 (18110) SS BOND : bond 0.00958 ( 11) SS BOND : angle 1.87538 ( 22) hydrogen bonds : bond 0.04181 ( 768) hydrogen bonds : angle 4.41056 ( 2208) link_BETA1-4 : bond 0.00419 ( 2) link_BETA1-4 : angle 2.10532 ( 6) link_NAG-ASN : bond 0.00643 ( 8) link_NAG-ASN : angle 2.64703 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 222 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 TYR cc_start: 0.5884 (t80) cc_final: 0.5611 (t80) REVERT: A 128 PHE cc_start: 0.7959 (t80) cc_final: 0.7594 (t80) REVERT: A 153 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8826 (mmmm) REVERT: A 163 TYR cc_start: 0.7385 (m-80) cc_final: 0.7097 (m-80) REVERT: A 165 PHE cc_start: 0.8447 (OUTLIER) cc_final: 0.7354 (p90) REVERT: A 247 ASP cc_start: 0.8588 (p0) cc_final: 0.8340 (p0) REVERT: A 362 TYR cc_start: 0.8838 (t80) cc_final: 0.8449 (t80) REVERT: A 783 PHE cc_start: 0.7977 (m-10) cc_final: 0.7724 (m-10) REVERT: A 791 MET cc_start: 0.8210 (ttm) cc_final: 0.7158 (tpt) REVERT: A 798 MET cc_start: 0.7401 (tmm) cc_final: 0.6987 (tmm) REVERT: A 943 MET cc_start: 0.8686 (mmm) cc_final: 0.8484 (mmp) REVERT: A 952 MET cc_start: 0.8351 (mmm) cc_final: 0.8145 (tpt) REVERT: A 1555 ILE cc_start: 0.8137 (tp) cc_final: 0.7892 (mt) REVERT: B 76 GLU cc_start: 0.8430 (tp30) cc_final: 0.8102 (tp30) REVERT: B 184 LYS cc_start: 0.9195 (tptp) cc_final: 0.8953 (tptp) REVERT: C 113 MET cc_start: 0.2780 (mmt) cc_final: 0.1827 (ttp) REVERT: C 135 ARG cc_start: 0.6414 (mmm160) cc_final: 0.5840 (mpt-90) outliers start: 37 outliers final: 22 residues processed: 246 average time/residue: 0.0952 time to fit residues: 36.4157 Evaluate side-chains 232 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 208 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 278 ASN Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1328 CYS Chi-restraints excluded: chain A residue 1366 ASN Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1571 HIS Chi-restraints excluded: chain A residue 1590 ILE Chi-restraints excluded: chain A residue 1602 TYR Chi-restraints excluded: chain A residue 1628 LYS Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain C residue 58 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 29 optimal weight: 0.8980 chunk 145 optimal weight: 40.0000 chunk 8 optimal weight: 20.0000 chunk 110 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 153 optimal weight: 20.0000 chunk 27 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 GLN A 765 HIS ** A 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1762 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.153175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.109742 restraints weight = 45978.624| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 4.10 r_work: 0.3354 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3361 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3361 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13424 Z= 0.124 Angle : 0.618 11.292 18162 Z= 0.316 Chirality : 0.043 0.347 2070 Planarity : 0.004 0.042 2194 Dihedral : 10.395 154.480 2157 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.69 % Allowed : 22.40 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.22), residues: 1556 helix: 1.29 (0.17), residues: 894 sheet: -0.59 (0.41), residues: 149 loop : -1.10 (0.30), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 135 TYR 0.026 0.001 TYR B 32 PHE 0.023 0.001 PHE A 733 TRP 0.012 0.001 TRP A1382 HIS 0.007 0.001 HIS A1571 Details of bonding type rmsd covalent geometry : bond 0.00273 (13403) covalent geometry : angle 0.60769 (18110) SS BOND : bond 0.00490 ( 11) SS BOND : angle 1.58178 ( 22) hydrogen bonds : bond 0.04112 ( 768) hydrogen bonds : angle 4.36586 ( 2208) link_BETA1-4 : bond 0.00381 ( 2) link_BETA1-4 : angle 2.02560 ( 6) link_NAG-ASN : bond 0.00611 ( 8) link_NAG-ASN : angle 2.59392 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 218 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 TYR cc_start: 0.5889 (t80) cc_final: 0.5608 (t80) REVERT: A 125 HIS cc_start: 0.7925 (OUTLIER) cc_final: 0.7637 (t70) REVERT: A 128 PHE cc_start: 0.7890 (t80) cc_final: 0.7563 (t80) REVERT: A 153 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8403 (mttp) REVERT: A 163 TYR cc_start: 0.7362 (m-80) cc_final: 0.7048 (m-80) REVERT: A 181 PHE cc_start: 0.7941 (m-80) cc_final: 0.7734 (m-10) REVERT: A 190 TRP cc_start: 0.8227 (m100) cc_final: 0.7968 (m100) REVERT: A 247 ASP cc_start: 0.8556 (p0) cc_final: 0.8344 (p0) REVERT: A 362 TYR cc_start: 0.8789 (t80) cc_final: 0.8388 (t80) REVERT: A 791 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7076 (tpt) REVERT: A 798 MET cc_start: 0.7382 (tmm) cc_final: 0.6947 (tmm) REVERT: A 1244 LYS cc_start: 0.9166 (OUTLIER) cc_final: 0.8912 (mttp) REVERT: A 1555 ILE cc_start: 0.8146 (tp) cc_final: 0.7902 (mt) REVERT: B 76 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8097 (tp30) REVERT: B 184 LYS cc_start: 0.9197 (tptp) cc_final: 0.8952 (tptp) REVERT: C 30 MET cc_start: 0.5316 (ptt) cc_final: 0.4054 (ppp) REVERT: C 113 MET cc_start: 0.2804 (mmt) cc_final: 0.1842 (ttp) REVERT: C 135 ARG cc_start: 0.6495 (mmm160) cc_final: 0.5925 (mpt-90) outliers start: 38 outliers final: 24 residues processed: 240 average time/residue: 0.0979 time to fit residues: 36.0015 Evaluate side-chains 236 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 207 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 791 MET Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 890 LYS Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1244 LYS Chi-restraints excluded: chain A residue 1328 CYS Chi-restraints excluded: chain A residue 1366 ASN Chi-restraints excluded: chain A residue 1374 MET Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1571 HIS Chi-restraints excluded: chain A residue 1590 ILE Chi-restraints excluded: chain A residue 1602 TYR Chi-restraints excluded: chain A residue 1628 LYS Chi-restraints excluded: chain A residue 1762 ASN Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain C residue 58 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 93 optimal weight: 3.9990 chunk 134 optimal weight: 8.9990 chunk 109 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 35 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 82 optimal weight: 0.0770 overall best weight: 1.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 GLN ** A 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1762 ASN B 102 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.152883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.110063 restraints weight = 38709.891| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 3.81 r_work: 0.3362 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3370 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3370 r_free = 0.3370 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3370 r_free = 0.3370 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3370 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13424 Z= 0.136 Angle : 0.648 12.650 18162 Z= 0.328 Chirality : 0.044 0.368 2070 Planarity : 0.004 0.042 2194 Dihedral : 10.372 154.080 2157 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.48 % Allowed : 22.82 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.22), residues: 1556 helix: 1.26 (0.17), residues: 896 sheet: -0.60 (0.42), residues: 141 loop : -1.04 (0.29), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 135 TYR 0.027 0.001 TYR B 32 PHE 0.024 0.001 PHE A 733 TRP 0.012 0.001 TRP A1382 HIS 0.007 0.001 HIS A1571 Details of bonding type rmsd covalent geometry : bond 0.00308 (13403) covalent geometry : angle 0.63906 (18110) SS BOND : bond 0.00462 ( 11) SS BOND : angle 1.52376 ( 22) hydrogen bonds : bond 0.04103 ( 768) hydrogen bonds : angle 4.38592 ( 2208) link_BETA1-4 : bond 0.00393 ( 2) link_BETA1-4 : angle 2.01179 ( 6) link_NAG-ASN : bond 0.00615 ( 8) link_NAG-ASN : angle 2.60107 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 211 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 TYR cc_start: 0.5862 (t80) cc_final: 0.5584 (t80) REVERT: A 125 HIS cc_start: 0.7825 (OUTLIER) cc_final: 0.7404 (t70) REVERT: A 128 PHE cc_start: 0.7949 (t80) cc_final: 0.7625 (t80) REVERT: A 153 LYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8320 (mttp) REVERT: A 157 TYR cc_start: 0.7838 (m-80) cc_final: 0.6705 (t80) REVERT: A 163 TYR cc_start: 0.7416 (m-80) cc_final: 0.7113 (m-80) REVERT: A 190 TRP cc_start: 0.8237 (m100) cc_final: 0.7904 (m100) REVERT: A 247 ASP cc_start: 0.8533 (p0) cc_final: 0.8331 (p0) REVERT: A 362 TYR cc_start: 0.8781 (t80) cc_final: 0.8396 (t80) REVERT: A 791 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.7019 (tpt) REVERT: A 798 MET cc_start: 0.7429 (tmm) cc_final: 0.7016 (tmm) REVERT: A 1244 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8914 (mttp) REVERT: A 1555 ILE cc_start: 0.8184 (tp) cc_final: 0.7939 (mt) REVERT: B 76 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7999 (tp30) REVERT: B 184 LYS cc_start: 0.9195 (tptp) cc_final: 0.8947 (tptp) REVERT: C 113 MET cc_start: 0.2805 (mmt) cc_final: 0.1918 (ttp) REVERT: C 135 ARG cc_start: 0.6568 (mmm160) cc_final: 0.5939 (mpt-90) outliers start: 35 outliers final: 22 residues processed: 230 average time/residue: 0.0972 time to fit residues: 34.6362 Evaluate side-chains 233 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 206 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 791 MET Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 890 LYS Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1244 LYS Chi-restraints excluded: chain A residue 1328 CYS Chi-restraints excluded: chain A residue 1366 ASN Chi-restraints excluded: chain A residue 1374 MET Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1590 ILE Chi-restraints excluded: chain A residue 1602 TYR Chi-restraints excluded: chain A residue 1628 LYS Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain C residue 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 45 optimal weight: 0.9980 chunk 115 optimal weight: 0.6980 chunk 35 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 116 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 78 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 GLN A 915 HIS A1762 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.153586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.109900 restraints weight = 47971.194| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 4.13 r_work: 0.3366 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3374 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3374 r_free = 0.3374 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3374 r_free = 0.3374 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3374 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13424 Z= 0.125 Angle : 0.657 15.606 18162 Z= 0.327 Chirality : 0.044 0.366 2070 Planarity : 0.004 0.042 2194 Dihedral : 10.193 153.840 2155 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.20 % Allowed : 23.25 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.22), residues: 1556 helix: 1.27 (0.17), residues: 897 sheet: -0.59 (0.43), residues: 141 loop : -1.00 (0.29), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 135 TYR 0.026 0.001 TYR B 32 PHE 0.024 0.001 PHE A 733 TRP 0.013 0.001 TRP A 188 HIS 0.005 0.001 HIS A1571 Details of bonding type rmsd covalent geometry : bond 0.00272 (13403) covalent geometry : angle 0.64844 (18110) SS BOND : bond 0.00429 ( 11) SS BOND : angle 1.44707 ( 22) hydrogen bonds : bond 0.04064 ( 768) hydrogen bonds : angle 4.33802 ( 2208) link_BETA1-4 : bond 0.00393 ( 2) link_BETA1-4 : angle 1.97723 ( 6) link_NAG-ASN : bond 0.00621 ( 8) link_NAG-ASN : angle 2.56145 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 217 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 TYR cc_start: 0.5828 (t80) cc_final: 0.5531 (t80) REVERT: A 125 HIS cc_start: 0.7845 (OUTLIER) cc_final: 0.7568 (t70) REVERT: A 153 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8681 (mmmm) REVERT: A 157 TYR cc_start: 0.7864 (m-80) cc_final: 0.6803 (t80) REVERT: A 163 TYR cc_start: 0.7375 (m-80) cc_final: 0.7096 (m-80) REVERT: A 176 PHE cc_start: 0.7976 (t80) cc_final: 0.7741 (t80) REVERT: A 247 ASP cc_start: 0.8556 (p0) cc_final: 0.8325 (p0) REVERT: A 362 TYR cc_start: 0.8777 (t80) cc_final: 0.8366 (t80) REVERT: A 791 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.7034 (tpt) REVERT: A 798 MET cc_start: 0.7296 (tmm) cc_final: 0.6929 (tmm) REVERT: A 1244 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8860 (mttp) REVERT: A 1555 ILE cc_start: 0.8173 (tp) cc_final: 0.7922 (mt) REVERT: B 76 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7980 (tp30) REVERT: B 184 LYS cc_start: 0.9173 (tptp) cc_final: 0.8931 (tptp) REVERT: C 30 MET cc_start: 0.5300 (ptt) cc_final: 0.4043 (ppp) REVERT: C 113 MET cc_start: 0.2719 (mmt) cc_final: 0.1848 (ttp) REVERT: C 135 ARG cc_start: 0.6771 (mmm160) cc_final: 0.6031 (mpt-90) outliers start: 31 outliers final: 23 residues processed: 235 average time/residue: 0.0931 time to fit residues: 33.9654 Evaluate side-chains 239 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 211 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 791 MET Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 890 LYS Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1244 LYS Chi-restraints excluded: chain A residue 1328 CYS Chi-restraints excluded: chain A residue 1366 ASN Chi-restraints excluded: chain A residue 1374 MET Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1571 HIS Chi-restraints excluded: chain A residue 1590 ILE Chi-restraints excluded: chain A residue 1602 TYR Chi-restraints excluded: chain A residue 1628 LYS Chi-restraints excluded: chain A residue 1762 ASN Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain C residue 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 102 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 111 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 91 optimal weight: 0.0670 chunk 119 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 135 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 overall best weight: 3.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.153316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.108517 restraints weight = 35592.147| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 3.16 r_work: 0.3413 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3418 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3418 r_free = 0.3418 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3418 r_free = 0.3418 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3418 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 13424 Z= 0.185 Angle : 0.859 59.196 18162 Z= 0.481 Chirality : 0.058 1.628 2070 Planarity : 0.004 0.078 2194 Dihedral : 10.198 153.772 2155 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.20 % Allowed : 23.74 % Favored : 74.06 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.22), residues: 1556 helix: 1.25 (0.17), residues: 897 sheet: -0.59 (0.43), residues: 141 loop : -1.00 (0.29), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 135 TYR 0.025 0.001 TYR B 32 PHE 0.024 0.001 PHE A 733 TRP 0.011 0.001 TRP A 188 HIS 0.005 0.001 HIS A1571 Details of bonding type rmsd covalent geometry : bond 0.00397 (13403) covalent geometry : angle 0.85283 (18110) SS BOND : bond 0.00475 ( 11) SS BOND : angle 1.45746 ( 22) hydrogen bonds : bond 0.04126 ( 768) hydrogen bonds : angle 4.34814 ( 2208) link_BETA1-4 : bond 0.00252 ( 2) link_BETA1-4 : angle 2.01991 ( 6) link_NAG-ASN : bond 0.00600 ( 8) link_NAG-ASN : angle 2.56890 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3829.14 seconds wall clock time: 66 minutes 13.39 seconds (3973.39 seconds total)