Starting phenix.real_space_refine on Thu Mar 5 11:28:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6l54_0837/03_2026/6l54_0837.cif Found real_map, /net/cci-nas-00/data/ceres_data/6l54_0837/03_2026/6l54_0837.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6l54_0837/03_2026/6l54_0837.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6l54_0837/03_2026/6l54_0837.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6l54_0837/03_2026/6l54_0837.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6l54_0837/03_2026/6l54_0837.map" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1617 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 109 5.16 5 C 12379 2.51 5 N 3340 2.21 5 O 3698 1.98 5 H 857 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20387 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 13859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1911, 13859 Classifications: {'peptide': 1911} Incomplete info: {'truncation_to_alanine': 288} Link IDs: {'CIS': 41, 'PCIS': 4, 'PTRANS': 62, 'TRANS': 1803} Chain breaks: 28 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 1401 Unresolved non-hydrogen angles: 1775 Unresolved non-hydrogen dihedrals: 1261 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'ARG:plan': 49, 'TYR:plan': 20, 'GLN:plan1': 22, 'PHE:plan': 15, 'ASN:plan1': 11, 'HIS:plan': 10, 'TRP:plan': 17, 'GLU:plan': 26, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 929 Chain: "B" Number of atoms: 3551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3551 Classifications: {'peptide': 389} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 369} Chain breaks: 7 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2944 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 289} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.23, per 1000 atoms: 0.21 Number of scatterers: 20387 At special positions: 0 Unit cell: (128.96, 178.88, 142.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 109 16.00 P 3 15.00 Mg 1 11.99 O 3698 8.00 N 3340 7.00 C 12379 6.00 H 857 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.48 Conformation dependent library (CDL) restraints added in 1.0 seconds 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4992 Finding SS restraints... Secondary structure from input PDB file: 139 helices and 6 sheets defined 61.2% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 37 through 43 Processing helix chain 'A' and resid 62 through 70 removed outlier: 3.634A pdb=" N ARG A 70 " --> pdb=" O VAL A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 80 through 89 removed outlier: 3.738A pdb=" N GLU A 84 " --> pdb=" O ILE A 80 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS A 85 " --> pdb=" O GLN A 81 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER A 89 " --> pdb=" O LYS A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 removed outlier: 3.737A pdb=" N SER A 103 " --> pdb=" O TYR A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 106 No H-bonds generated for 'chain 'A' and resid 104 through 106' Processing helix chain 'A' and resid 113 through 118 removed outlier: 3.809A pdb=" N GLU A 117 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N PHE A 118 " --> pdb=" O THR A 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 113 through 118' Processing helix chain 'A' and resid 123 through 142 removed outlier: 3.722A pdb=" N THR A 130 " --> pdb=" O ARG A 126 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N SER A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 152 No H-bonds generated for 'chain 'A' and resid 150 through 152' Processing helix chain 'A' and resid 153 through 163 Processing helix chain 'A' and resid 170 through 175 removed outlier: 3.776A pdb=" N PHE A 175 " --> pdb=" O GLN A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 182 Processing helix chain 'A' and resid 188 through 199 removed outlier: 3.795A pdb=" N ILE A 192 " --> pdb=" O GLN A 188 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N HIS A 197 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL A 199 " --> pdb=" O ALA A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 205 removed outlier: 3.648A pdb=" N SER A 204 " --> pdb=" O ASN A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 223 removed outlier: 3.768A pdb=" N CYS A 217 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU A 218 " --> pdb=" O GLY A 214 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY A 219 " --> pdb=" O ALA A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 246 removed outlier: 4.185A pdb=" N PHE A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LYS A 239 " --> pdb=" O TRP A 235 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE A 240 " --> pdb=" O ILE A 236 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER A 242 " --> pdb=" O SER A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 269 Processing helix chain 'A' and resid 278 through 293 removed outlier: 3.737A pdb=" N SER A 282 " --> pdb=" O THR A 278 " (cutoff:3.500A) Proline residue: A 290 - end of helix removed outlier: 3.967A pdb=" N LEU A 293 " --> pdb=" O THR A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 313 removed outlier: 4.447A pdb=" N ALA A 304 " --> pdb=" O ILE A 300 " (cutoff:3.500A) Proline residue: A 308 - end of helix Processing helix chain 'A' and resid 321 through 324 Processing helix chain 'A' and resid 325 through 331 Processing helix chain 'A' and resid 338 through 356 removed outlier: 3.865A pdb=" N LEU A 343 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Proline residue: A 348 - end of helix Processing helix chain 'A' and resid 362 through 367 removed outlier: 3.567A pdb=" N GLU A 366 " --> pdb=" O GLY A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 388 Processing helix chain 'A' and resid 388 through 395 Processing helix chain 'A' and resid 398 through 420 removed outlier: 4.099A pdb=" N VAL A 404 " --> pdb=" O ALA A 400 " (cutoff:3.500A) Proline residue: A 418 - end of helix Processing helix chain 'A' and resid 420 through 425 Processing helix chain 'A' and resid 444 through 456 removed outlier: 3.732A pdb=" N PHE A 448 " --> pdb=" O ASN A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 460 Processing helix chain 'A' and resid 472 through 480 removed outlier: 4.324A pdb=" N VAL A 478 " --> pdb=" O HIS A 474 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR A 480 " --> pdb=" O ASP A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 485 Processing helix chain 'A' and resid 487 through 492 Processing helix chain 'A' and resid 493 through 509 removed outlier: 3.996A pdb=" N ILE A 497 " --> pdb=" O GLY A 493 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL A 508 " --> pdb=" O LEU A 504 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU A 509 " --> pdb=" O THR A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 558 removed outlier: 4.284A pdb=" N GLN A 550 " --> pdb=" O HIS A 546 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU A 555 " --> pdb=" O ALA A 551 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ILE A 558 " --> pdb=" O SER A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 581 removed outlier: 3.704A pdb=" N LYS A 566 " --> pdb=" O GLU A 562 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ILE A 568 " --> pdb=" O ALA A 564 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU A 571 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A 579 " --> pdb=" O ALA A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 601 removed outlier: 4.042A pdb=" N HIS A 600 " --> pdb=" O PHE A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 617 removed outlier: 4.064A pdb=" N VAL A 611 " --> pdb=" O ALA A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 631 Processing helix chain 'A' and resid 641 through 653 removed outlier: 3.806A pdb=" N ASN A 645 " --> pdb=" O LEU A 641 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER A 651 " --> pdb=" O MET A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 668 removed outlier: 3.783A pdb=" N TYR A 662 " --> pdb=" O PRO A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 726 Processing helix chain 'A' and resid 734 through 746 removed outlier: 3.902A pdb=" N ALA A 739 " --> pdb=" O ALA A 735 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N VAL A 740 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS A 744 " --> pdb=" O VAL A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 768 removed outlier: 3.684A pdb=" N THR A 768 " --> pdb=" O LEU A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 824 removed outlier: 3.954A pdb=" N ALA A 816 " --> pdb=" O ARG A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 850 removed outlier: 3.674A pdb=" N HIS A 848 " --> pdb=" O ALA A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 890 removed outlier: 4.010A pdb=" N ASN A 873 " --> pdb=" O ILE A 869 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER A 874 " --> pdb=" O LEU A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 907 Processing helix chain 'A' and resid 908 through 913 Processing helix chain 'A' and resid 915 through 922 Processing helix chain 'A' and resid 924 through 931 removed outlier: 3.688A pdb=" N THR A 931 " --> pdb=" O SER A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 948 removed outlier: 4.165A pdb=" N ASP A 938 " --> pdb=" O GLY A 934 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N THR A 939 " --> pdb=" O ARG A 935 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N PHE A 940 " --> pdb=" O ALA A 936 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE A 943 " --> pdb=" O THR A 939 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ILE A 946 " --> pdb=" O THR A 942 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG A 948 " --> pdb=" O GLU A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 985 removed outlier: 3.511A pdb=" N ASN A 976 " --> pdb=" O GLY A 972 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLN A 977 " --> pdb=" O HIS A 973 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N LEU A 978 " --> pdb=" O GLY A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 999 removed outlier: 3.537A pdb=" N TYR A 995 " --> pdb=" O GLU A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1016 removed outlier: 3.907A pdb=" N THR A1014 " --> pdb=" O LYS A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1021 Processing helix chain 'A' and resid 1026 through 1034 removed outlier: 3.547A pdb=" N ILE A1030 " --> pdb=" O TRP A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1073 through 1078 Processing helix chain 'A' and resid 1080 through 1085 Processing helix chain 'A' and resid 1092 through 1104 Processing helix chain 'A' and resid 1117 through 1122 removed outlier: 3.524A pdb=" N ALA A1121 " --> pdb=" O PHE A1118 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N SER A1122 " --> pdb=" O GLU A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1132 Processing helix chain 'A' and resid 1195 through 1205 removed outlier: 3.558A pdb=" N ASP A1199 " --> pdb=" O ILE A1195 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A1203 " --> pdb=" O ASP A1199 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLN A1204 " --> pdb=" O TRP A1200 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU A1205 " --> pdb=" O ALA A1201 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1215 removed outlier: 4.608A pdb=" N HIS A1211 " --> pdb=" O GLN A1207 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP A1212 " --> pdb=" O ASN A1208 " (cutoff:3.500A) Processing helix chain 'A' and resid 1282 through 1297 removed outlier: 4.233A pdb=" N LYS A1287 " --> pdb=" O ARG A1283 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER A1288 " --> pdb=" O GLU A1284 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL A1291 " --> pdb=" O LYS A1287 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLN A1292 " --> pdb=" O SER A1288 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG A1295 " --> pdb=" O VAL A1291 " (cutoff:3.500A) Processing helix chain 'A' and resid 1297 through 1302 Processing helix chain 'A' and resid 1303 through 1305 No H-bonds generated for 'chain 'A' and resid 1303 through 1305' Processing helix chain 'A' and resid 1315 through 1331 removed outlier: 3.617A pdb=" N ALA A1331 " --> pdb=" O THR A1327 " (cutoff:3.500A) Processing helix chain 'A' and resid 1350 through 1355 Processing helix chain 'A' and resid 1355 through 1368 removed outlier: 3.897A pdb=" N GLU A1361 " --> pdb=" O SER A1357 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL A1364 " --> pdb=" O LEU A1360 " (cutoff:3.500A) Processing helix chain 'A' and resid 1399 through 1411 Processing helix chain 'A' and resid 1416 through 1428 Processing helix chain 'A' and resid 1453 through 1466 removed outlier: 3.875A pdb=" N THR A1458 " --> pdb=" O GLY A1454 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA A1459 " --> pdb=" O LYS A1455 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN A1460 " --> pdb=" O THR A1456 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP A1461 " --> pdb=" O THR A1457 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU A1462 " --> pdb=" O THR A1458 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A1463 " --> pdb=" O ALA A1459 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N HIS A1465 " --> pdb=" O ASP A1461 " (cutoff:3.500A) Processing helix chain 'A' and resid 1466 through 1480 removed outlier: 3.564A pdb=" N GLY A1480 " --> pdb=" O ASP A1476 " (cutoff:3.500A) Processing helix chain 'A' and resid 1485 through 1500 removed outlier: 3.769A pdb=" N LYS A1489 " --> pdb=" O ILE A1485 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU A1491 " --> pdb=" O LYS A1487 " (cutoff:3.500A) Processing helix chain 'A' and resid 1511 through 1517 removed outlier: 4.074A pdb=" N ALA A1517 " --> pdb=" O SER A1514 " (cutoff:3.500A) Processing helix chain 'A' and resid 1523 through 1534 Processing helix chain 'A' and resid 1535 through 1539 Processing helix chain 'A' and resid 1598 through 1608 removed outlier: 3.787A pdb=" N GLY A1602 " --> pdb=" O ASP A1598 " (cutoff:3.500A) Processing helix chain 'A' and resid 1617 through 1640 removed outlier: 3.795A pdb=" N ALA A1621 " --> pdb=" O LYS A1617 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU A1622 " --> pdb=" O SER A1618 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TRP A1625 " --> pdb=" O ALA A1621 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS A1632 " --> pdb=" O ARG A1628 " (cutoff:3.500A) Processing helix chain 'A' and resid 1644 through 1655 Processing helix chain 'A' and resid 1660 through 1677 removed outlier: 3.646A pdb=" N GLU A1665 " --> pdb=" O ILE A1661 " (cutoff:3.500A) Processing helix chain 'A' and resid 1701 through 1713 removed outlier: 3.875A pdb=" N ASP A1705 " --> pdb=" O ASP A1701 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL A1706 " --> pdb=" O ASP A1702 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU A1711 " --> pdb=" O ILE A1707 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE A1712 " --> pdb=" O TRP A1708 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER A1713 " --> pdb=" O ARG A1709 " (cutoff:3.500A) Processing helix chain 'A' and resid 1727 through 1739 removed outlier: 3.730A pdb=" N VAL A1732 " --> pdb=" O GLY A1728 " (cutoff:3.500A) Processing helix chain 'A' and resid 1739 through 1760 removed outlier: 3.697A pdb=" N LEU A1743 " --> pdb=" O ARG A1739 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LYS A1745 " --> pdb=" O PHE A1741 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N LEU A1746 " --> pdb=" O SER A1742 " (cutoff:3.500A) Processing helix chain 'A' and resid 1785 through 1799 Processing helix chain 'A' and resid 1803 through 1811 removed outlier: 3.989A pdb=" N HIS A1809 " --> pdb=" O GLN A1805 " (cutoff:3.500A) Processing helix chain 'A' and resid 1823 through 1827 removed outlier: 4.137A pdb=" N LEU A1826 " --> pdb=" O ILE A1823 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE A1827 " --> pdb=" O PRO A1824 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1823 through 1827' Processing helix chain 'A' and resid 1837 through 1851 removed outlier: 3.566A pdb=" N ASN A1843 " --> pdb=" O GLN A1839 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP A1851 " --> pdb=" O ARG A1847 " (cutoff:3.500A) Processing helix chain 'A' and resid 1852 through 1856 Processing helix chain 'A' and resid 1860 through 1865 removed outlier: 3.572A pdb=" N ILE A1865 " --> pdb=" O ILE A1861 " (cutoff:3.500A) Processing helix chain 'A' and resid 1927 through 1939 removed outlier: 4.056A pdb=" N LYS A1932 " --> pdb=" O ASP A1928 " (cutoff:3.500A) Processing helix chain 'A' and resid 1941 through 1959 removed outlier: 3.950A pdb=" N VAL A1945 " --> pdb=" O ASN A1941 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL A1948 " --> pdb=" O MET A1944 " (cutoff:3.500A) Processing helix chain 'A' and resid 1964 through 1971 Processing helix chain 'A' and resid 1975 through 1991 Processing helix chain 'A' and resid 2010 through 2013 Processing helix chain 'A' and resid 2014 through 2028 removed outlier: 3.692A pdb=" N ARG A2025 " --> pdb=" O LEU A2021 " (cutoff:3.500A) Processing helix chain 'A' and resid 2039 through 2044 Processing helix chain 'A' and resid 2048 through 2053 removed outlier: 3.933A pdb=" N GLU A2053 " --> pdb=" O GLU A2049 " (cutoff:3.500A) Processing helix chain 'A' and resid 2071 through 2084 removed outlier: 3.942A pdb=" N MET A2075 " --> pdb=" O PHE A2071 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A2078 " --> pdb=" O ILE A2074 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ARG A2081 " --> pdb=" O SER A2077 " (cutoff:3.500A) Processing helix chain 'A' and resid 2097 through 2102 Processing helix chain 'A' and resid 2161 through 2179 removed outlier: 4.299A pdb=" N THR A2179 " --> pdb=" O THR A2175 " (cutoff:3.500A) Processing helix chain 'A' and resid 2214 through 2231 Processing helix chain 'A' and resid 2250 through 2256 removed outlier: 3.728A pdb=" N TYR A2254 " --> pdb=" O SER A2250 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS A2256 " --> pdb=" O LEU A2252 " (cutoff:3.500A) Processing helix chain 'A' and resid 2279 through 2289 removed outlier: 3.563A pdb=" N GLU A2285 " --> pdb=" O LYS A2281 " (cutoff:3.500A) Processing helix chain 'A' and resid 2294 through 2303 Processing helix chain 'A' and resid 2306 through 2331 removed outlier: 3.752A pdb=" N TRP A2311 " --> pdb=" O PRO A2307 " (cutoff:3.500A) Processing helix chain 'A' and resid 2360 through 2364 Processing helix chain 'A' and resid 2377 through 2382 removed outlier: 3.688A pdb=" N ALA A2382 " --> pdb=" O ASN A2378 " (cutoff:3.500A) Processing helix chain 'A' and resid 2391 through 2406 removed outlier: 3.675A pdb=" N GLN A2398 " --> pdb=" O LEU A2394 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL A2399 " --> pdb=" O SER A2395 " (cutoff:3.500A) Processing helix chain 'A' and resid 2407 through 2419 removed outlier: 3.797A pdb=" N LEU A2411 " --> pdb=" O ARG A2407 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU A2414 " --> pdb=" O LEU A2410 " (cutoff:3.500A) Processing helix chain 'A' and resid 3608 through 3621 Processing helix chain 'A' and resid 3632 through 3644 Processing helix chain 'A' and resid 3646 through 3652 Processing helix chain 'A' and resid 3654 through 3658 Processing helix chain 'B' and resid 6 through 11 Processing helix chain 'B' and resid 62 through 72 removed outlier: 3.501A pdb=" N CYS B 72 " --> pdb=" O VAL B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 171 removed outlier: 3.765A pdb=" N ARG B 164 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER B 171 " --> pdb=" O ARG B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 206 removed outlier: 3.617A pdb=" N LEU B 203 " --> pdb=" O SER B 199 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL B 206 " --> pdb=" O TYR B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.802A pdb=" N ARG B 225 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP B 231 " --> pdb=" O PHE B 227 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLY B 232 " --> pdb=" O ARG B 228 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU B 233 " --> pdb=" O ALA B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 243 Processing helix chain 'B' and resid 251 through 258 removed outlier: 3.631A pdb=" N LYS B 255 " --> pdb=" O GLY B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 315 removed outlier: 3.523A pdb=" N LEU B 300 " --> pdb=" O PRO B 296 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N HIS B 302 " --> pdb=" O ARG B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 361 removed outlier: 3.752A pdb=" N ARG B 356 " --> pdb=" O LEU B 352 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N SER B 357 " --> pdb=" O ASP B 353 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR B 360 " --> pdb=" O ARG B 356 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL B 361 " --> pdb=" O SER B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 423 removed outlier: 4.464A pdb=" N HIS B 417 " --> pdb=" O PHE B 413 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LEU B 420 " --> pdb=" O GLN B 416 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL B 421 " --> pdb=" O HIS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 460 removed outlier: 3.773A pdb=" N LYS B 454 " --> pdb=" O SER B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 486 removed outlier: 3.950A pdb=" N LYS B 483 " --> pdb=" O SER B 480 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N VAL B 484 " --> pdb=" O SER B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 514 Proline residue: B 505 - end of helix removed outlier: 3.786A pdb=" N SER B 509 " --> pdb=" O PRO B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 537 removed outlier: 4.683A pdb=" N GLN B 530 " --> pdb=" O ASN B 526 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ARG B 533 " --> pdb=" O ALA B 529 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN B 537 " --> pdb=" O ARG B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 557 removed outlier: 3.968A pdb=" N ALA B 548 " --> pdb=" O PHE B 544 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET B 549 " --> pdb=" O HIS B 545 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N HIS B 552 " --> pdb=" O ALA B 548 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N GLU B 553 " --> pdb=" O MET B 549 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP B 554 " --> pdb=" O GLN B 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 198 Processing helix chain 'C' and resid 218 through 226 Processing helix chain 'C' and resid 275 through 285 Processing helix chain 'C' and resid 296 through 314 removed outlier: 3.747A pdb=" N GLU C 301 " --> pdb=" O HIS C 297 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N MET C 302 " --> pdb=" O THR C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 341 removed outlier: 3.549A pdb=" N GLN C 335 " --> pdb=" O TYR C 331 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR C 336 " --> pdb=" O ARG C 332 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N MET C 339 " --> pdb=" O GLN C 335 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL C 340 " --> pdb=" O THR C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 379 Processing helix chain 'C' and resid 380 through 395 Processing helix chain 'C' and resid 465 through 480 Processing helix chain 'C' and resid 491 through 508 removed outlier: 3.556A pdb=" N PHE C 496 " --> pdb=" O GLU C 492 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ARG C 501 " --> pdb=" O HIS C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 518 removed outlier: 3.905A pdb=" N ARG C 517 " --> pdb=" O ALA C 513 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2128 through 2129 Processing sheet with id=AA2, first strand: chain 'A' and resid 2153 through 2154 Processing sheet with id=AA3, first strand: chain 'A' and resid 2212 through 2213 Processing sheet with id=AA4, first strand: chain 'B' and resid 139 through 143 removed outlier: 6.503A pdb=" N CYS B 48 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N LEU B 151 " --> pdb=" O CYS B 48 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL B 50 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE B 209 " --> pdb=" O VAL B 49 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 267 through 270 removed outlier: 6.601A pdb=" N PHE B 267 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N TYR B 337 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N PHE B 269 " --> pdb=" O TYR B 337 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 259 through 260 removed outlier: 6.154A pdb=" N LEU C 205 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N LEU C 268 " --> pdb=" O LEU C 205 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL C 207 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL C 206 " --> pdb=" O VAL C 317 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ILE C 319 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLY C 208 " --> pdb=" O ILE C 319 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL C 321 " --> pdb=" O GLY C 208 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LEU C 210 " --> pdb=" O VAL C 321 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL C 318 " --> pdb=" O VAL C 368 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LEU C 370 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL C 320 " --> pdb=" O LEU C 370 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N PHE C 369 " --> pdb=" O SER C 424 " (cutoff:3.500A) 891 hydrogen bonds defined for protein. 2574 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: 4.07 Time building geometry restraints manager: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 857 1.03 - 1.23: 0 1.23 - 1.42: 8033 1.42 - 1.62: 11661 1.62 - 1.81: 161 Bond restraints: 20712 Sorted by residual: bond pdb=" CA ASP A2420 " pdb=" C ASP A2420 " ideal model delta sigma weight residual 1.532 1.525 0.007 6.50e-03 2.37e+04 1.33e+00 bond pdb=" N VAL B 348 " pdb=" CA VAL B 348 " ideal model delta sigma weight residual 1.474 1.458 0.017 1.57e-02 4.06e+03 1.11e+00 bond pdb=" C ASP A2420 " pdb=" O ASP A2420 " ideal model delta sigma weight residual 1.233 1.238 -0.005 4.80e-03 4.34e+04 9.52e-01 bond pdb=" CA VAL A3637 " pdb=" CB VAL A3637 " ideal model delta sigma weight residual 1.540 1.528 0.012 1.25e-02 6.40e+03 9.32e-01 bond pdb=" C HIS A 675 " pdb=" N ASP A 676 " ideal model delta sigma weight residual 1.329 1.342 -0.013 1.40e-02 5.10e+03 9.21e-01 ... (remaining 20707 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.56: 29104 10.56 - 21.12: 3 21.12 - 31.68: 0 31.68 - 42.24: 0 42.24 - 52.80: 6 Bond angle restraints: 29113 Sorted by residual: angle pdb=" C LEU B 137 " pdb=" N LEU B 138 " pdb=" H LEU B 138 " ideal model delta sigma weight residual 124.53 71.73 52.80 3.00e+00 1.11e-01 3.10e+02 angle pdb=" CA LEU B 138 " pdb=" N LEU B 138 " pdb=" H LEU B 138 " ideal model delta sigma weight residual 114.23 61.60 52.63 3.00e+00 1.11e-01 3.08e+02 angle pdb=" C HIS C 399 " pdb=" N LEU C 400 " pdb=" H LEU C 400 " ideal model delta sigma weight residual 124.11 72.13 51.98 3.00e+00 1.11e-01 3.00e+02 angle pdb=" CA LEU C 400 " pdb=" N LEU C 400 " pdb=" H LEU C 400 " ideal model delta sigma weight residual 113.81 62.54 51.27 3.00e+00 1.11e-01 2.92e+02 angle pdb=" C PHE C 325 " pdb=" N THR C 326 " pdb=" H THR C 326 " ideal model delta sigma weight residual 123.83 72.65 51.19 3.00e+00 1.11e-01 2.91e+02 ... (remaining 29108 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.30: 12165 20.30 - 40.60: 173 40.60 - 60.90: 21 60.90 - 81.20: 8 81.20 - 101.50: 3 Dihedral angle restraints: 12370 sinusoidal: 4717 harmonic: 7653 Sorted by residual: dihedral pdb=" O5' GTP C 601 " pdb=" O3A GTP C 601 " pdb=" PA GTP C 601 " pdb=" PB GTP C 601 " ideal model delta sinusoidal sigma weight residual 274.12 172.62 101.50 1 2.00e+01 2.50e-03 2.88e+01 dihedral pdb=" CA ALA A1088 " pdb=" C ALA A1088 " pdb=" N ILE A1089 " pdb=" CA ILE A1089 " ideal model delta harmonic sigma weight residual 180.00 -154.21 -25.79 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA LEU A1657 " pdb=" C LEU A1657 " pdb=" N PRO A1658 " pdb=" CA PRO A1658 " ideal model delta harmonic sigma weight residual -180.00 -155.34 -24.66 0 5.00e+00 4.00e-02 2.43e+01 ... (remaining 12367 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2828 0.051 - 0.102: 399 0.102 - 0.153: 39 0.153 - 0.204: 0 0.204 - 0.255: 1 Chirality restraints: 3267 Sorted by residual: chirality pdb=" CA PRO A3627 " pdb=" N PRO A3627 " pdb=" C PRO A3627 " pdb=" CB PRO A3627 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA PRO A1658 " pdb=" N PRO A1658 " pdb=" C PRO A1658 " pdb=" CB PRO A1658 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 5.01e-01 chirality pdb=" CA VAL A2367 " pdb=" N VAL A2367 " pdb=" C VAL A2367 " pdb=" CB VAL A2367 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.51e-01 ... (remaining 3264 not shown) Planarity restraints: 3786 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A1346 " 0.040 5.00e-02 4.00e+02 6.06e-02 5.87e+00 pdb=" N PRO A1347 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO A1347 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A1347 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A2275 " 0.030 5.00e-02 4.00e+02 4.57e-02 3.34e+00 pdb=" N PRO A2276 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A2276 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A2276 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A2246 " 0.027 5.00e-02 4.00e+02 4.16e-02 2.76e+00 pdb=" N PRO A2247 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A2247 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A2247 " 0.021 5.00e-02 4.00e+02 ... (remaining 3783 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.10: 57 2.10 - 2.72: 4505 2.72 - 3.35: 31910 3.35 - 3.97: 42449 3.97 - 4.60: 64486 Nonbonded interactions: 143407 Sorted by model distance: nonbonded pdb=" H LEU C 400 " pdb=" HA LEU C 400 " model vdw 1.469 1.816 nonbonded pdb=" H LEU B 138 " pdb=" HA LEU B 138 " model vdw 1.552 1.816 nonbonded pdb=" O LEU C 212 " pdb=" HZ2 LYS C 217 " model vdw 1.646 2.450 nonbonded pdb=" O GLU B 44 " pdb=" H TYR B 445 " model vdw 1.686 2.450 nonbonded pdb=" O GLY C 208 " pdb=" H ILE C 319 " model vdw 1.712 2.450 ... (remaining 143402 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.180 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 19.410 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 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:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 19856 Z= 0.090 Angle : 0.492 12.576 27014 Z= 0.294 Chirality : 0.035 0.255 3267 Planarity : 0.003 0.061 3422 Dihedral : 7.603 101.504 6981 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 61.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.79 % Favored : 91.17 % Rotamer: Outliers : 0.79 % Allowed : 4.34 % Favored : 94.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 1.66 % 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: -3.87 (0.15), residues: 2526 helix: -1.52 (0.13), residues: 1356 sheet: -4.08 (0.37), residues: 109 loop : -3.85 (0.18), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 474 TYR 0.005 0.000 TYR A 143 PHE 0.007 0.000 PHE A 240 TRP 0.007 0.001 TRP A1819 HIS 0.002 0.000 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00157 (19855) covalent geometry : angle 0.49188 (27014) hydrogen bonds : bond 0.19579 ( 891) hydrogen bonds : angle 6.68245 ( 2574) Misc. bond : bond 0.00057 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 5 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue VAL 50 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue LYS 55 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue ALA 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue ALA 140 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue TYR 150 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LEU 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue ALA 165 is missing expected H atoms. Skipping. Residue ALA 185 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue TYR 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue LEU 210 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue LEU 212 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue THR 216 is missing expected H atoms. Skipping. Residue SER 218 is missing expected H atoms. Skipping. Residue ILE 221 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue TYR 223 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LYS 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue LEU 300 is missing expected H atoms. Skipping. Residue ALA 303 is missing expected H atoms. Skipping. Residue LEU 304 is missing expected H atoms. Skipping. Residue ILE 308 is missing expected H atoms. Skipping. Residue TYR 309 is missing expected H atoms. Skipping. Residue ILE 311 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue SER 315 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue ALA 334 is missing expected H atoms. Skipping. Residue VAL 336 is missing expected H atoms. Skipping. Residue TYR 337 is missing expected H atoms. Skipping. Residue ILE 338 is missing expected H atoms. Skipping. Residue VAL 339 is missing expected H atoms. Skipping. Residue THR 409 is missing expected H atoms. Skipping. Residue VAL 418 is missing expected H atoms. Skipping. Residue LEU 420 is missing expected H atoms. Skipping. Residue THR 444 is missing expected H atoms. Skipping. Residue TYR 445 is missing expected H atoms. Skipping. Residue LYS 447 is missing expected H atoms. Skipping. Residue ILE 449 is missing expected H atoms. Skipping. Residue SER 450 is missing expected H atoms. Skipping. Residue ALA 451 is missing expected H atoms. Skipping. Residue SER 453 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue TYR 456 is missing expected H atoms. Skipping. Residue VAL 458 is missing expected H atoms. Skipping. Residue ALA 459 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 493 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue SER 496 is missing expected H atoms. Skipping. Residue LEU 528 is missing expected H atoms. Skipping. Residue ALA 529 is missing expected H atoms. Skipping. Residue ALA 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue VAL 534 is missing expected H atoms. Skipping. Residue TYR 535 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue ALA 539 is missing expected H atoms. Skipping. Residue ALA 543 is missing expected H atoms. Skipping. Residue LYS 546 is missing expected H atoms. Skipping. Residue TYR 547 is missing expected H atoms. Skipping. Residue ALA 548 is missing expected H atoms. Skipping. Residue MET 549 is missing expected H atoms. Skipping. Residue LEU 551 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 181 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 183 is missing expected H atoms. Skipping. Residue VAL 184 is missing expected H atoms. Skipping. Residue MET 188 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue ALA 194 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue TYR 197 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue THR 202 is missing expected H atoms. Skipping. Residue VAL 204 is missing expected H atoms. Skipping. Residue LEU 205 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue VAL 209 is missing expected H atoms. Skipping. Residue LEU 210 is missing expected H atoms. Skipping. Residue LEU 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue MET 221 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue ALA 226 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue ILE 256 is missing expected H atoms. Skipping. Residue ILE 265 is missing expected H atoms. Skipping. Residue VAL 266 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue MET 302 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue ILE 307 is missing expected H atoms. Skipping. Residue ALA 308 is missing expected H atoms. Skipping. Residue ALA 309 is missing expected H atoms. Skipping. Residue LEU 311 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue VAL 318 is missing expected H atoms. Skipping. Residue ILE 319 is missing expected H atoms. Skipping. Residue VAL 320 is missing expected H atoms. Skipping. Residue VAL 321 is missing expected H atoms. Skipping. Residue THR 326 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LEU 330 is missing expected H atoms. Skipping. Residue TYR 331 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 336 is missing expected H atoms. Skipping. Residue ALA 337 is missing expected H atoms. Skipping. Residue MET 339 is missing expected H atoms. Skipping. Residue VAL 340 is missing expected H atoms. Skipping. Residue LYS 341 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue VAL 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue ALA 374 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue LEU 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue LEU 394 is missing expected H atoms. Skipping. Residue MET 395 is missing expected H atoms. Skipping. Residue ALA 396 is missing expected H atoms. Skipping. Residue SER 398 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue SER 424 is missing expected H atoms. Skipping. Residue VAL 426 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue SER 468 is missing expected H atoms. Skipping. Residue LEU 469 is missing expected H atoms. Skipping. Residue VAL 470 is missing expected H atoms. Skipping. Residue SER 471 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue SER 475 is missing expected H atoms. Skipping. Residue VAL 477 is missing expected H atoms. Skipping. Residue MET 478 is missing expected H atoms. Skipping. Residue THR 491 is missing expected H atoms. Skipping. Residue LYS 493 is missing expected H atoms. Skipping. Residue ALA 499 is missing expected H atoms. Skipping. Residue ALA 500 is missing expected H atoms. Skipping. Residue ILE 502 is missing expected H atoms. Skipping. Residue SER 510 is missing expected H atoms. Skipping. Residue ALA 511 is missing expected H atoms. Skipping. Residue ALA 513 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Evaluate side-chains 635 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 619 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 PHE cc_start: 0.7733 (m-80) cc_final: 0.4593 (m-80) REVERT: A 252 TYR cc_start: 0.6642 (m-80) cc_final: 0.6282 (m-10) REVERT: A 257 TYR cc_start: 0.5499 (t80) cc_final: 0.4543 (t80) REVERT: A 267 LYS cc_start: 0.7054 (tptt) cc_final: 0.6745 (tttp) REVERT: A 331 GLN cc_start: 0.8162 (tt0) cc_final: 0.7944 (tm-30) REVERT: A 368 MET cc_start: 0.5817 (mmt) cc_final: 0.5217 (ttp) REVERT: A 500 VAL cc_start: 0.8009 (t) cc_final: 0.6822 (m) REVERT: A 565 TYR cc_start: 0.5132 (m-80) cc_final: 0.4088 (m-80) REVERT: A 666 TYR cc_start: 0.6537 (t80) cc_final: 0.6082 (t80) REVERT: A 721 ASP cc_start: 0.6941 (t70) cc_final: 0.6638 (t0) REVERT: A 903 ARG cc_start: 0.4549 (mpt90) cc_final: 0.2139 (mmp80) REVERT: A 905 LEU cc_start: 0.5752 (pp) cc_final: 0.5501 (pp) REVERT: A 1090 GLN cc_start: 0.4429 (tp-100) cc_final: 0.4104 (tp40) REVERT: A 1129 LEU cc_start: 0.8523 (mt) cc_final: 0.8034 (mm) REVERT: A 1293 LEU cc_start: 0.8516 (mm) cc_final: 0.8264 (mm) REVERT: A 1496 GLN cc_start: 0.8153 (tm-30) cc_final: 0.7899 (tm-30) REVERT: A 1666 LYS cc_start: 0.8182 (mmtt) cc_final: 0.7021 (mmtt) REVERT: A 1703 MET cc_start: 0.6397 (mmm) cc_final: 0.6058 (mmm) REVERT: A 2128 ILE cc_start: 0.7706 (pt) cc_final: 0.7470 (mp) REVERT: A 2176 MET cc_start: 0.7838 (mtp) cc_final: 0.7602 (ttm) REVERT: A 2276 PRO cc_start: 0.7861 (Cg_exo) cc_final: 0.7460 (Cg_endo) REVERT: A 2299 GLU cc_start: 0.7480 (tp30) cc_final: 0.7043 (tp30) REVERT: A 2315 GLN cc_start: 0.7991 (mm-40) cc_final: 0.7768 (mm-40) REVERT: A 2374 ARG cc_start: 0.7890 (pmt170) cc_final: 0.7177 (pmt170) REVERT: A 2393 ARG cc_start: 0.7199 (ptm-80) cc_final: 0.6879 (mtt90) REVERT: B 268 LEU cc_start: 0.8578 (mt) cc_final: 0.8329 (mt) REVERT: B 445 TYR cc_start: 0.8756 (t80) cc_final: 0.8460 (t80) REVERT: C 269 ASP cc_start: 0.7231 (p0) cc_final: 0.6745 (p0) outliers start: 16 outliers final: 8 residues processed: 631 average time/residue: 0.1635 time to fit residues: 153.3364 Evaluate side-chains 406 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 398 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 613 PHE Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1464 GLN Chi-restraints excluded: chain A residue 1521 VAL Chi-restraints excluded: chain A residue 1816 THR Chi-restraints excluded: chain A residue 1964 GLU Chi-restraints excluded: chain A residue 2279 VAL Chi-restraints excluded: chain B residue 408 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.1980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 5.9990 chunk 258 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS A 171 GLN ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 ASN A 326 HIS ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 ASN ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 ASN ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 881 ASN A 904 ASN A 989 ASN A1090 GLN A1103 ASN ** A1184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1305 ASN ** A1362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1591 HIS ** A1654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1832 HIS A2023 HIS A2050 ASN ** A2189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2206 GLN A2229 GLN A2315 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 GLN B 196 GLN ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 GLN ** B 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 HIS ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 GLN ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 HIS C 484 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.140456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.118885 restraints weight = 55325.162| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 2.54 r_work: 0.3633 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19856 Z= 0.165 Angle : 0.583 12.462 27014 Z= 0.308 Chirality : 0.038 0.148 3267 Planarity : 0.004 0.055 3422 Dihedral : 5.662 97.772 2750 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 63.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.69 % Favored : 89.27 % Rotamer: Outliers : 2.86 % Allowed : 13.12 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 1.66 % 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: -2.97 (0.17), residues: 2526 helix: -0.62 (0.14), residues: 1410 sheet: -4.02 (0.40), residues: 107 loop : -3.78 (0.18), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 8 TYR 0.024 0.001 TYR A1017 PHE 0.019 0.001 PHE A 609 TRP 0.014 0.002 TRP A1106 HIS 0.011 0.001 HIS A2401 Details of bonding type rmsd covalent geometry : bond 0.00351 (19855) covalent geometry : angle 0.58274 (27014) hydrogen bonds : bond 0.03655 ( 891) hydrogen bonds : angle 4.96279 ( 2574) Misc. bond : bond 0.00080 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 5 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue VAL 50 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue LYS 55 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue ALA 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue ALA 140 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue TYR 150 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LEU 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue ALA 165 is missing expected H atoms. Skipping. Residue ALA 185 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue TYR 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue LEU 210 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue LEU 212 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue THR 216 is missing expected H atoms. Skipping. Residue SER 218 is missing expected H atoms. Skipping. Residue ILE 221 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue TYR 223 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LYS 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue LEU 300 is missing expected H atoms. Skipping. Residue ALA 303 is missing expected H atoms. Skipping. Residue LEU 304 is missing expected H atoms. Skipping. Residue ILE 308 is missing expected H atoms. Skipping. Residue TYR 309 is missing expected H atoms. Skipping. Residue ILE 311 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue SER 315 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue ALA 334 is missing expected H atoms. Skipping. Residue VAL 336 is missing expected H atoms. Skipping. Residue TYR 337 is missing expected H atoms. Skipping. Residue ILE 338 is missing expected H atoms. Skipping. Residue VAL 339 is missing expected H atoms. Skipping. Residue THR 409 is missing expected H atoms. Skipping. Residue VAL 418 is missing expected H atoms. Skipping. Residue LEU 420 is missing expected H atoms. Skipping. Residue THR 444 is missing expected H atoms. Skipping. Residue TYR 445 is missing expected H atoms. Skipping. Residue LYS 447 is missing expected H atoms. Skipping. Residue ILE 449 is missing expected H atoms. Skipping. Residue SER 450 is missing expected H atoms. Skipping. Residue ALA 451 is missing expected H atoms. Skipping. Residue SER 453 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue TYR 456 is missing expected H atoms. Skipping. Residue VAL 458 is missing expected H atoms. Skipping. Residue ALA 459 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 493 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue SER 496 is missing expected H atoms. Skipping. Residue LEU 528 is missing expected H atoms. Skipping. Residue ALA 529 is missing expected H atoms. Skipping. Residue ALA 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue VAL 534 is missing expected H atoms. Skipping. Residue TYR 535 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue ALA 539 is missing expected H atoms. Skipping. Residue ALA 543 is missing expected H atoms. Skipping. Residue LYS 546 is missing expected H atoms. Skipping. Residue TYR 547 is missing expected H atoms. Skipping. Residue ALA 548 is missing expected H atoms. Skipping. Residue MET 549 is missing expected H atoms. Skipping. Residue LEU 551 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 181 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 183 is missing expected H atoms. Skipping. Residue VAL 184 is missing expected H atoms. Skipping. Residue MET 188 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue ALA 194 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue TYR 197 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue THR 202 is missing expected H atoms. Skipping. Residue VAL 204 is missing expected H atoms. Skipping. Residue LEU 205 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue VAL 209 is missing expected H atoms. Skipping. Residue LEU 210 is missing expected H atoms. Skipping. Residue LEU 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue MET 221 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue ALA 226 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue ILE 256 is missing expected H atoms. Skipping. Residue ILE 265 is missing expected H atoms. Skipping. Residue VAL 266 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue MET 302 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue ILE 307 is missing expected H atoms. Skipping. Residue ALA 308 is missing expected H atoms. Skipping. Residue ALA 309 is missing expected H atoms. Skipping. Residue LEU 311 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue VAL 318 is missing expected H atoms. Skipping. Residue ILE 319 is missing expected H atoms. Skipping. Residue VAL 320 is missing expected H atoms. Skipping. Residue VAL 321 is missing expected H atoms. Skipping. Residue THR 326 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LEU 330 is missing expected H atoms. Skipping. Residue TYR 331 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 336 is missing expected H atoms. Skipping. Residue ALA 337 is missing expected H atoms. Skipping. Residue MET 339 is missing expected H atoms. Skipping. Residue VAL 340 is missing expected H atoms. Skipping. Residue LYS 341 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue VAL 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue ALA 374 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue LEU 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue LEU 394 is missing expected H atoms. Skipping. Residue MET 395 is missing expected H atoms. Skipping. Residue ALA 396 is missing expected H atoms. Skipping. Residue SER 398 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue SER 424 is missing expected H atoms. Skipping. Residue VAL 426 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue SER 468 is missing expected H atoms. Skipping. Residue LEU 469 is missing expected H atoms. Skipping. Residue VAL 470 is missing expected H atoms. Skipping. Residue SER 471 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue SER 475 is missing expected H atoms. Skipping. Residue VAL 477 is missing expected H atoms. Skipping. Residue MET 478 is missing expected H atoms. Skipping. Residue THR 491 is missing expected H atoms. Skipping. Residue LYS 493 is missing expected H atoms. Skipping. Residue ALA 499 is missing expected H atoms. Skipping. Residue ALA 500 is missing expected H atoms. Skipping. Residue ILE 502 is missing expected H atoms. Skipping. Residue SER 510 is missing expected H atoms. Skipping. Residue ALA 511 is missing expected H atoms. Skipping. Residue ALA 513 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Evaluate side-chains 475 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 417 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 TYR cc_start: 0.7162 (m-80) cc_final: 0.6862 (m-10) REVERT: A 331 GLN cc_start: 0.8431 (tt0) cc_final: 0.8067 (tm-30) REVERT: A 338 GLN cc_start: 0.7286 (pt0) cc_final: 0.6872 (pt0) REVERT: A 342 TRP cc_start: 0.6303 (m100) cc_final: 0.5795 (m100) REVERT: A 368 MET cc_start: 0.6544 (mmt) cc_final: 0.5389 (ttp) REVERT: A 492 CYS cc_start: 0.6804 (p) cc_final: 0.6508 (t) REVERT: A 565 TYR cc_start: 0.6057 (m-80) cc_final: 0.4684 (m-80) REVERT: A 645 ASN cc_start: 0.8097 (m110) cc_final: 0.7821 (m110) REVERT: A 666 TYR cc_start: 0.7720 (t80) cc_final: 0.7369 (t80) REVERT: A 721 ASP cc_start: 0.7997 (t70) cc_final: 0.7729 (t0) REVERT: A 820 LEU cc_start: 0.7639 (mt) cc_final: 0.7428 (mt) REVERT: A 882 TRP cc_start: 0.8105 (t60) cc_final: 0.7483 (t60) REVERT: A 903 ARG cc_start: 0.6123 (mpt90) cc_final: 0.2324 (mpt90) REVERT: A 1017 TYR cc_start: 0.7344 (t80) cc_final: 0.7103 (t80) REVERT: A 1368 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7853 (pp) REVERT: A 1648 ARG cc_start: 0.8566 (ptm160) cc_final: 0.8265 (ptm160) REVERT: A 1666 LYS cc_start: 0.8195 (mmtt) cc_final: 0.7942 (mmtt) REVERT: A 1703 MET cc_start: 0.6499 (mmm) cc_final: 0.6213 (mmm) REVERT: A 2276 PRO cc_start: 0.7723 (Cg_exo) cc_final: 0.7419 (Cg_endo) REVERT: A 2393 ARG cc_start: 0.7813 (ptm-80) cc_final: 0.7036 (mtt180) REVERT: B 445 TYR cc_start: 0.8945 (t80) cc_final: 0.8672 (t80) REVERT: B 490 ASP cc_start: 0.5561 (OUTLIER) cc_final: 0.5236 (p0) REVERT: B 549 MET cc_start: 0.7685 (tmm) cc_final: 0.7337 (tmm) REVERT: B 550 GLN cc_start: 0.7374 (mt0) cc_final: 0.6756 (mt0) REVERT: C 197 TYR cc_start: 0.8608 (m-80) cc_final: 0.8268 (m-80) REVERT: C 269 ASP cc_start: 0.8109 (p0) cc_final: 0.7824 (p0) REVERT: C 405 THR cc_start: 0.7816 (p) cc_final: 0.7559 (p) outliers start: 58 outliers final: 44 residues processed: 452 average time/residue: 0.1529 time to fit residues: 105.9089 Evaluate side-chains 414 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 368 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 613 PHE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain A residue 1081 CYS Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1316 ILE Chi-restraints excluded: chain A residue 1358 SER Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1422 MET Chi-restraints excluded: chain A residue 1521 VAL Chi-restraints excluded: chain A residue 1599 PHE Chi-restraints excluded: chain A residue 1729 VAL Chi-restraints excluded: chain A residue 1858 TYR Chi-restraints excluded: chain A residue 1964 GLU Chi-restraints excluded: chain A residue 2279 VAL Chi-restraints excluded: chain A residue 2320 SER Chi-restraints excluded: chain A residue 2327 VAL Chi-restraints excluded: chain A residue 2337 HIS Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 281 HIS Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 380 CYS Chi-restraints excluded: chain C residue 411 CYS Chi-restraints excluded: chain C residue 417 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 78 optimal weight: 0.2980 chunk 68 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 208 optimal weight: 4.9990 chunk 219 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 231 optimal weight: 3.9990 chunk 122 optimal weight: 0.5980 chunk 140 optimal weight: 6.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 GLN ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 623 ASN ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 ASN ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 989 ASN ** A1184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1413 GLN A2023 HIS ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 GLN C 271 GLN C 322 GLN ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.138032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.116070 restraints weight = 55236.985| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.60 r_work: 0.3573 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 19856 Z= 0.155 Angle : 0.570 12.444 27014 Z= 0.299 Chirality : 0.038 0.190 3267 Planarity : 0.004 0.053 3422 Dihedral : 5.677 99.526 2746 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 63.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.36 % Favored : 88.60 % Rotamer: Outliers : 3.80 % Allowed : 13.91 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 1.66 % 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: -2.55 (0.17), residues: 2526 helix: -0.23 (0.14), residues: 1413 sheet: -3.64 (0.42), residues: 113 loop : -3.71 (0.18), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 420 TYR 0.019 0.001 TYR A1670 PHE 0.017 0.001 PHE A 609 TRP 0.012 0.001 TRP A2301 HIS 0.010 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00331 (19855) covalent geometry : angle 0.56957 (27014) hydrogen bonds : bond 0.03280 ( 891) hydrogen bonds : angle 4.67235 ( 2574) Misc. bond : bond 0.00050 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 5 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue VAL 50 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue LYS 55 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue ALA 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue ALA 140 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue TYR 150 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LEU 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue ALA 165 is missing expected H atoms. Skipping. Residue ALA 185 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue TYR 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue LEU 210 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue LEU 212 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue THR 216 is missing expected H atoms. Skipping. Residue SER 218 is missing expected H atoms. Skipping. Residue ILE 221 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue TYR 223 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LYS 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue LEU 300 is missing expected H atoms. Skipping. Residue ALA 303 is missing expected H atoms. Skipping. Residue LEU 304 is missing expected H atoms. Skipping. Residue ILE 308 is missing expected H atoms. Skipping. Residue TYR 309 is missing expected H atoms. Skipping. Residue ILE 311 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue SER 315 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue ALA 334 is missing expected H atoms. Skipping. Residue VAL 336 is missing expected H atoms. Skipping. Residue TYR 337 is missing expected H atoms. Skipping. Residue ILE 338 is missing expected H atoms. Skipping. Residue VAL 339 is missing expected H atoms. Skipping. Residue THR 409 is missing expected H atoms. Skipping. Residue VAL 418 is missing expected H atoms. Skipping. Residue LEU 420 is missing expected H atoms. Skipping. Residue THR 444 is missing expected H atoms. Skipping. Residue TYR 445 is missing expected H atoms. Skipping. Residue LYS 447 is missing expected H atoms. Skipping. Residue ILE 449 is missing expected H atoms. Skipping. Residue SER 450 is missing expected H atoms. Skipping. Residue ALA 451 is missing expected H atoms. Skipping. Residue SER 453 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue TYR 456 is missing expected H atoms. Skipping. Residue VAL 458 is missing expected H atoms. Skipping. Residue ALA 459 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 493 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue SER 496 is missing expected H atoms. Skipping. Residue LEU 528 is missing expected H atoms. Skipping. Residue ALA 529 is missing expected H atoms. Skipping. Residue ALA 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue VAL 534 is missing expected H atoms. Skipping. Residue TYR 535 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue ALA 539 is missing expected H atoms. Skipping. Residue ALA 543 is missing expected H atoms. Skipping. Residue LYS 546 is missing expected H atoms. Skipping. Residue TYR 547 is missing expected H atoms. Skipping. Residue ALA 548 is missing expected H atoms. Skipping. Residue MET 549 is missing expected H atoms. Skipping. Residue LEU 551 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 181 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 183 is missing expected H atoms. Skipping. Residue VAL 184 is missing expected H atoms. Skipping. Residue MET 188 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue ALA 194 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue TYR 197 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue THR 202 is missing expected H atoms. Skipping. Residue VAL 204 is missing expected H atoms. Skipping. Residue LEU 205 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue VAL 209 is missing expected H atoms. Skipping. Residue LEU 210 is missing expected H atoms. Skipping. Residue LEU 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue MET 221 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue ALA 226 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue ILE 256 is missing expected H atoms. Skipping. Residue ILE 265 is missing expected H atoms. Skipping. Residue VAL 266 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue MET 302 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue ILE 307 is missing expected H atoms. Skipping. Residue ALA 308 is missing expected H atoms. Skipping. Residue ALA 309 is missing expected H atoms. Skipping. Residue LEU 311 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue VAL 318 is missing expected H atoms. Skipping. Residue ILE 319 is missing expected H atoms. Skipping. Residue VAL 320 is missing expected H atoms. Skipping. Residue VAL 321 is missing expected H atoms. Skipping. Residue THR 326 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LEU 330 is missing expected H atoms. Skipping. Residue TYR 331 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 336 is missing expected H atoms. Skipping. Residue ALA 337 is missing expected H atoms. Skipping. Residue MET 339 is missing expected H atoms. Skipping. Residue VAL 340 is missing expected H atoms. Skipping. Residue LYS 341 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue VAL 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue ALA 374 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue LEU 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue LEU 394 is missing expected H atoms. Skipping. Residue MET 395 is missing expected H atoms. Skipping. Residue ALA 396 is missing expected H atoms. Skipping. Residue SER 398 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue SER 424 is missing expected H atoms. Skipping. Residue VAL 426 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue SER 468 is missing expected H atoms. Skipping. Residue LEU 469 is missing expected H atoms. Skipping. Residue VAL 470 is missing expected H atoms. Skipping. Residue SER 471 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue SER 475 is missing expected H atoms. Skipping. Residue VAL 477 is missing expected H atoms. Skipping. Residue MET 478 is missing expected H atoms. Skipping. Residue THR 491 is missing expected H atoms. Skipping. Residue LYS 493 is missing expected H atoms. Skipping. Residue ALA 499 is missing expected H atoms. Skipping. Residue ALA 500 is missing expected H atoms. Skipping. Residue ILE 502 is missing expected H atoms. Skipping. Residue SER 510 is missing expected H atoms. Skipping. Residue ALA 511 is missing expected H atoms. Skipping. Residue ALA 513 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Evaluate side-chains 464 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 387 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 LEU cc_start: 0.3605 (OUTLIER) cc_final: 0.3098 (pt) REVERT: A 252 TYR cc_start: 0.7129 (m-80) cc_final: 0.6810 (m-10) REVERT: A 331 GLN cc_start: 0.8563 (tt0) cc_final: 0.8137 (tm-30) REVERT: A 338 GLN cc_start: 0.7323 (pt0) cc_final: 0.6897 (pt0) REVERT: A 342 TRP cc_start: 0.6417 (m100) cc_final: 0.5946 (m100) REVERT: A 368 MET cc_start: 0.6823 (mmt) cc_final: 0.5491 (ttp) REVERT: A 645 ASN cc_start: 0.8195 (m110) cc_final: 0.7963 (m110) REVERT: A 666 TYR cc_start: 0.7749 (t80) cc_final: 0.7354 (t80) REVERT: A 716 ILE cc_start: 0.9139 (mm) cc_final: 0.8877 (mt) REVERT: A 721 ASP cc_start: 0.8078 (t70) cc_final: 0.7835 (t0) REVERT: A 882 TRP cc_start: 0.8182 (t60) cc_final: 0.7555 (t60) REVERT: A 903 ARG cc_start: 0.6750 (mpt90) cc_final: 0.3764 (mpt90) REVERT: A 1017 TYR cc_start: 0.7547 (t80) cc_final: 0.7319 (t80) REVERT: A 1126 GLN cc_start: 0.7614 (tp-100) cc_final: 0.7305 (tp-100) REVERT: A 1648 ARG cc_start: 0.8610 (ptm160) cc_final: 0.8277 (ptm160) REVERT: A 1666 LYS cc_start: 0.8352 (mmtt) cc_final: 0.8058 (mmtt) REVERT: A 1703 MET cc_start: 0.6399 (mmm) cc_final: 0.6153 (mmm) REVERT: A 1708 TRP cc_start: 0.7478 (m100) cc_final: 0.6917 (m100) REVERT: A 2276 PRO cc_start: 0.7749 (Cg_exo) cc_final: 0.7518 (Cg_endo) REVERT: A 2393 ARG cc_start: 0.7808 (ptm-80) cc_final: 0.6905 (mtt180) REVERT: B 190 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8747 (mtpt) REVERT: C 197 TYR cc_start: 0.8647 (m-80) cc_final: 0.8336 (m-80) REVERT: C 269 ASP cc_start: 0.8276 (p0) cc_final: 0.8051 (p0) outliers start: 77 outliers final: 54 residues processed: 426 average time/residue: 0.1555 time to fit residues: 102.4168 Evaluate side-chains 423 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 367 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 613 PHE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1316 ILE Chi-restraints excluded: chain A residue 1358 SER Chi-restraints excluded: chain A residue 1397 LEU Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1423 GLU Chi-restraints excluded: chain A residue 1521 VAL Chi-restraints excluded: chain A residue 1599 PHE Chi-restraints excluded: chain A residue 1729 VAL Chi-restraints excluded: chain A residue 1785 ILE Chi-restraints excluded: chain A residue 1858 TYR Chi-restraints excluded: chain A residue 1964 GLU Chi-restraints excluded: chain A residue 2128 ILE Chi-restraints excluded: chain A residue 2279 VAL Chi-restraints excluded: chain A residue 2299 GLU Chi-restraints excluded: chain A residue 2327 VAL Chi-restraints excluded: chain A residue 2337 HIS Chi-restraints excluded: chain A residue 2367 VAL Chi-restraints excluded: chain A residue 2381 THR Chi-restraints excluded: chain A residue 2386 THR Chi-restraints excluded: chain A residue 2403 MET Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 258 CYS Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 380 CYS Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 411 CYS Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 487 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 188 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 213 optimal weight: 4.9990 chunk 106 optimal weight: 0.0470 chunk 113 optimal weight: 1.9990 chunk 185 optimal weight: 3.9990 chunk 204 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 160 optimal weight: 8.9990 overall best weight: 1.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 ASN ** A 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1496 GLN A2023 HIS ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.133272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.111673 restraints weight = 55022.649| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.42 r_work: 0.3496 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 19856 Z= 0.210 Angle : 0.636 12.929 27014 Z= 0.336 Chirality : 0.040 0.192 3267 Planarity : 0.005 0.056 3422 Dihedral : 6.209 98.589 2744 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 66.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 13.46 % Favored : 86.50 % Rotamer: Outliers : 4.49 % Allowed : 15.04 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 1.66 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.45 (0.17), residues: 2526 helix: -0.15 (0.14), residues: 1415 sheet: -3.54 (0.43), residues: 113 loop : -3.67 (0.18), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 420 TYR 0.033 0.002 TYR A1670 PHE 0.020 0.002 PHE A 609 TRP 0.015 0.001 TRP A2301 HIS 0.007 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00451 (19855) covalent geometry : angle 0.63596 (27014) hydrogen bonds : bond 0.03461 ( 891) hydrogen bonds : angle 4.78473 ( 2574) Misc. bond : bond 0.00019 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 5 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue VAL 50 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue LYS 55 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue ALA 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue ALA 140 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue TYR 150 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LEU 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue ALA 165 is missing expected H atoms. Skipping. Residue ALA 185 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue TYR 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue LEU 210 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue LEU 212 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue THR 216 is missing expected H atoms. Skipping. Residue SER 218 is missing expected H atoms. Skipping. Residue ILE 221 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue TYR 223 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LYS 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue LEU 300 is missing expected H atoms. Skipping. Residue ALA 303 is missing expected H atoms. Skipping. Residue LEU 304 is missing expected H atoms. Skipping. Residue ILE 308 is missing expected H atoms. Skipping. Residue TYR 309 is missing expected H atoms. Skipping. Residue ILE 311 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue SER 315 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue ALA 334 is missing expected H atoms. Skipping. Residue VAL 336 is missing expected H atoms. Skipping. Residue TYR 337 is missing expected H atoms. Skipping. Residue ILE 338 is missing expected H atoms. Skipping. Residue VAL 339 is missing expected H atoms. Skipping. Residue THR 409 is missing expected H atoms. Skipping. Residue VAL 418 is missing expected H atoms. Skipping. Residue LEU 420 is missing expected H atoms. Skipping. Residue THR 444 is missing expected H atoms. Skipping. Residue TYR 445 is missing expected H atoms. Skipping. Residue LYS 447 is missing expected H atoms. Skipping. Residue ILE 449 is missing expected H atoms. Skipping. Residue SER 450 is missing expected H atoms. Skipping. Residue ALA 451 is missing expected H atoms. Skipping. Residue SER 453 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue TYR 456 is missing expected H atoms. Skipping. Residue VAL 458 is missing expected H atoms. Skipping. Residue ALA 459 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 493 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue SER 496 is missing expected H atoms. Skipping. Residue LEU 528 is missing expected H atoms. Skipping. Residue ALA 529 is missing expected H atoms. Skipping. Residue ALA 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue VAL 534 is missing expected H atoms. Skipping. Residue TYR 535 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue ALA 539 is missing expected H atoms. Skipping. Residue ALA 543 is missing expected H atoms. Skipping. Residue LYS 546 is missing expected H atoms. Skipping. Residue TYR 547 is missing expected H atoms. Skipping. Residue ALA 548 is missing expected H atoms. Skipping. Residue MET 549 is missing expected H atoms. Skipping. Residue LEU 551 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 181 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 183 is missing expected H atoms. Skipping. Residue VAL 184 is missing expected H atoms. Skipping. Residue MET 188 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue ALA 194 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue TYR 197 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue THR 202 is missing expected H atoms. Skipping. Residue VAL 204 is missing expected H atoms. Skipping. Residue LEU 205 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue VAL 209 is missing expected H atoms. Skipping. Residue LEU 210 is missing expected H atoms. Skipping. Residue LEU 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue MET 221 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue ALA 226 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue ILE 256 is missing expected H atoms. Skipping. Residue ILE 265 is missing expected H atoms. Skipping. Residue VAL 266 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue MET 302 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue ILE 307 is missing expected H atoms. Skipping. Residue ALA 308 is missing expected H atoms. Skipping. Residue ALA 309 is missing expected H atoms. Skipping. Residue LEU 311 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue VAL 318 is missing expected H atoms. Skipping. Residue ILE 319 is missing expected H atoms. Skipping. Residue VAL 320 is missing expected H atoms. Skipping. Residue VAL 321 is missing expected H atoms. Skipping. Residue THR 326 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LEU 330 is missing expected H atoms. Skipping. Residue TYR 331 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 336 is missing expected H atoms. Skipping. Residue ALA 337 is missing expected H atoms. Skipping. Residue MET 339 is missing expected H atoms. Skipping. Residue VAL 340 is missing expected H atoms. Skipping. Residue LYS 341 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue VAL 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue ALA 374 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue LEU 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue LEU 394 is missing expected H atoms. Skipping. Residue MET 395 is missing expected H atoms. Skipping. Residue ALA 396 is missing expected H atoms. Skipping. Residue SER 398 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue SER 424 is missing expected H atoms. Skipping. Residue VAL 426 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue SER 468 is missing expected H atoms. Skipping. Residue LEU 469 is missing expected H atoms. Skipping. Residue VAL 470 is missing expected H atoms. Skipping. Residue SER 471 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue SER 475 is missing expected H atoms. Skipping. Residue VAL 477 is missing expected H atoms. Skipping. Residue MET 478 is missing expected H atoms. Skipping. Residue THR 491 is missing expected H atoms. Skipping. Residue LYS 493 is missing expected H atoms. Skipping. Residue ALA 499 is missing expected H atoms. Skipping. Residue ALA 500 is missing expected H atoms. Skipping. Residue ILE 502 is missing expected H atoms. Skipping. Residue SER 510 is missing expected H atoms. Skipping. Residue ALA 511 is missing expected H atoms. Skipping. Residue ALA 513 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Evaluate side-chains 467 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 376 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 GLU cc_start: 0.3356 (tp30) cc_final: 0.1268 (tm-30) REVERT: A 149 LEU cc_start: 0.3452 (OUTLIER) cc_final: 0.2468 (pt) REVERT: A 252 TYR cc_start: 0.7057 (m-80) cc_final: 0.6764 (m-10) REVERT: A 331 GLN cc_start: 0.8608 (tt0) cc_final: 0.8129 (tm-30) REVERT: A 342 TRP cc_start: 0.6584 (m100) cc_final: 0.6163 (m100) REVERT: A 368 MET cc_start: 0.7238 (mmt) cc_final: 0.5762 (ttp) REVERT: A 426 GLU cc_start: 0.6079 (pt0) cc_final: 0.5612 (pt0) REVERT: A 557 ASN cc_start: 0.8302 (OUTLIER) cc_final: 0.8015 (t160) REVERT: A 645 ASN cc_start: 0.8233 (m110) cc_final: 0.7960 (m110) REVERT: A 666 TYR cc_start: 0.7819 (t80) cc_final: 0.7441 (t80) REVERT: A 721 ASP cc_start: 0.8060 (t70) cc_final: 0.7852 (t0) REVERT: A 894 ASP cc_start: 0.7724 (t0) cc_final: 0.7471 (t0) REVERT: A 903 ARG cc_start: 0.7555 (mpt90) cc_final: 0.4587 (mpt90) REVERT: A 922 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8318 (pp30) REVERT: A 1017 TYR cc_start: 0.7640 (t80) cc_final: 0.7349 (t80) REVERT: A 1126 GLN cc_start: 0.7765 (tp-100) cc_final: 0.7489 (tp-100) REVERT: A 1703 MET cc_start: 0.6338 (mmm) cc_final: 0.5863 (mmm) REVERT: A 1708 TRP cc_start: 0.7494 (m100) cc_final: 0.6858 (m100) REVERT: A 1842 CYS cc_start: 0.8295 (p) cc_final: 0.7768 (m) REVERT: A 1929 CYS cc_start: 0.7599 (m) cc_final: 0.7112 (t) REVERT: A 2326 MET cc_start: 0.8905 (mmp) cc_final: 0.8473 (mmp) REVERT: A 2393 ARG cc_start: 0.7854 (ptm-80) cc_final: 0.6840 (mtt180) REVERT: B 190 LYS cc_start: 0.9183 (OUTLIER) cc_final: 0.8733 (ttpp) REVERT: B 506 MET cc_start: 0.8039 (ttp) cc_final: 0.7827 (ptt) REVERT: B 550 GLN cc_start: 0.7459 (mt0) cc_final: 0.7124 (mt0) REVERT: C 421 PHE cc_start: 0.8108 (p90) cc_final: 0.7736 (p90) outliers start: 91 outliers final: 62 residues processed: 434 average time/residue: 0.1483 time to fit residues: 99.7668 Evaluate side-chains 430 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 364 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 325 TRP Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 557 ASN Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 833 ASN Chi-restraints excluded: chain A residue 922 GLN Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1012 ILE Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1309 GLN Chi-restraints excluded: chain A residue 1316 ILE Chi-restraints excluded: chain A residue 1358 SER Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1423 GLU Chi-restraints excluded: chain A residue 1521 VAL Chi-restraints excluded: chain A residue 1599 PHE Chi-restraints excluded: chain A residue 1712 ILE Chi-restraints excluded: chain A residue 1729 VAL Chi-restraints excluded: chain A residue 1816 THR Chi-restraints excluded: chain A residue 1858 TYR Chi-restraints excluded: chain A residue 1964 GLU Chi-restraints excluded: chain A residue 2128 ILE Chi-restraints excluded: chain A residue 2180 ILE Chi-restraints excluded: chain A residue 2193 TYR Chi-restraints excluded: chain A residue 2279 VAL Chi-restraints excluded: chain A residue 2320 SER Chi-restraints excluded: chain A residue 2337 HIS Chi-restraints excluded: chain A residue 2367 VAL Chi-restraints excluded: chain A residue 2381 THR Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 380 CYS Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 411 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 205 optimal weight: 1.9990 chunk 82 optimal weight: 0.0870 chunk 21 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 252 optimal weight: 0.6980 chunk 150 optimal weight: 10.0000 chunk 99 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 212 optimal weight: 3.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 326 HIS ** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 600 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 ASN A 858 HIS ** A 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1362 ASN ** A1405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1496 GLN A1636 ASN A2023 HIS ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 GLN ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 ASN B 307 GLN ** B 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.135811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.114121 restraints weight = 54876.069| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.37 r_work: 0.3549 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 19856 Z= 0.113 Angle : 0.546 12.489 27014 Z= 0.288 Chirality : 0.037 0.211 3267 Planarity : 0.004 0.055 3422 Dihedral : 5.982 101.863 2742 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 65.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.72 % Favored : 88.24 % Rotamer: Outliers : 3.06 % Allowed : 16.91 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 1.66 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.03 (0.17), residues: 2526 helix: 0.21 (0.14), residues: 1425 sheet: -3.38 (0.45), residues: 113 loop : -3.55 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 8 TYR 0.041 0.001 TYR A1670 PHE 0.017 0.001 PHE A 609 TRP 0.012 0.001 TRP A 350 HIS 0.006 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00248 (19855) covalent geometry : angle 0.54559 (27014) hydrogen bonds : bond 0.02828 ( 891) hydrogen bonds : angle 4.44074 ( 2574) Misc. bond : bond 0.00026 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 5 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue VAL 50 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue LYS 55 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue ALA 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue ALA 140 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue TYR 150 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LEU 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue ALA 165 is missing expected H atoms. Skipping. Residue ALA 185 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue TYR 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue LEU 210 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue LEU 212 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue THR 216 is missing expected H atoms. Skipping. Residue SER 218 is missing expected H atoms. Skipping. Residue ILE 221 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue TYR 223 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LYS 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue LEU 300 is missing expected H atoms. Skipping. Residue ALA 303 is missing expected H atoms. Skipping. Residue LEU 304 is missing expected H atoms. Skipping. Residue ILE 308 is missing expected H atoms. Skipping. Residue TYR 309 is missing expected H atoms. Skipping. Residue ILE 311 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue SER 315 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue ALA 334 is missing expected H atoms. Skipping. Residue VAL 336 is missing expected H atoms. Skipping. Residue TYR 337 is missing expected H atoms. Skipping. Residue ILE 338 is missing expected H atoms. Skipping. Residue VAL 339 is missing expected H atoms. Skipping. Residue THR 409 is missing expected H atoms. Skipping. Residue VAL 418 is missing expected H atoms. Skipping. Residue LEU 420 is missing expected H atoms. Skipping. Residue THR 444 is missing expected H atoms. Skipping. Residue TYR 445 is missing expected H atoms. Skipping. Residue LYS 447 is missing expected H atoms. Skipping. Residue ILE 449 is missing expected H atoms. Skipping. Residue SER 450 is missing expected H atoms. Skipping. Residue ALA 451 is missing expected H atoms. Skipping. Residue SER 453 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue TYR 456 is missing expected H atoms. Skipping. Residue VAL 458 is missing expected H atoms. Skipping. Residue ALA 459 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 493 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue SER 496 is missing expected H atoms. Skipping. Residue LEU 528 is missing expected H atoms. Skipping. Residue ALA 529 is missing expected H atoms. Skipping. Residue ALA 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue VAL 534 is missing expected H atoms. Skipping. Residue TYR 535 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue ALA 539 is missing expected H atoms. Skipping. Residue ALA 543 is missing expected H atoms. Skipping. Residue LYS 546 is missing expected H atoms. Skipping. Residue TYR 547 is missing expected H atoms. Skipping. Residue ALA 548 is missing expected H atoms. Skipping. Residue MET 549 is missing expected H atoms. Skipping. Residue LEU 551 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 181 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 183 is missing expected H atoms. Skipping. Residue VAL 184 is missing expected H atoms. Skipping. Residue MET 188 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue ALA 194 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue TYR 197 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue THR 202 is missing expected H atoms. Skipping. Residue VAL 204 is missing expected H atoms. Skipping. Residue LEU 205 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue VAL 209 is missing expected H atoms. Skipping. Residue LEU 210 is missing expected H atoms. Skipping. Residue LEU 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue MET 221 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue ALA 226 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue ILE 256 is missing expected H atoms. Skipping. Residue ILE 265 is missing expected H atoms. Skipping. Residue VAL 266 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue MET 302 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue ILE 307 is missing expected H atoms. Skipping. Residue ALA 308 is missing expected H atoms. Skipping. Residue ALA 309 is missing expected H atoms. Skipping. Residue LEU 311 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue VAL 318 is missing expected H atoms. Skipping. Residue ILE 319 is missing expected H atoms. Skipping. Residue VAL 320 is missing expected H atoms. Skipping. Residue VAL 321 is missing expected H atoms. Skipping. Residue THR 326 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LEU 330 is missing expected H atoms. Skipping. Residue TYR 331 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 336 is missing expected H atoms. Skipping. Residue ALA 337 is missing expected H atoms. Skipping. Residue MET 339 is missing expected H atoms. Skipping. Residue VAL 340 is missing expected H atoms. Skipping. Residue LYS 341 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue VAL 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue ALA 374 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue LEU 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue LEU 394 is missing expected H atoms. Skipping. Residue MET 395 is missing expected H atoms. Skipping. Residue ALA 396 is missing expected H atoms. Skipping. Residue SER 398 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue SER 424 is missing expected H atoms. Skipping. Residue VAL 426 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue SER 468 is missing expected H atoms. Skipping. Residue LEU 469 is missing expected H atoms. Skipping. Residue VAL 470 is missing expected H atoms. Skipping. Residue SER 471 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue SER 475 is missing expected H atoms. Skipping. Residue VAL 477 is missing expected H atoms. Skipping. Residue MET 478 is missing expected H atoms. Skipping. Residue THR 491 is missing expected H atoms. Skipping. Residue LYS 493 is missing expected H atoms. Skipping. Residue ALA 499 is missing expected H atoms. Skipping. Residue ALA 500 is missing expected H atoms. Skipping. Residue ILE 502 is missing expected H atoms. Skipping. Residue SER 510 is missing expected H atoms. Skipping. Residue ALA 511 is missing expected H atoms. Skipping. Residue ALA 513 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Evaluate side-chains 442 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 380 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 GLU cc_start: 0.3240 (tp30) cc_final: 0.1372 (tm-30) REVERT: A 149 LEU cc_start: 0.3015 (OUTLIER) cc_final: 0.2164 (pt) REVERT: A 233 PHE cc_start: 0.7498 (m-10) cc_final: 0.7212 (m-10) REVERT: A 252 TYR cc_start: 0.6983 (m-80) cc_final: 0.6663 (m-10) REVERT: A 267 LYS cc_start: 0.7532 (tptt) cc_final: 0.6451 (tptt) REVERT: A 342 TRP cc_start: 0.6450 (m100) cc_final: 0.6118 (m100) REVERT: A 368 MET cc_start: 0.7106 (mmt) cc_final: 0.5712 (ttp) REVERT: A 426 GLU cc_start: 0.5863 (pt0) cc_final: 0.5132 (pt0) REVERT: A 645 ASN cc_start: 0.8180 (m110) cc_final: 0.7914 (m110) REVERT: A 666 TYR cc_start: 0.7755 (t80) cc_final: 0.7371 (t80) REVERT: A 721 ASP cc_start: 0.8022 (t70) cc_final: 0.7793 (t0) REVERT: A 903 ARG cc_start: 0.7368 (mpt90) cc_final: 0.3912 (tpp-160) REVERT: A 919 GLU cc_start: 0.7190 (tm-30) cc_final: 0.6943 (tm-30) REVERT: A 1017 TYR cc_start: 0.7605 (t80) cc_final: 0.7372 (t80) REVERT: A 1126 GLN cc_start: 0.7625 (tp-100) cc_final: 0.7313 (tp-100) REVERT: A 1208 ASN cc_start: 0.6725 (t0) cc_final: 0.6255 (t0) REVERT: A 1703 MET cc_start: 0.6380 (mmm) cc_final: 0.6150 (mmm) REVERT: A 1708 TRP cc_start: 0.7452 (m100) cc_final: 0.6803 (m100) REVERT: A 2326 MET cc_start: 0.8837 (mmp) cc_final: 0.8399 (mmp) REVERT: A 2393 ARG cc_start: 0.7653 (ptm-80) cc_final: 0.6651 (mtt90) REVERT: B 190 LYS cc_start: 0.9138 (OUTLIER) cc_final: 0.8713 (ttpp) REVERT: B 550 GLN cc_start: 0.7144 (mt0) cc_final: 0.6752 (mt0) REVERT: C 421 PHE cc_start: 0.7840 (p90) cc_final: 0.7475 (p90) outliers start: 62 outliers final: 54 residues processed: 418 average time/residue: 0.1487 time to fit residues: 96.5839 Evaluate side-chains 423 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 367 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 613 PHE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 867 SER Chi-restraints excluded: chain A residue 985 GLN Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1085 CYS Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1285 LEU Chi-restraints excluded: chain A residue 1316 ILE Chi-restraints excluded: chain A residue 1358 SER Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1423 GLU Chi-restraints excluded: chain A residue 1521 VAL Chi-restraints excluded: chain A residue 1590 VAL Chi-restraints excluded: chain A residue 1599 PHE Chi-restraints excluded: chain A residue 1790 LEU Chi-restraints excluded: chain A residue 1816 THR Chi-restraints excluded: chain A residue 1858 TYR Chi-restraints excluded: chain A residue 1964 GLU Chi-restraints excluded: chain A residue 2128 ILE Chi-restraints excluded: chain A residue 2176 MET Chi-restraints excluded: chain A residue 2180 ILE Chi-restraints excluded: chain A residue 2279 VAL Chi-restraints excluded: chain A residue 2320 SER Chi-restraints excluded: chain A residue 2337 HIS Chi-restraints excluded: chain A residue 2367 VAL Chi-restraints excluded: chain A residue 2381 THR Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 258 CYS Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 380 CYS Chi-restraints excluded: chain C residue 411 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 133 optimal weight: 3.9990 chunk 231 optimal weight: 3.9990 chunk 225 optimal weight: 4.9990 chunk 141 optimal weight: 6.9990 chunk 104 optimal weight: 0.4980 chunk 183 optimal weight: 2.9990 chunk 160 optimal weight: 7.9990 chunk 229 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 233 optimal weight: 0.7980 chunk 8 optimal weight: 7.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 600 HIS ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1472 GLN A1496 GLN A1636 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 GLN ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.133757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.111842 restraints weight = 54932.477| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.55 r_work: 0.3502 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19856 Z= 0.168 Angle : 0.582 12.613 27014 Z= 0.307 Chirality : 0.038 0.189 3267 Planarity : 0.004 0.058 3422 Dihedral : 6.070 98.920 2742 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 65.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.22 % Favored : 86.70 % Rotamer: Outliers : 3.99 % Allowed : 16.42 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 1.66 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.99 (0.17), residues: 2526 helix: 0.25 (0.14), residues: 1431 sheet: -3.29 (0.46), residues: 113 loop : -3.57 (0.19), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2224 TYR 0.037 0.001 TYR A1670 PHE 0.018 0.001 PHE A 609 TRP 0.022 0.001 TRP A1106 HIS 0.007 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00365 (19855) covalent geometry : angle 0.58180 (27014) hydrogen bonds : bond 0.02986 ( 891) hydrogen bonds : angle 4.49707 ( 2574) Misc. bond : bond 0.00023 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 5 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue VAL 50 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue LYS 55 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue ALA 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue ALA 140 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue TYR 150 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LEU 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue ALA 165 is missing expected H atoms. Skipping. Residue ALA 185 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue TYR 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue LEU 210 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue LEU 212 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue THR 216 is missing expected H atoms. Skipping. Residue SER 218 is missing expected H atoms. Skipping. Residue ILE 221 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue TYR 223 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LYS 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue LEU 300 is missing expected H atoms. Skipping. Residue ALA 303 is missing expected H atoms. Skipping. Residue LEU 304 is missing expected H atoms. Skipping. Residue ILE 308 is missing expected H atoms. Skipping. Residue TYR 309 is missing expected H atoms. Skipping. Residue ILE 311 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue SER 315 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue ALA 334 is missing expected H atoms. Skipping. Residue VAL 336 is missing expected H atoms. Skipping. Residue TYR 337 is missing expected H atoms. Skipping. Residue ILE 338 is missing expected H atoms. Skipping. Residue VAL 339 is missing expected H atoms. Skipping. Residue THR 409 is missing expected H atoms. Skipping. Residue VAL 418 is missing expected H atoms. Skipping. Residue LEU 420 is missing expected H atoms. Skipping. Residue THR 444 is missing expected H atoms. Skipping. Residue TYR 445 is missing expected H atoms. Skipping. Residue LYS 447 is missing expected H atoms. Skipping. Residue ILE 449 is missing expected H atoms. Skipping. Residue SER 450 is missing expected H atoms. Skipping. Residue ALA 451 is missing expected H atoms. Skipping. Residue SER 453 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue TYR 456 is missing expected H atoms. Skipping. Residue VAL 458 is missing expected H atoms. Skipping. Residue ALA 459 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 493 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue SER 496 is missing expected H atoms. Skipping. Residue LEU 528 is missing expected H atoms. Skipping. Residue ALA 529 is missing expected H atoms. Skipping. Residue ALA 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue VAL 534 is missing expected H atoms. Skipping. Residue TYR 535 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue ALA 539 is missing expected H atoms. Skipping. Residue ALA 543 is missing expected H atoms. Skipping. Residue LYS 546 is missing expected H atoms. Skipping. Residue TYR 547 is missing expected H atoms. Skipping. Residue ALA 548 is missing expected H atoms. Skipping. Residue MET 549 is missing expected H atoms. Skipping. Residue LEU 551 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 181 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 183 is missing expected H atoms. Skipping. Residue VAL 184 is missing expected H atoms. Skipping. Residue MET 188 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue ALA 194 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue TYR 197 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue THR 202 is missing expected H atoms. Skipping. Residue VAL 204 is missing expected H atoms. Skipping. Residue LEU 205 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue VAL 209 is missing expected H atoms. Skipping. Residue LEU 210 is missing expected H atoms. Skipping. Residue LEU 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue MET 221 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue ALA 226 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue ILE 256 is missing expected H atoms. Skipping. Residue ILE 265 is missing expected H atoms. Skipping. Residue VAL 266 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue MET 302 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue ILE 307 is missing expected H atoms. Skipping. Residue ALA 308 is missing expected H atoms. Skipping. Residue ALA 309 is missing expected H atoms. Skipping. Residue LEU 311 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue VAL 318 is missing expected H atoms. Skipping. Residue ILE 319 is missing expected H atoms. Skipping. Residue VAL 320 is missing expected H atoms. Skipping. Residue VAL 321 is missing expected H atoms. Skipping. Residue THR 326 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LEU 330 is missing expected H atoms. Skipping. Residue TYR 331 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 336 is missing expected H atoms. Skipping. Residue ALA 337 is missing expected H atoms. Skipping. Residue MET 339 is missing expected H atoms. Skipping. Residue VAL 340 is missing expected H atoms. Skipping. Residue LYS 341 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue VAL 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue ALA 374 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue LEU 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue LEU 394 is missing expected H atoms. Skipping. Residue MET 395 is missing expected H atoms. Skipping. Residue ALA 396 is missing expected H atoms. Skipping. Residue SER 398 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue SER 424 is missing expected H atoms. Skipping. Residue VAL 426 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue SER 468 is missing expected H atoms. Skipping. Residue LEU 469 is missing expected H atoms. Skipping. Residue VAL 470 is missing expected H atoms. Skipping. Residue SER 471 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue SER 475 is missing expected H atoms. Skipping. Residue VAL 477 is missing expected H atoms. Skipping. Residue MET 478 is missing expected H atoms. Skipping. Residue THR 491 is missing expected H atoms. Skipping. Residue LYS 493 is missing expected H atoms. Skipping. Residue ALA 499 is missing expected H atoms. Skipping. Residue ALA 500 is missing expected H atoms. Skipping. Residue ILE 502 is missing expected H atoms. Skipping. Residue SER 510 is missing expected H atoms. Skipping. Residue ALA 511 is missing expected H atoms. Skipping. Residue ALA 513 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Evaluate side-chains 450 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 369 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 GLU cc_start: 0.3314 (tp30) cc_final: 0.1508 (tm-30) REVERT: A 149 LEU cc_start: 0.3165 (OUTLIER) cc_final: 0.2094 (pt) REVERT: A 252 TYR cc_start: 0.7024 (m-80) cc_final: 0.6687 (m-10) REVERT: A 267 LYS cc_start: 0.7494 (tptt) cc_final: 0.6438 (tptt) REVERT: A 342 TRP cc_start: 0.6640 (m100) cc_final: 0.6264 (m100) REVERT: A 368 MET cc_start: 0.7298 (mmt) cc_final: 0.5764 (ttp) REVERT: A 645 ASN cc_start: 0.8201 (m110) cc_final: 0.7930 (m110) REVERT: A 666 TYR cc_start: 0.7746 (t80) cc_final: 0.7345 (t80) REVERT: A 716 ILE cc_start: 0.9049 (mm) cc_final: 0.8610 (mp) REVERT: A 721 ASP cc_start: 0.8082 (t70) cc_final: 0.7873 (t0) REVERT: A 903 ARG cc_start: 0.7607 (mpt90) cc_final: 0.4223 (tpp-160) REVERT: A 1017 TYR cc_start: 0.7621 (t80) cc_final: 0.7413 (t80) REVERT: A 1126 GLN cc_start: 0.7686 (tp-100) cc_final: 0.7405 (tp-100) REVERT: A 1194 TYR cc_start: 0.5553 (t80) cc_final: 0.5036 (t80) REVERT: A 1326 GLN cc_start: 0.8407 (tt0) cc_final: 0.8187 (tt0) REVERT: A 1703 MET cc_start: 0.6467 (mmm) cc_final: 0.6227 (mmm) REVERT: A 1708 TRP cc_start: 0.7461 (m100) cc_final: 0.6827 (m100) REVERT: A 1842 CYS cc_start: 0.8203 (p) cc_final: 0.7734 (m) REVERT: A 2326 MET cc_start: 0.8800 (mmp) cc_final: 0.8379 (mmp) REVERT: A 2393 ARG cc_start: 0.7773 (ptm-80) cc_final: 0.6850 (mtt180) REVERT: B 190 LYS cc_start: 0.9165 (OUTLIER) cc_final: 0.8742 (ttpp) REVERT: B 506 MET cc_start: 0.8044 (ttp) cc_final: 0.7680 (ptt) REVERT: C 421 PHE cc_start: 0.7982 (p90) cc_final: 0.7617 (p90) outliers start: 81 outliers final: 64 residues processed: 420 average time/residue: 0.1503 time to fit residues: 97.9374 Evaluate side-chains 422 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 356 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 613 PHE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 833 ASN Chi-restraints excluded: chain A residue 867 SER Chi-restraints excluded: chain A residue 942 THR Chi-restraints excluded: chain A residue 985 GLN Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1285 LEU Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1309 GLN Chi-restraints excluded: chain A residue 1316 ILE Chi-restraints excluded: chain A residue 1358 SER Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1423 GLU Chi-restraints excluded: chain A residue 1521 VAL Chi-restraints excluded: chain A residue 1590 VAL Chi-restraints excluded: chain A residue 1599 PHE Chi-restraints excluded: chain A residue 1785 ILE Chi-restraints excluded: chain A residue 1816 THR Chi-restraints excluded: chain A residue 1856 ILE Chi-restraints excluded: chain A residue 1858 TYR Chi-restraints excluded: chain A residue 1964 GLU Chi-restraints excluded: chain A residue 2128 ILE Chi-restraints excluded: chain A residue 2180 ILE Chi-restraints excluded: chain A residue 2204 LEU Chi-restraints excluded: chain A residue 2279 VAL Chi-restraints excluded: chain A residue 2337 HIS Chi-restraints excluded: chain A residue 2367 VAL Chi-restraints excluded: chain A residue 2381 THR Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 258 CYS Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 380 CYS Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 411 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 158 optimal weight: 2.9990 chunk 74 optimal weight: 0.0970 chunk 32 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 168 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 chunk 112 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 169 optimal weight: 0.0770 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1496 GLN A1636 ASN B 61 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.136251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.114555 restraints weight = 55350.019| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.59 r_work: 0.3546 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 19856 Z= 0.097 Angle : 0.545 16.431 27014 Z= 0.284 Chirality : 0.037 0.188 3267 Planarity : 0.004 0.053 3422 Dihedral : 5.912 100.636 2742 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 63.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.20 % Favored : 88.76 % Rotamer: Outliers : 3.06 % Allowed : 17.55 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 1.66 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.71 (0.18), residues: 2526 helix: 0.45 (0.15), residues: 1449 sheet: -3.21 (0.45), residues: 116 loop : -3.47 (0.19), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 8 TYR 0.042 0.001 TYR A1670 PHE 0.015 0.001 PHE A 609 TRP 0.018 0.001 TRP A1106 HIS 0.004 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00212 (19855) covalent geometry : angle 0.54473 (27014) hydrogen bonds : bond 0.02613 ( 891) hydrogen bonds : angle 4.25065 ( 2574) Misc. bond : bond 0.00035 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 5 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue VAL 50 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue LYS 55 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue ALA 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue ALA 140 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue TYR 150 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LEU 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue ALA 165 is missing expected H atoms. Skipping. Residue ALA 185 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue TYR 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue LEU 210 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue LEU 212 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue THR 216 is missing expected H atoms. Skipping. Residue SER 218 is missing expected H atoms. Skipping. Residue ILE 221 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue TYR 223 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LYS 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue LEU 300 is missing expected H atoms. Skipping. Residue ALA 303 is missing expected H atoms. Skipping. Residue LEU 304 is missing expected H atoms. Skipping. Residue ILE 308 is missing expected H atoms. Skipping. Residue TYR 309 is missing expected H atoms. Skipping. Residue ILE 311 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue SER 315 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue ALA 334 is missing expected H atoms. Skipping. Residue VAL 336 is missing expected H atoms. Skipping. Residue TYR 337 is missing expected H atoms. Skipping. Residue ILE 338 is missing expected H atoms. Skipping. Residue VAL 339 is missing expected H atoms. Skipping. Residue THR 409 is missing expected H atoms. Skipping. Residue VAL 418 is missing expected H atoms. Skipping. Residue LEU 420 is missing expected H atoms. Skipping. Residue THR 444 is missing expected H atoms. Skipping. Residue TYR 445 is missing expected H atoms. Skipping. Residue LYS 447 is missing expected H atoms. Skipping. Residue ILE 449 is missing expected H atoms. Skipping. Residue SER 450 is missing expected H atoms. Skipping. Residue ALA 451 is missing expected H atoms. Skipping. Residue SER 453 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue TYR 456 is missing expected H atoms. Skipping. Residue VAL 458 is missing expected H atoms. Skipping. Residue ALA 459 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 493 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue SER 496 is missing expected H atoms. Skipping. Residue LEU 528 is missing expected H atoms. Skipping. Residue ALA 529 is missing expected H atoms. Skipping. Residue ALA 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue VAL 534 is missing expected H atoms. Skipping. Residue TYR 535 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue ALA 539 is missing expected H atoms. Skipping. Residue ALA 543 is missing expected H atoms. Skipping. Residue LYS 546 is missing expected H atoms. Skipping. Residue TYR 547 is missing expected H atoms. Skipping. Residue ALA 548 is missing expected H atoms. Skipping. Residue MET 549 is missing expected H atoms. Skipping. Residue LEU 551 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 181 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 183 is missing expected H atoms. Skipping. Residue VAL 184 is missing expected H atoms. Skipping. Residue MET 188 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue ALA 194 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue TYR 197 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue THR 202 is missing expected H atoms. Skipping. Residue VAL 204 is missing expected H atoms. Skipping. Residue LEU 205 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue VAL 209 is missing expected H atoms. Skipping. Residue LEU 210 is missing expected H atoms. Skipping. Residue LEU 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue MET 221 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue ALA 226 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue ILE 256 is missing expected H atoms. Skipping. Residue ILE 265 is missing expected H atoms. Skipping. Residue VAL 266 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue MET 302 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue ILE 307 is missing expected H atoms. Skipping. Residue ALA 308 is missing expected H atoms. Skipping. Residue ALA 309 is missing expected H atoms. Skipping. Residue LEU 311 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue VAL 318 is missing expected H atoms. Skipping. Residue ILE 319 is missing expected H atoms. Skipping. Residue VAL 320 is missing expected H atoms. Skipping. Residue VAL 321 is missing expected H atoms. Skipping. Residue THR 326 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LEU 330 is missing expected H atoms. Skipping. Residue TYR 331 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 336 is missing expected H atoms. Skipping. Residue ALA 337 is missing expected H atoms. Skipping. Residue MET 339 is missing expected H atoms. Skipping. Residue VAL 340 is missing expected H atoms. Skipping. Residue LYS 341 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue VAL 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue ALA 374 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue LEU 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue LEU 394 is missing expected H atoms. Skipping. Residue MET 395 is missing expected H atoms. Skipping. Residue ALA 396 is missing expected H atoms. Skipping. Residue SER 398 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue SER 424 is missing expected H atoms. Skipping. Residue VAL 426 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue SER 468 is missing expected H atoms. Skipping. Residue LEU 469 is missing expected H atoms. Skipping. Residue VAL 470 is missing expected H atoms. Skipping. Residue SER 471 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue SER 475 is missing expected H atoms. Skipping. Residue VAL 477 is missing expected H atoms. Skipping. Residue MET 478 is missing expected H atoms. Skipping. Residue THR 491 is missing expected H atoms. Skipping. Residue LYS 493 is missing expected H atoms. Skipping. Residue ALA 499 is missing expected H atoms. Skipping. Residue ALA 500 is missing expected H atoms. Skipping. Residue ILE 502 is missing expected H atoms. Skipping. Residue SER 510 is missing expected H atoms. Skipping. Residue ALA 511 is missing expected H atoms. Skipping. Residue ALA 513 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Evaluate side-chains 439 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 377 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 GLU cc_start: 0.3387 (tp30) cc_final: 0.1722 (tm-30) REVERT: A 149 LEU cc_start: 0.2881 (OUTLIER) cc_final: 0.2074 (pt) REVERT: A 233 PHE cc_start: 0.7555 (m-10) cc_final: 0.7243 (m-10) REVERT: A 252 TYR cc_start: 0.7162 (m-80) cc_final: 0.6817 (m-10) REVERT: A 267 LYS cc_start: 0.7434 (tptt) cc_final: 0.6447 (tptt) REVERT: A 342 TRP cc_start: 0.6586 (m100) cc_final: 0.6284 (m100) REVERT: A 368 MET cc_start: 0.7262 (mmt) cc_final: 0.5565 (ttp) REVERT: A 420 ARG cc_start: 0.7647 (mtm110) cc_final: 0.7415 (mtp180) REVERT: A 500 VAL cc_start: 0.8489 (t) cc_final: 0.7035 (m) REVERT: A 666 TYR cc_start: 0.7658 (t80) cc_final: 0.7295 (t80) REVERT: A 716 ILE cc_start: 0.9018 (mm) cc_final: 0.8597 (mp) REVERT: A 721 ASP cc_start: 0.8029 (t70) cc_final: 0.7815 (t0) REVERT: A 903 ARG cc_start: 0.7415 (mpt90) cc_final: 0.3896 (tpp-160) REVERT: A 1126 GLN cc_start: 0.7555 (tp-100) cc_final: 0.7249 (tp-100) REVERT: A 1194 TYR cc_start: 0.5391 (t80) cc_final: 0.4950 (t80) REVERT: A 1326 GLN cc_start: 0.8399 (tt0) cc_final: 0.8152 (tt0) REVERT: A 1703 MET cc_start: 0.6462 (mmm) cc_final: 0.6233 (mmm) REVERT: A 1708 TRP cc_start: 0.7495 (m100) cc_final: 0.6863 (m100) REVERT: A 1842 CYS cc_start: 0.8299 (p) cc_final: 0.7757 (m) REVERT: A 2326 MET cc_start: 0.8765 (mmp) cc_final: 0.8326 (mmp) REVERT: A 2393 ARG cc_start: 0.7696 (ptm-80) cc_final: 0.6555 (mtt90) REVERT: B 190 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8697 (ttpp) outliers start: 62 outliers final: 55 residues processed: 414 average time/residue: 0.1506 time to fit residues: 96.6400 Evaluate side-chains 422 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 365 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 613 PHE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 650 HIS Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 985 GLN Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1019 ASN Chi-restraints excluded: chain A residue 1085 CYS Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1285 LEU Chi-restraints excluded: chain A residue 1316 ILE Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1423 GLU Chi-restraints excluded: chain A residue 1521 VAL Chi-restraints excluded: chain A residue 1590 VAL Chi-restraints excluded: chain A residue 1599 PHE Chi-restraints excluded: chain A residue 1729 VAL Chi-restraints excluded: chain A residue 1816 THR Chi-restraints excluded: chain A residue 1856 ILE Chi-restraints excluded: chain A residue 1858 TYR Chi-restraints excluded: chain A residue 1964 GLU Chi-restraints excluded: chain A residue 2128 ILE Chi-restraints excluded: chain A residue 2176 MET Chi-restraints excluded: chain A residue 2204 LEU Chi-restraints excluded: chain A residue 2279 VAL Chi-restraints excluded: chain A residue 2306 THR Chi-restraints excluded: chain A residue 2320 SER Chi-restraints excluded: chain A residue 2337 HIS Chi-restraints excluded: chain A residue 2367 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 258 CYS Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 411 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 116 optimal weight: 0.0370 chunk 193 optimal weight: 3.9990 chunk 130 optimal weight: 0.0020 chunk 0 optimal weight: 10.0000 chunk 184 optimal weight: 9.9990 chunk 83 optimal weight: 0.6980 chunk 142 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 252 optimal weight: 2.9990 chunk 215 optimal weight: 0.7980 overall best weight: 0.5068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 ASN ** A 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 ASN ** A 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1496 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.136293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.114596 restraints weight = 55152.508| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.59 r_work: 0.3546 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 19856 Z= 0.104 Angle : 0.548 14.919 27014 Z= 0.285 Chirality : 0.037 0.245 3267 Planarity : 0.004 0.054 3422 Dihedral : 5.829 99.143 2742 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 64.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 12.11 % Favored : 87.85 % Rotamer: Outliers : 3.16 % Allowed : 18.20 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 1.66 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.59 (0.18), residues: 2526 helix: 0.55 (0.15), residues: 1456 sheet: -3.10 (0.46), residues: 116 loop : -3.46 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 8 TYR 0.042 0.001 TYR A1670 PHE 0.015 0.001 PHE A 609 TRP 0.014 0.001 TRP A1106 HIS 0.004 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00233 (19855) covalent geometry : angle 0.54751 (27014) hydrogen bonds : bond 0.02595 ( 891) hydrogen bonds : angle 4.17287 ( 2574) Misc. bond : bond 0.00029 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 5 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue VAL 50 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue LYS 55 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue ALA 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue ALA 140 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue TYR 150 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LEU 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue ALA 165 is missing expected H atoms. Skipping. Residue ALA 185 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue TYR 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue LEU 210 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue LEU 212 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue THR 216 is missing expected H atoms. Skipping. Residue SER 218 is missing expected H atoms. Skipping. Residue ILE 221 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue TYR 223 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LYS 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue LEU 300 is missing expected H atoms. Skipping. Residue ALA 303 is missing expected H atoms. Skipping. Residue LEU 304 is missing expected H atoms. Skipping. Residue ILE 308 is missing expected H atoms. Skipping. Residue TYR 309 is missing expected H atoms. Skipping. Residue ILE 311 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue SER 315 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue ALA 334 is missing expected H atoms. Skipping. Residue VAL 336 is missing expected H atoms. Skipping. Residue TYR 337 is missing expected H atoms. Skipping. Residue ILE 338 is missing expected H atoms. Skipping. Residue VAL 339 is missing expected H atoms. Skipping. Residue THR 409 is missing expected H atoms. Skipping. Residue VAL 418 is missing expected H atoms. Skipping. Residue LEU 420 is missing expected H atoms. Skipping. Residue THR 444 is missing expected H atoms. Skipping. Residue TYR 445 is missing expected H atoms. Skipping. Residue LYS 447 is missing expected H atoms. Skipping. Residue ILE 449 is missing expected H atoms. Skipping. Residue SER 450 is missing expected H atoms. Skipping. Residue ALA 451 is missing expected H atoms. Skipping. Residue SER 453 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue TYR 456 is missing expected H atoms. Skipping. Residue VAL 458 is missing expected H atoms. Skipping. Residue ALA 459 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 493 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue SER 496 is missing expected H atoms. Skipping. Residue LEU 528 is missing expected H atoms. Skipping. Residue ALA 529 is missing expected H atoms. Skipping. Residue ALA 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue VAL 534 is missing expected H atoms. Skipping. Residue TYR 535 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue ALA 539 is missing expected H atoms. Skipping. Residue ALA 543 is missing expected H atoms. Skipping. Residue LYS 546 is missing expected H atoms. Skipping. Residue TYR 547 is missing expected H atoms. Skipping. Residue ALA 548 is missing expected H atoms. Skipping. Residue MET 549 is missing expected H atoms. Skipping. Residue LEU 551 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 181 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 183 is missing expected H atoms. Skipping. Residue VAL 184 is missing expected H atoms. Skipping. Residue MET 188 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue ALA 194 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue TYR 197 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue THR 202 is missing expected H atoms. Skipping. Residue VAL 204 is missing expected H atoms. Skipping. Residue LEU 205 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue VAL 209 is missing expected H atoms. Skipping. Residue LEU 210 is missing expected H atoms. Skipping. Residue LEU 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue MET 221 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue ALA 226 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue ILE 256 is missing expected H atoms. Skipping. Residue ILE 265 is missing expected H atoms. Skipping. Residue VAL 266 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue MET 302 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue ILE 307 is missing expected H atoms. Skipping. Residue ALA 308 is missing expected H atoms. Skipping. Residue ALA 309 is missing expected H atoms. Skipping. Residue LEU 311 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue VAL 318 is missing expected H atoms. Skipping. Residue ILE 319 is missing expected H atoms. Skipping. Residue VAL 320 is missing expected H atoms. Skipping. Residue VAL 321 is missing expected H atoms. Skipping. Residue THR 326 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LEU 330 is missing expected H atoms. Skipping. Residue TYR 331 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 336 is missing expected H atoms. Skipping. Residue ALA 337 is missing expected H atoms. Skipping. Residue MET 339 is missing expected H atoms. Skipping. Residue VAL 340 is missing expected H atoms. Skipping. Residue LYS 341 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue VAL 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue ALA 374 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue LEU 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue LEU 394 is missing expected H atoms. Skipping. Residue MET 395 is missing expected H atoms. Skipping. Residue ALA 396 is missing expected H atoms. Skipping. Residue SER 398 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue SER 424 is missing expected H atoms. Skipping. Residue VAL 426 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue SER 468 is missing expected H atoms. Skipping. Residue LEU 469 is missing expected H atoms. Skipping. Residue VAL 470 is missing expected H atoms. Skipping. Residue SER 471 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue SER 475 is missing expected H atoms. Skipping. Residue VAL 477 is missing expected H atoms. Skipping. Residue MET 478 is missing expected H atoms. Skipping. Residue THR 491 is missing expected H atoms. Skipping. Residue LYS 493 is missing expected H atoms. Skipping. Residue ALA 499 is missing expected H atoms. Skipping. Residue ALA 500 is missing expected H atoms. Skipping. Residue ILE 502 is missing expected H atoms. Skipping. Residue SER 510 is missing expected H atoms. Skipping. Residue ALA 511 is missing expected H atoms. Skipping. Residue ALA 513 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Evaluate side-chains 436 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 372 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 GLU cc_start: 0.3285 (tp30) cc_final: 0.1664 (tm-30) REVERT: A 149 LEU cc_start: 0.2893 (OUTLIER) cc_final: 0.2053 (pt) REVERT: A 233 PHE cc_start: 0.7574 (m-10) cc_final: 0.7259 (m-10) REVERT: A 252 TYR cc_start: 0.7202 (m-80) cc_final: 0.6852 (m-10) REVERT: A 267 LYS cc_start: 0.7502 (tptt) cc_final: 0.6550 (tptt) REVERT: A 314 ASN cc_start: 0.3807 (OUTLIER) cc_final: 0.3564 (t0) REVERT: A 342 TRP cc_start: 0.6595 (m100) cc_final: 0.6285 (m100) REVERT: A 368 MET cc_start: 0.7238 (mmt) cc_final: 0.5470 (ttp) REVERT: A 420 ARG cc_start: 0.7639 (mtm110) cc_final: 0.7415 (mtp180) REVERT: A 500 VAL cc_start: 0.8471 (t) cc_final: 0.6967 (m) REVERT: A 629 ILE cc_start: 0.8887 (mm) cc_final: 0.8635 (mm) REVERT: A 666 TYR cc_start: 0.7637 (t80) cc_final: 0.7410 (t80) REVERT: A 716 ILE cc_start: 0.9018 (mm) cc_final: 0.8643 (mp) REVERT: A 721 ASP cc_start: 0.8018 (t70) cc_final: 0.7804 (t0) REVERT: A 903 ARG cc_start: 0.7392 (mpt90) cc_final: 0.3721 (tpp-160) REVERT: A 1017 TYR cc_start: 0.7599 (t80) cc_final: 0.7390 (t80) REVERT: A 1075 MET cc_start: 0.8117 (mmm) cc_final: 0.7699 (mmm) REVERT: A 1126 GLN cc_start: 0.7600 (tp-100) cc_final: 0.7290 (tp-100) REVERT: A 1194 TYR cc_start: 0.5408 (t80) cc_final: 0.4955 (t80) REVERT: A 1212 ASP cc_start: 0.7038 (t0) cc_final: 0.6690 (t0) REVERT: A 1703 MET cc_start: 0.6445 (mmm) cc_final: 0.6216 (mmm) REVERT: A 1708 TRP cc_start: 0.7497 (m100) cc_final: 0.6844 (m100) REVERT: A 1842 CYS cc_start: 0.8241 (p) cc_final: 0.7577 (m) REVERT: A 2326 MET cc_start: 0.8779 (mmp) cc_final: 0.8351 (mmp) REVERT: A 2393 ARG cc_start: 0.7920 (ptm-80) cc_final: 0.6669 (mtt90) REVERT: B 190 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8699 (ttpp) REVERT: B 550 GLN cc_start: 0.6799 (mt0) cc_final: 0.5198 (mt0) outliers start: 64 outliers final: 56 residues processed: 413 average time/residue: 0.1519 time to fit residues: 97.5497 Evaluate side-chains 422 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 363 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 613 PHE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 867 SER Chi-restraints excluded: chain A residue 942 THR Chi-restraints excluded: chain A residue 985 GLN Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1019 ASN Chi-restraints excluded: chain A residue 1085 CYS Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1285 LEU Chi-restraints excluded: chain A residue 1316 ILE Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1423 GLU Chi-restraints excluded: chain A residue 1521 VAL Chi-restraints excluded: chain A residue 1590 VAL Chi-restraints excluded: chain A residue 1599 PHE Chi-restraints excluded: chain A residue 1729 VAL Chi-restraints excluded: chain A residue 1816 THR Chi-restraints excluded: chain A residue 1856 ILE Chi-restraints excluded: chain A residue 1858 TYR Chi-restraints excluded: chain A residue 1964 GLU Chi-restraints excluded: chain A residue 2128 ILE Chi-restraints excluded: chain A residue 2204 LEU Chi-restraints excluded: chain A residue 2279 VAL Chi-restraints excluded: chain A residue 2306 THR Chi-restraints excluded: chain A residue 2320 SER Chi-restraints excluded: chain A residue 2337 HIS Chi-restraints excluded: chain A residue 2367 VAL Chi-restraints excluded: chain A residue 2391 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 258 CYS Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 411 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 24 optimal weight: 5.9990 chunk 197 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 244 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 109 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 251 optimal weight: 0.0060 chunk 80 optimal weight: 1.9990 overall best weight: 1.1000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 ASN A 577 ASN ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 ASN ** A 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1496 GLN B 61 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 GLN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.134333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.113182 restraints weight = 55130.456| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.43 r_work: 0.3517 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 19856 Z= 0.152 Angle : 0.584 16.178 27014 Z= 0.305 Chirality : 0.038 0.270 3267 Planarity : 0.004 0.055 3422 Dihedral : 5.976 95.218 2742 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 65.53 Ramachandran Plot: Outliers : 0.04 % Allowed : 12.91 % Favored : 87.05 % Rotamer: Outliers : 3.60 % Allowed : 18.24 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 1.66 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.58 (0.18), residues: 2526 helix: 0.57 (0.15), residues: 1450 sheet: -3.08 (0.46), residues: 116 loop : -3.46 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 8 TYR 0.041 0.001 TYR A1670 PHE 0.017 0.001 PHE A 609 TRP 0.014 0.001 TRP A1106 HIS 0.005 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00333 (19855) covalent geometry : angle 0.58374 (27014) hydrogen bonds : bond 0.02849 ( 891) hydrogen bonds : angle 4.30060 ( 2574) Misc. bond : bond 0.00025 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 5 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue VAL 50 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue LYS 55 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue ALA 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue ALA 140 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue TYR 150 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LEU 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue ALA 165 is missing expected H atoms. Skipping. Residue ALA 185 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue TYR 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue LEU 210 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue LEU 212 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue THR 216 is missing expected H atoms. Skipping. Residue SER 218 is missing expected H atoms. Skipping. Residue ILE 221 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue TYR 223 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LYS 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue LEU 300 is missing expected H atoms. Skipping. Residue ALA 303 is missing expected H atoms. Skipping. Residue LEU 304 is missing expected H atoms. Skipping. Residue ILE 308 is missing expected H atoms. Skipping. Residue TYR 309 is missing expected H atoms. Skipping. Residue ILE 311 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue SER 315 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue ALA 334 is missing expected H atoms. Skipping. Residue VAL 336 is missing expected H atoms. Skipping. Residue TYR 337 is missing expected H atoms. Skipping. Residue ILE 338 is missing expected H atoms. Skipping. Residue VAL 339 is missing expected H atoms. Skipping. Residue THR 409 is missing expected H atoms. Skipping. Residue VAL 418 is missing expected H atoms. Skipping. Residue LEU 420 is missing expected H atoms. Skipping. Residue THR 444 is missing expected H atoms. Skipping. Residue TYR 445 is missing expected H atoms. Skipping. Residue LYS 447 is missing expected H atoms. Skipping. Residue ILE 449 is missing expected H atoms. Skipping. Residue SER 450 is missing expected H atoms. Skipping. Residue ALA 451 is missing expected H atoms. Skipping. Residue SER 453 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue TYR 456 is missing expected H atoms. Skipping. Residue VAL 458 is missing expected H atoms. Skipping. Residue ALA 459 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 493 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue SER 496 is missing expected H atoms. Skipping. Residue LEU 528 is missing expected H atoms. Skipping. Residue ALA 529 is missing expected H atoms. Skipping. Residue ALA 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue VAL 534 is missing expected H atoms. Skipping. Residue TYR 535 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue ALA 539 is missing expected H atoms. Skipping. Residue ALA 543 is missing expected H atoms. Skipping. Residue LYS 546 is missing expected H atoms. Skipping. Residue TYR 547 is missing expected H atoms. Skipping. Residue ALA 548 is missing expected H atoms. Skipping. Residue MET 549 is missing expected H atoms. Skipping. Residue LEU 551 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 181 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 183 is missing expected H atoms. Skipping. Residue VAL 184 is missing expected H atoms. Skipping. Residue MET 188 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue ALA 194 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue TYR 197 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue THR 202 is missing expected H atoms. Skipping. Residue VAL 204 is missing expected H atoms. Skipping. Residue LEU 205 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue VAL 209 is missing expected H atoms. Skipping. Residue LEU 210 is missing expected H atoms. Skipping. Residue LEU 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue MET 221 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue ALA 226 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue ILE 256 is missing expected H atoms. Skipping. Residue ILE 265 is missing expected H atoms. Skipping. Residue VAL 266 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue MET 302 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue ILE 307 is missing expected H atoms. Skipping. Residue ALA 308 is missing expected H atoms. Skipping. Residue ALA 309 is missing expected H atoms. Skipping. Residue LEU 311 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue VAL 318 is missing expected H atoms. Skipping. Residue ILE 319 is missing expected H atoms. Skipping. Residue VAL 320 is missing expected H atoms. Skipping. Residue VAL 321 is missing expected H atoms. Skipping. Residue THR 326 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LEU 330 is missing expected H atoms. Skipping. Residue TYR 331 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 336 is missing expected H atoms. Skipping. Residue ALA 337 is missing expected H atoms. Skipping. Residue MET 339 is missing expected H atoms. Skipping. Residue VAL 340 is missing expected H atoms. Skipping. Residue LYS 341 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue VAL 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue ALA 374 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue LEU 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue LEU 394 is missing expected H atoms. Skipping. Residue MET 395 is missing expected H atoms. Skipping. Residue ALA 396 is missing expected H atoms. Skipping. Residue SER 398 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue SER 424 is missing expected H atoms. Skipping. Residue VAL 426 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue SER 468 is missing expected H atoms. Skipping. Residue LEU 469 is missing expected H atoms. Skipping. Residue VAL 470 is missing expected H atoms. Skipping. Residue SER 471 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue SER 475 is missing expected H atoms. Skipping. Residue VAL 477 is missing expected H atoms. Skipping. Residue MET 478 is missing expected H atoms. Skipping. Residue THR 491 is missing expected H atoms. Skipping. Residue LYS 493 is missing expected H atoms. Skipping. Residue ALA 499 is missing expected H atoms. Skipping. Residue ALA 500 is missing expected H atoms. Skipping. Residue ILE 502 is missing expected H atoms. Skipping. Residue SER 510 is missing expected H atoms. Skipping. Residue ALA 511 is missing expected H atoms. Skipping. Residue ALA 513 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Evaluate side-chains 430 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 357 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 LEU cc_start: 0.2682 (OUTLIER) cc_final: 0.2175 (pt) REVERT: A 233 PHE cc_start: 0.7533 (m-10) cc_final: 0.7261 (m-10) REVERT: A 252 TYR cc_start: 0.7137 (m-80) cc_final: 0.6774 (m-10) REVERT: A 267 LYS cc_start: 0.7422 (tptt) cc_final: 0.6495 (tptt) REVERT: A 342 TRP cc_start: 0.6527 (m100) cc_final: 0.6173 (m100) REVERT: A 368 MET cc_start: 0.7255 (mmt) cc_final: 0.5619 (ttp) REVERT: A 426 GLU cc_start: 0.6290 (pt0) cc_final: 0.5403 (pt0) REVERT: A 471 MET cc_start: 0.7845 (tpp) cc_final: 0.7582 (tpp) REVERT: A 629 ILE cc_start: 0.8936 (mm) cc_final: 0.8661 (mm) REVERT: A 716 ILE cc_start: 0.9070 (mm) cc_final: 0.8653 (mp) REVERT: A 721 ASP cc_start: 0.8107 (t70) cc_final: 0.7904 (t0) REVERT: A 737 GLU cc_start: 0.6703 (tt0) cc_final: 0.6404 (tt0) REVERT: A 1017 TYR cc_start: 0.7688 (t80) cc_final: 0.7367 (t80) REVERT: A 1075 MET cc_start: 0.8179 (mmm) cc_final: 0.7752 (mmm) REVERT: A 1126 GLN cc_start: 0.7709 (tp-100) cc_final: 0.7420 (tp-100) REVERT: A 1326 GLN cc_start: 0.8082 (tt0) cc_final: 0.7784 (tt0) REVERT: A 1703 MET cc_start: 0.6430 (mmm) cc_final: 0.6214 (mmm) REVERT: A 1708 TRP cc_start: 0.7458 (m100) cc_final: 0.6864 (m100) REVERT: A 1842 CYS cc_start: 0.8199 (p) cc_final: 0.7582 (m) REVERT: A 2326 MET cc_start: 0.8824 (mmp) cc_final: 0.8404 (mmp) REVERT: A 2393 ARG cc_start: 0.7986 (ptm-80) cc_final: 0.6682 (mtt180) REVERT: B 190 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.8740 (ttpp) REVERT: C 421 PHE cc_start: 0.7992 (p90) cc_final: 0.7610 (p90) outliers start: 73 outliers final: 65 residues processed: 404 average time/residue: 0.1506 time to fit residues: 94.6981 Evaluate side-chains 421 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 354 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 557 ASN Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 613 PHE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 833 ASN Chi-restraints excluded: chain A residue 867 SER Chi-restraints excluded: chain A residue 942 THR Chi-restraints excluded: chain A residue 985 GLN Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1019 ASN Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1316 ILE Chi-restraints excluded: chain A residue 1358 SER Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1590 VAL Chi-restraints excluded: chain A residue 1599 PHE Chi-restraints excluded: chain A residue 1729 VAL Chi-restraints excluded: chain A residue 1785 ILE Chi-restraints excluded: chain A residue 1816 THR Chi-restraints excluded: chain A residue 1856 ILE Chi-restraints excluded: chain A residue 1858 TYR Chi-restraints excluded: chain A residue 2128 ILE Chi-restraints excluded: chain A residue 2204 LEU Chi-restraints excluded: chain A residue 2279 VAL Chi-restraints excluded: chain A residue 2306 THR Chi-restraints excluded: chain A residue 2320 SER Chi-restraints excluded: chain A residue 2337 HIS Chi-restraints excluded: chain A residue 2367 VAL Chi-restraints excluded: chain A residue 2381 THR Chi-restraints excluded: chain A residue 2391 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 258 CYS Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 411 CYS Chi-restraints excluded: chain C residue 487 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 215 optimal weight: 0.9980 chunk 11 optimal weight: 9.9990 chunk 67 optimal weight: 1.9990 chunk 229 optimal weight: 5.9990 chunk 193 optimal weight: 2.9990 chunk 190 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 129 optimal weight: 0.0970 chunk 32 optimal weight: 0.0030 chunk 213 optimal weight: 0.0570 overall best weight: 0.4308 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 ASN ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 677 HIS ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1496 GLN B 61 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.136151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.114577 restraints weight = 55416.416| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.51 r_work: 0.3551 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 19856 Z= 0.100 Angle : 0.555 16.166 27014 Z= 0.290 Chirality : 0.037 0.284 3267 Planarity : 0.004 0.054 3422 Dihedral : 5.599 96.293 2738 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 64.53 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.72 % Favored : 88.24 % Rotamer: Outliers : 2.81 % Allowed : 19.28 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 1.66 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.36 (0.18), residues: 2526 helix: 0.76 (0.15), residues: 1449 sheet: -2.99 (0.47), residues: 116 loop : -3.39 (0.19), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 8 TYR 0.041 0.001 TYR A1670 PHE 0.016 0.001 PHE A 609 TRP 0.015 0.001 TRP A 235 HIS 0.004 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00220 (19855) covalent geometry : angle 0.55483 (27014) hydrogen bonds : bond 0.02601 ( 891) hydrogen bonds : angle 4.14441 ( 2574) Misc. bond : bond 0.00025 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 5 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue VAL 50 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue LYS 55 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue ALA 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue ALA 140 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue TYR 150 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LEU 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue ALA 165 is missing expected H atoms. Skipping. Residue ALA 185 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue TYR 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue LEU 210 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue LEU 212 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue THR 216 is missing expected H atoms. Skipping. Residue SER 218 is missing expected H atoms. Skipping. Residue ILE 221 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue TYR 223 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LYS 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue LEU 300 is missing expected H atoms. Skipping. Residue ALA 303 is missing expected H atoms. Skipping. Residue LEU 304 is missing expected H atoms. Skipping. Residue ILE 308 is missing expected H atoms. Skipping. Residue TYR 309 is missing expected H atoms. Skipping. Residue ILE 311 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue SER 315 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue ALA 334 is missing expected H atoms. Skipping. Residue VAL 336 is missing expected H atoms. Skipping. Residue TYR 337 is missing expected H atoms. Skipping. Residue ILE 338 is missing expected H atoms. Skipping. Residue VAL 339 is missing expected H atoms. Skipping. Residue THR 409 is missing expected H atoms. Skipping. Residue VAL 418 is missing expected H atoms. Skipping. Residue LEU 420 is missing expected H atoms. Skipping. Residue THR 444 is missing expected H atoms. Skipping. Residue TYR 445 is missing expected H atoms. Skipping. Residue LYS 447 is missing expected H atoms. Skipping. Residue ILE 449 is missing expected H atoms. Skipping. Residue SER 450 is missing expected H atoms. Skipping. Residue ALA 451 is missing expected H atoms. Skipping. Residue SER 453 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue TYR 456 is missing expected H atoms. Skipping. Residue VAL 458 is missing expected H atoms. Skipping. Residue ALA 459 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 493 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue SER 496 is missing expected H atoms. Skipping. Residue LEU 528 is missing expected H atoms. Skipping. Residue ALA 529 is missing expected H atoms. Skipping. Residue ALA 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue VAL 534 is missing expected H atoms. Skipping. Residue TYR 535 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue ALA 539 is missing expected H atoms. Skipping. Residue ALA 543 is missing expected H atoms. Skipping. Residue LYS 546 is missing expected H atoms. Skipping. Residue TYR 547 is missing expected H atoms. Skipping. Residue ALA 548 is missing expected H atoms. Skipping. Residue MET 549 is missing expected H atoms. Skipping. Residue LEU 551 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 181 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 183 is missing expected H atoms. Skipping. Residue VAL 184 is missing expected H atoms. Skipping. Residue MET 188 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue ALA 194 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue TYR 197 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue THR 202 is missing expected H atoms. Skipping. Residue VAL 204 is missing expected H atoms. Skipping. Residue LEU 205 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue VAL 209 is missing expected H atoms. Skipping. Residue LEU 210 is missing expected H atoms. Skipping. Residue LEU 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue MET 221 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue ALA 226 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue ILE 256 is missing expected H atoms. Skipping. Residue ILE 265 is missing expected H atoms. Skipping. Residue VAL 266 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue MET 302 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue ILE 307 is missing expected H atoms. Skipping. Residue ALA 308 is missing expected H atoms. Skipping. Residue ALA 309 is missing expected H atoms. Skipping. Residue LEU 311 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue VAL 318 is missing expected H atoms. Skipping. Residue ILE 319 is missing expected H atoms. Skipping. Residue VAL 320 is missing expected H atoms. Skipping. Residue VAL 321 is missing expected H atoms. Skipping. Residue THR 326 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LEU 330 is missing expected H atoms. Skipping. Residue TYR 331 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 336 is missing expected H atoms. Skipping. Residue ALA 337 is missing expected H atoms. Skipping. Residue MET 339 is missing expected H atoms. Skipping. Residue VAL 340 is missing expected H atoms. Skipping. Residue LYS 341 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue VAL 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue ALA 374 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue LEU 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue LEU 394 is missing expected H atoms. Skipping. Residue MET 395 is missing expected H atoms. Skipping. Residue ALA 396 is missing expected H atoms. Skipping. Residue SER 398 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue SER 424 is missing expected H atoms. Skipping. Residue VAL 426 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue SER 468 is missing expected H atoms. Skipping. Residue LEU 469 is missing expected H atoms. Skipping. Residue VAL 470 is missing expected H atoms. Skipping. Residue SER 471 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue SER 475 is missing expected H atoms. Skipping. Residue VAL 477 is missing expected H atoms. Skipping. Residue MET 478 is missing expected H atoms. Skipping. Residue THR 491 is missing expected H atoms. Skipping. Residue LYS 493 is missing expected H atoms. Skipping. Residue ALA 499 is missing expected H atoms. Skipping. Residue ALA 500 is missing expected H atoms. Skipping. Residue ILE 502 is missing expected H atoms. Skipping. Residue SER 510 is missing expected H atoms. Skipping. Residue ALA 511 is missing expected H atoms. Skipping. Residue ALA 513 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Evaluate side-chains 425 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 368 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 LEU cc_start: 0.2679 (OUTLIER) cc_final: 0.2123 (pt) REVERT: A 233 PHE cc_start: 0.7599 (m-10) cc_final: 0.7251 (m-10) REVERT: A 252 TYR cc_start: 0.7273 (m-80) cc_final: 0.6914 (m-10) REVERT: A 267 LYS cc_start: 0.7523 (tptt) cc_final: 0.6621 (tptt) REVERT: A 342 TRP cc_start: 0.6556 (m100) cc_final: 0.6270 (m100) REVERT: A 368 MET cc_start: 0.7260 (mmt) cc_final: 0.5499 (ttp) REVERT: A 426 GLU cc_start: 0.6106 (pt0) cc_final: 0.5275 (pt0) REVERT: A 471 MET cc_start: 0.7795 (tpp) cc_final: 0.7525 (tpp) REVERT: A 500 VAL cc_start: 0.8484 (t) cc_final: 0.6961 (m) REVERT: A 557 ASN cc_start: 0.7431 (OUTLIER) cc_final: 0.7164 (t0) REVERT: A 629 ILE cc_start: 0.8820 (mm) cc_final: 0.8579 (mm) REVERT: A 716 ILE cc_start: 0.9007 (mm) cc_final: 0.8662 (mp) REVERT: A 721 ASP cc_start: 0.8014 (t70) cc_final: 0.7811 (t0) REVERT: A 737 GLU cc_start: 0.6625 (tt0) cc_final: 0.6320 (tt0) REVERT: A 903 ARG cc_start: 0.7378 (mpt90) cc_final: 0.4037 (mpt90) REVERT: A 1017 TYR cc_start: 0.7684 (t80) cc_final: 0.7472 (t80) REVERT: A 1075 MET cc_start: 0.8001 (mmm) cc_final: 0.7633 (mmm) REVERT: A 1212 ASP cc_start: 0.7069 (t0) cc_final: 0.6707 (t0) REVERT: A 1326 GLN cc_start: 0.7905 (tt0) cc_final: 0.7504 (tt0) REVERT: A 1703 MET cc_start: 0.6444 (mmm) cc_final: 0.6224 (mmm) REVERT: A 1708 TRP cc_start: 0.7443 (m100) cc_final: 0.6879 (m100) REVERT: A 1842 CYS cc_start: 0.8220 (p) cc_final: 0.7569 (m) REVERT: A 1973 GLN cc_start: 0.5015 (mt0) cc_final: 0.4673 (mm110) REVERT: A 2306 THR cc_start: 0.9393 (OUTLIER) cc_final: 0.9131 (t) REVERT: A 2326 MET cc_start: 0.8744 (mmp) cc_final: 0.8340 (mmp) REVERT: A 2393 ARG cc_start: 0.7888 (ptm-80) cc_final: 0.6699 (mtt90) REVERT: B 190 LYS cc_start: 0.9106 (OUTLIER) cc_final: 0.8695 (ttpp) REVERT: B 506 MET cc_start: 0.7598 (ptt) cc_final: 0.7186 (ptm) outliers start: 57 outliers final: 49 residues processed: 400 average time/residue: 0.1511 time to fit residues: 93.8148 Evaluate side-chains 410 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 357 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 475 CYS Chi-restraints excluded: chain A residue 557 ASN Chi-restraints excluded: chain A residue 613 PHE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 867 SER Chi-restraints excluded: chain A residue 985 GLN Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1019 ASN Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1316 ILE Chi-restraints excluded: chain A residue 1358 SER Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1599 PHE Chi-restraints excluded: chain A residue 1729 VAL Chi-restraints excluded: chain A residue 1785 ILE Chi-restraints excluded: chain A residue 1816 THR Chi-restraints excluded: chain A residue 1856 ILE Chi-restraints excluded: chain A residue 1858 TYR Chi-restraints excluded: chain A residue 2128 ILE Chi-restraints excluded: chain A residue 2204 LEU Chi-restraints excluded: chain A residue 2279 VAL Chi-restraints excluded: chain A residue 2306 THR Chi-restraints excluded: chain A residue 2320 SER Chi-restraints excluded: chain A residue 2337 HIS Chi-restraints excluded: chain A residue 2367 VAL Chi-restraints excluded: chain A residue 2381 THR Chi-restraints excluded: chain A residue 2391 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 258 CYS Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 411 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 199 optimal weight: 2.9990 chunk 214 optimal weight: 1.9990 chunk 242 optimal weight: 2.9990 chunk 253 optimal weight: 4.9990 chunk 159 optimal weight: 7.9990 chunk 232 optimal weight: 0.7980 chunk 129 optimal weight: 5.9990 chunk 211 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 chunk 236 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 ASN ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 ASN ** A1184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1496 GLN B 61 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 GLN ** B 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.131153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.108903 restraints weight = 55142.363| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.69 r_work: 0.3448 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 19856 Z= 0.241 Angle : 0.682 13.487 27014 Z= 0.357 Chirality : 0.041 0.305 3267 Planarity : 0.005 0.061 3422 Dihedral : 6.036 87.266 2738 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 69.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.78 % Favored : 86.14 % Rotamer: Outliers : 3.50 % Allowed : 18.74 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 1.66 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.82 (0.17), residues: 2526 helix: 0.37 (0.14), residues: 1443 sheet: -3.08 (0.46), residues: 116 loop : -3.54 (0.19), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 482 TYR 0.040 0.002 TYR A1670 PHE 0.020 0.002 PHE A 609 TRP 0.014 0.001 TRP A1106 HIS 0.007 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00523 (19855) covalent geometry : angle 0.68167 (27014) hydrogen bonds : bond 0.03384 ( 891) hydrogen bonds : angle 4.59956 ( 2574) Misc. bond : bond 0.00011 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5292.72 seconds wall clock time: 91 minutes 47.67 seconds (5507.67 seconds total)