Starting phenix.real_space_refine on Thu Mar 5 04:52:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v1n_31628/03_2026/7v1n_31628.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v1n_31628/03_2026/7v1n_31628.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7v1n_31628/03_2026/7v1n_31628.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v1n_31628/03_2026/7v1n_31628.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v1n_31628/03_2026/7v1n_31628.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v1n_31628/03_2026/7v1n_31628.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 12209 2.51 5 N 3016 2.21 5 O 3881 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 219 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19156 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 18665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2344, 18665 Classifications: {'peptide': 2344} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 22} Link IDs: {'PTRANS': 52, 'TRANS': 2291} Chain breaks: 1 Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 245 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'ASP:plan': 9, 'GLU:plan': 2, 'ASN:plan1': 7, 'TYR:plan': 2, 'ARG:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 80 Chain: "K" Number of atoms: 491 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 59, 485 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 2, 'TRANS': 56} Conformer: "B" Number of residues, atoms: 59, 485 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 2, 'TRANS': 56} bond proxies already assigned to first conformer: 488 Time building chain proxies: 3.95, per 1000 atoms: 0.21 Number of scatterers: 19156 At special positions: 0 Unit cell: (215.226, 176.094, 166.311, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 3881 8.00 N 3016 7.00 C 12209 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS K 125 " - pdb=" SG CYS K 175 " distance=2.02 Simple disulfide: pdb=" SG CYS K 134 " - pdb=" SG CYS K 158 " distance=2.03 Simple disulfide: pdb=" SG CYS K 150 " - pdb=" SG CYS K 171 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.45 Conformation dependent library (CDL) restraints added in 929.3 milliseconds 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4524 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 41 sheets defined 22.6% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 Processing helix chain 'A' and resid 26 through 31 removed outlier: 3.916A pdb=" N ALA A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 53 Processing helix chain 'A' and resid 53 through 63 removed outlier: 3.717A pdb=" N TYR A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 122 removed outlier: 3.593A pdb=" N ILE A 112 " --> pdb=" O ASN A 108 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLN A 117 " --> pdb=" O ASN A 113 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N TRP A 118 " --> pdb=" O TYR A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 154 removed outlier: 4.054A pdb=" N LYS A 143 " --> pdb=" O ASN A 139 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER A 148 " --> pdb=" O THR A 144 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASN A 151 " --> pdb=" O GLU A 147 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASP A 152 " --> pdb=" O SER A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 159 removed outlier: 4.114A pdb=" N GLU A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 171 Processing helix chain 'A' and resid 175 through 197 removed outlier: 3.644A pdb=" N TYR A 180 " --> pdb=" O MET A 176 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ASP A 181 " --> pdb=" O GLN A 177 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS A 182 " --> pdb=" O ILE A 178 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N PHE A 186 " --> pdb=" O LYS A 182 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 215 Processing helix chain 'A' and resid 219 through 227 Processing helix chain 'A' and resid 256 through 261 Processing helix chain 'A' and resid 264 through 280 removed outlier: 4.077A pdb=" N ASP A 270 " --> pdb=" O ALA A 266 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N VAL A 274 " --> pdb=" O ASP A 270 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU A 277 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS A 278 " --> pdb=" O VAL A 274 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASN A 279 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE A 280 " --> pdb=" O ILE A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 325 removed outlier: 3.556A pdb=" N TRP A 313 " --> pdb=" O THR A 309 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLU A 315 " --> pdb=" O VAL A 311 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU A 318 " --> pdb=" O GLU A 314 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE A 321 " --> pdb=" O GLN A 317 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N MET A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS A 323 " --> pdb=" O GLU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 345 Processing helix chain 'A' and resid 345 through 353 removed outlier: 3.555A pdb=" N SER A 349 " --> pdb=" O SER A 345 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N VAL A 350 " --> pdb=" O SER A 346 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N LEU A 351 " --> pdb=" O PHE A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 361 removed outlier: 3.882A pdb=" N ILE A 360 " --> pdb=" O ASP A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 421 removed outlier: 3.587A pdb=" N ILE A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN A 405 " --> pdb=" O ILE A 401 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR A 408 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N THR A 414 " --> pdb=" O ILE A 410 " (cutoff:3.500A) Proline residue: A 417 - end of helix Processing helix chain 'A' and resid 424 through 438 Processing helix chain 'A' and resid 444 through 449 Processing helix chain 'A' and resid 453 through 457 removed outlier: 3.756A pdb=" N VAL A 457 " --> pdb=" O TYR A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 470 removed outlier: 3.505A pdb=" N SER A 470 " --> pdb=" O THR A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 484 removed outlier: 4.063A pdb=" N TYR A 475 " --> pdb=" O GLY A 471 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA A 476 " --> pdb=" O PRO A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 519 Processing helix chain 'A' and resid 524 through 538 removed outlier: 3.502A pdb=" N ASN A 538 " --> pdb=" O GLU A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 601 Processing helix chain 'A' and resid 668 through 682 removed outlier: 3.554A pdb=" N ILE A 680 " --> pdb=" O ILE A 676 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 682 " --> pdb=" O THR A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 686 removed outlier: 3.844A pdb=" N ASP A 686 " --> pdb=" O ALA A 683 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 683 through 686' Processing helix chain 'A' and resid 711 through 721 removed outlier: 3.558A pdb=" N LEU A 718 " --> pdb=" O GLY A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 728 removed outlier: 3.737A pdb=" N LEU A 727 " --> pdb=" O VAL A 724 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET A 728 " --> pdb=" O SER A 725 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 724 through 728' Processing helix chain 'A' and resid 765 through 775 Processing helix chain 'A' and resid 794 through 810 removed outlier: 3.511A pdb=" N ASN A 807 " --> pdb=" O GLN A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 839 removed outlier: 3.592A pdb=" N GLN A 836 " --> pdb=" O ASN A 832 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL A 837 " --> pdb=" O ILE A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 863 removed outlier: 3.932A pdb=" N TYR A 855 " --> pdb=" O ASP A 851 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ILE A 856 " --> pdb=" O SER A 852 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE A 863 " --> pdb=" O GLU A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 874 removed outlier: 3.972A pdb=" N LYS A 874 " --> pdb=" O TYR A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 936 removed outlier: 3.734A pdb=" N THR A 936 " --> pdb=" O LYS A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 991 removed outlier: 3.905A pdb=" N MET A 986 " --> pdb=" O LEU A 982 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS A 987 " --> pdb=" O SER A 983 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR A 991 " --> pdb=" O LYS A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1117 through 1134 removed outlier: 3.843A pdb=" N ASP A1123 " --> pdb=" O LYS A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1246 through 1259 Processing helix chain 'A' and resid 1306 through 1312 removed outlier: 3.990A pdb=" N GLU A1311 " --> pdb=" O GLU A1307 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS A1312 " --> pdb=" O TYR A1308 " (cutoff:3.500A) Processing helix chain 'A' and resid 1349 through 1354 Processing helix chain 'A' and resid 1433 through 1451 removed outlier: 7.031A pdb=" N ASN A1442 " --> pdb=" O MET A1438 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N SER A1443 " --> pdb=" O ALA A1439 " (cutoff:3.500A) Processing helix chain 'A' and resid 1561 through 1572 removed outlier: 3.626A pdb=" N ILE A1566 " --> pdb=" O GLY A1562 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET A1570 " --> pdb=" O ILE A1566 " (cutoff:3.500A) Processing helix chain 'A' and resid 1580 through 1589 Processing helix chain 'A' and resid 1678 through 1682 removed outlier: 3.540A pdb=" N TYR A1681 " --> pdb=" O SER A1678 " (cutoff:3.500A) Processing helix chain 'A' and resid 1793 through 1799 Processing helix chain 'A' and resid 1838 through 1842 removed outlier: 3.726A pdb=" N ASP A1841 " --> pdb=" O TYR A1838 " (cutoff:3.500A) Processing helix chain 'A' and resid 1868 through 1872 removed outlier: 4.011A pdb=" N GLY A1872 " --> pdb=" O PRO A1869 " (cutoff:3.500A) Processing helix chain 'K' and resid 168 through 176 removed outlier: 3.542A pdb=" N LYS K 172 " --> pdb=" O LEU K 168 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ILE K 174 " --> pdb=" O GLU K 170 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 93 Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 101 removed outlier: 6.034A pdb=" N ASN A 238 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N VAL A 129 " --> pdb=" O ASN A 238 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 282 through 285 removed outlier: 3.664A pdb=" N ALA A 377 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N GLN A 386 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 11.139A pdb=" N LYS A 375 " --> pdb=" O GLN A 386 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 609 through 610 removed outlier: 7.085A pdb=" N VAL A 583 " --> pdb=" O ILE A 652 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 646 through 647 removed outlier: 6.617A pdb=" N ILE A 647 " --> pdb=" O GLU A 693 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE A 692 " --> pdb=" O ILE A 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 696 through 697 removed outlier: 6.171A pdb=" N LEU A 696 " --> pdb=" O ASN A 741 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 745 through 747 Processing sheet with id=AA8, first strand: chain 'A' and resid 778 through 781 removed outlier: 4.647A pdb=" N TYR A 778 " --> pdb=" O LYS A 791 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1162 through 1163 removed outlier: 3.960A pdb=" N ILE A1290 " --> pdb=" O SER A1316 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR A1318 " --> pdb=" O ILE A1290 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU A1338 " --> pdb=" O PHE A1317 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE A1335 " --> pdb=" O ASN A1391 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N SER A1393 " --> pdb=" O ILE A1335 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ILE A1337 " --> pdb=" O SER A1393 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1168 through 1170 removed outlier: 6.896A pdb=" N GLU A1169 " --> pdb=" O PHE A1231 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N TRP A1233 " --> pdb=" O GLU A1169 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU A1234 " --> pdb=" O LYS A1278 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS A1278 " --> pdb=" O GLU A1234 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N GLY A1236 " --> pdb=" O ILE A1276 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ILE A1276 " --> pdb=" O GLY A1236 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1172 through 1173 removed outlier: 3.636A pdb=" N ARG A1172 " --> pdb=" O THR A1194 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1323 through 1327 removed outlier: 3.971A pdb=" N SER A1404 " --> pdb=" O TRP A1345 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A1419 " --> pdb=" O VAL A1403 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1323 through 1327 removed outlier: 3.971A pdb=" N SER A1404 " --> pdb=" O TRP A1345 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A1419 " --> pdb=" O VAL A1403 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1356 through 1359 Processing sheet with id=AB6, first strand: chain 'A' and resid 1376 through 1378 Processing sheet with id=AB7, first strand: chain 'A' and resid 1460 through 1464 removed outlier: 3.534A pdb=" N TYR A1463 " --> pdb=" O GLY A1474 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY A1474 " --> pdb=" O TYR A1463 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1486 through 1489 removed outlier: 3.530A pdb=" N LEU A1489 " --> pdb=" O VAL A1492 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR A1509 " --> pdb=" O ILE A1495 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1542 through 1545 removed outlier: 7.245A pdb=" N SER A1542 " --> pdb=" O ASN A1554 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASN A1554 " --> pdb=" O SER A1542 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ILE A1551 " --> pdb=" O ILE A1606 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1542 through 1545 removed outlier: 7.245A pdb=" N SER A1542 " --> pdb=" O ASN A1554 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASN A1554 " --> pdb=" O SER A1542 " (cutoff:3.500A) removed outlier: 9.684A pdb=" N ILE A1612 " --> pdb=" O LYS A1552 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASN A1554 " --> pdb=" O ILE A1612 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N SER A1614 " --> pdb=" O ASN A1554 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL A1556 " --> pdb=" O SER A1614 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLN A1621 " --> pdb=" O ILE A1637 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ILE A1637 " --> pdb=" O GLN A1621 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N GLU A1623 " --> pdb=" O TYR A1635 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1644 through 1647 removed outlier: 6.327A pdb=" N MET A1656 " --> pdb=" O ILE A1693 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL A1718 " --> pdb=" O ARG A1767 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N THR A1769 " --> pdb=" O VAL A1718 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N VAL A1720 " --> pdb=" O THR A1769 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1702 through 1705 removed outlier: 6.321A pdb=" N ILE A1703 " --> pdb=" O ASN A1733 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1815 through 1819 Processing sheet with id=AC5, first strand: chain 'A' and resid 1835 through 1837 Processing sheet with id=AC6, first strand: chain 'A' and resid 1857 through 1860 Processing sheet with id=AC7, first strand: chain 'A' and resid 1878 through 1882 Processing sheet with id=AC8, first strand: chain 'A' and resid 1898 through 1900 removed outlier: 3.712A pdb=" N GLU A1922 " --> pdb=" O ALA A1910 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 1928 through 1932 Processing sheet with id=AD1, first strand: chain 'A' and resid 1951 through 1952 Processing sheet with id=AD2, first strand: chain 'A' and resid 1969 through 1972 Processing sheet with id=AD3, first strand: chain 'A' and resid 2011 through 2013 Processing sheet with id=AD4, first strand: chain 'A' and resid 2030 through 2032 removed outlier: 3.970A pdb=" N PHE A2031 " --> pdb=" O LYS A2038 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS A2038 " --> pdb=" O PHE A2031 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU A2053 " --> pdb=" O ALA A2041 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 2059 through 2063 Processing sheet with id=AD6, first strand: chain 'A' and resid 2081 through 2083 removed outlier: 7.562A pdb=" N LYS A2081 " --> pdb=" O LYS A2088 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N LYS A2088 " --> pdb=" O LYS A2081 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 2152 through 2153 removed outlier: 4.026A pdb=" N LEU A2157 " --> pdb=" O SER A2153 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 2171 through 2172 removed outlier: 4.066A pdb=" N TYR A2171 " --> pdb=" O VAL A2187 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 2235 through 2239 removed outlier: 3.560A pdb=" N GLY A2235 " --> pdb=" O PHE A2246 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASN A2237 " --> pdb=" O TYR A2244 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR A2244 " --> pdb=" O ASN A2237 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 2257 through 2258 Processing sheet with id=AE2, first strand: chain 'A' and resid 2295 through 2299 removed outlier: 3.531A pdb=" N GLY A2295 " --> pdb=" O PHE A2306 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 2327 through 2328 Processing sheet with id=AE4, first strand: chain 'A' and resid 2346 through 2349 removed outlier: 4.047A pdb=" N ILE A2349 " --> pdb=" O GLU A2352 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 138 through 144 removed outlier: 3.862A pdb=" N GLN K 149 " --> pdb=" O ASN K 144 " (cutoff:3.500A) 460 hydrogen bonds defined for protein. 1251 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.05 Time building geometry restraints manager: 1.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4903 1.33 - 1.46: 5269 1.46 - 1.59: 9271 1.59 - 1.71: 0 1.71 - 1.84: 86 Bond restraints: 19529 Sorted by residual: bond pdb=" C TYR A 581 " pdb=" N ILE A 582 " ideal model delta sigma weight residual 1.330 1.233 0.097 1.00e-02 1.00e+04 9.35e+01 bond pdb=" CA GLU A 859 " pdb=" C GLU A 859 " ideal model delta sigma weight residual 1.522 1.415 0.107 1.40e-02 5.10e+03 5.85e+01 bond pdb=" C GLU A1198 " pdb=" N PRO A1199 " ideal model delta sigma weight residual 1.334 1.499 -0.165 2.34e-02 1.83e+03 4.99e+01 bond pdb=" C LEU A 91 " pdb=" N THR A 92 " ideal model delta sigma weight residual 1.328 1.241 0.086 1.45e-02 4.76e+03 3.55e+01 bond pdb=" N GLY A 943 " pdb=" CA GLY A 943 " ideal model delta sigma weight residual 1.447 1.476 -0.029 7.50e-03 1.78e+04 1.46e+01 ... (remaining 19524 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.62: 25966 3.62 - 7.25: 432 7.25 - 10.87: 26 10.87 - 14.49: 1 14.49 - 18.11: 2 Bond angle restraints: 26427 Sorted by residual: angle pdb=" C GLU A1198 " pdb=" N PRO A1199 " pdb=" CA PRO A1199 " ideal model delta sigma weight residual 119.84 137.95 -18.11 1.25e+00 6.40e-01 2.10e+02 angle pdb=" N LEU A 960 " pdb=" CA LEU A 960 " pdb=" C LEU A 960 " ideal model delta sigma weight residual 113.38 104.56 8.82 1.23e+00 6.61e-01 5.14e+01 angle pdb=" N GLU A 245 " pdb=" CA GLU A 245 " pdb=" C GLU A 245 " ideal model delta sigma weight residual 113.89 103.58 10.31 1.58e+00 4.01e-01 4.26e+01 angle pdb=" C ARG A1058 " pdb=" N GLN A1059 " pdb=" CA GLN A1059 " ideal model delta sigma weight residual 121.90 114.55 7.35 1.26e+00 6.30e-01 3.41e+01 angle pdb=" N ARG A 173 " pdb=" CA ARG A 173 " pdb=" C ARG A 173 " ideal model delta sigma weight residual 114.62 108.00 6.62 1.14e+00 7.69e-01 3.37e+01 ... (remaining 26422 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 9613 17.96 - 35.93: 1483 35.93 - 53.89: 447 53.89 - 71.86: 113 71.86 - 89.82: 30 Dihedral angle restraints: 11686 sinusoidal: 4624 harmonic: 7062 Sorted by residual: dihedral pdb=" CA GLY A1029 " pdb=" C GLY A1029 " pdb=" N LEU A1030 " pdb=" CA LEU A1030 " ideal model delta harmonic sigma weight residual -180.00 -150.42 -29.58 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA ASP A 300 " pdb=" C ASP A 300 " pdb=" N ILE A 301 " pdb=" CA ILE A 301 " ideal model delta harmonic sigma weight residual 180.00 150.95 29.05 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA ILE A1037 " pdb=" C ILE A1037 " pdb=" N ASP A1038 " pdb=" CA ASP A1038 " ideal model delta harmonic sigma weight residual -180.00 -150.97 -29.03 0 5.00e+00 4.00e-02 3.37e+01 ... (remaining 11683 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 2061 0.068 - 0.137: 734 0.137 - 0.205: 95 0.205 - 0.274: 18 0.274 - 0.342: 6 Chirality restraints: 2914 Sorted by residual: chirality pdb=" CA ASP A 163 " pdb=" N ASP A 163 " pdb=" C ASP A 163 " pdb=" CB ASP A 163 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" CG LEU A1558 " pdb=" CB LEU A1558 " pdb=" CD1 LEU A1558 " pdb=" CD2 LEU A1558 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.32 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CA ARG A1197 " pdb=" N ARG A1197 " pdb=" C ARG A1197 " pdb=" CB ARG A1197 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.53e+00 ... (remaining 2911 not shown) Planarity restraints: 3443 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A2099 " 0.017 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C SER A2099 " -0.064 2.00e-02 2.50e+03 pdb=" O SER A2099 " 0.025 2.00e-02 2.50e+03 pdb=" N ILE A2100 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A1847 " -0.060 5.00e-02 4.00e+02 9.24e-02 1.37e+01 pdb=" N PRO A1848 " 0.160 5.00e-02 4.00e+02 pdb=" CA PRO A1848 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO A1848 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 243 " -0.026 2.00e-02 2.50e+03 2.05e-02 7.34e+00 pdb=" CG PHE A 243 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE A 243 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE A 243 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 243 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 243 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 243 " -0.009 2.00e-02 2.50e+03 ... (remaining 3440 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 339 2.56 - 3.14: 16514 3.14 - 3.73: 28572 3.73 - 4.31: 41467 4.31 - 4.90: 67807 Nonbonded interactions: 154699 Sorted by model distance: nonbonded pdb=" O SER A1738 " pdb=" OG SER A1738 " model vdw 1.973 3.040 nonbonded pdb=" OE2 GLU A1048 " pdb=" OG1 THR A1052 " model vdw 2.088 3.040 nonbonded pdb=" NZ LYS A 278 " pdb=" OD1 ASP A 398 " model vdw 2.089 3.120 nonbonded pdb=" ND2 ASN A 40 " pdb=" OE1 GLU A 44 " model vdw 2.100 3.120 nonbonded pdb=" O ASP A1686 " pdb=" OG1 THR A1714 " model vdw 2.102 3.040 ... (remaining 154694 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=0.30 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.560 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 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 : 0.013 0.165 19532 Z= 0.607 Angle : 1.207 18.114 26433 Z= 0.728 Chirality : 0.068 0.342 2914 Planarity : 0.006 0.092 3443 Dihedral : 19.761 89.821 7153 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 28.47 Ramachandran Plot: Outliers : 1.00 % Allowed : 20.11 % Favored : 78.89 % Rotamer: Outliers : 16.75 % Allowed : 22.63 % Favored : 60.63 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.88 (0.12), residues: 2398 helix: -4.28 (0.12), residues: 546 sheet: -3.62 (0.23), residues: 360 loop : -4.04 (0.12), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1229 TYR 0.033 0.003 TYR A1463 PHE 0.046 0.004 PHE A 243 TRP 0.023 0.003 TRP A 118 HIS 0.011 0.002 HIS A 654 Details of bonding type rmsd covalent geometry : bond 0.01308 (19529) covalent geometry : angle 1.20618 (26427) SS BOND : bond 0.00535 ( 3) SS BOND : angle 2.72392 ( 6) hydrogen bonds : bond 0.24486 ( 447) hydrogen bonds : angle 10.04630 ( 1251) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 351 poor density : 135 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 GLU cc_start: 0.6480 (OUTLIER) cc_final: 0.6079 (mp0) REVERT: A 194 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.7608 (mptm) REVERT: A 288 ASP cc_start: 0.8480 (OUTLIER) cc_final: 0.8198 (m-30) REVERT: A 400 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8389 (tp) REVERT: A 617 GLU cc_start: 0.6888 (mm-30) cc_final: 0.5742 (tt0) REVERT: A 634 LYS cc_start: 0.7287 (OUTLIER) cc_final: 0.6564 (mtmt) REVERT: A 721 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7643 (ptmm) REVERT: A 777 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7590 (mm-30) REVERT: A 818 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7154 (pm20) REVERT: A 860 PHE cc_start: 0.8364 (OUTLIER) cc_final: 0.7686 (m-10) REVERT: A 982 LEU cc_start: 0.7042 (OUTLIER) cc_final: 0.6472 (tt) REVERT: A 986 MET cc_start: 0.7032 (mmm) cc_final: 0.6781 (mmm) REVERT: A 1139 LEU cc_start: 0.4778 (OUTLIER) cc_final: 0.2198 (tt) REVERT: A 1196 TYR cc_start: 0.2627 (OUTLIER) cc_final: 0.1491 (m-10) REVERT: A 1251 LEU cc_start: 0.1358 (OUTLIER) cc_final: 0.1007 (tp) REVERT: A 1426 TYR cc_start: 0.5439 (OUTLIER) cc_final: 0.4643 (p90) REVERT: A 1509 TYR cc_start: 0.5317 (OUTLIER) cc_final: 0.4392 (m-80) REVERT: A 1560 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6727 (tp30) REVERT: A 1605 LEU cc_start: 0.6489 (OUTLIER) cc_final: 0.6238 (mp) REVERT: A 1640 ASN cc_start: 0.7902 (OUTLIER) cc_final: 0.7646 (m-40) REVERT: A 1781 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8177 (mm) REVERT: A 2026 MET cc_start: -0.2981 (tpt) cc_final: -0.3439 (mtp) REVERT: A 2130 PHE cc_start: 0.1562 (OUTLIER) cc_final: 0.0890 (p90) REVERT: A 2143 GLN cc_start: 0.5407 (OUTLIER) cc_final: 0.3867 (pp30) REVERT: A 2154 GLU cc_start: 0.1918 (OUTLIER) cc_final: 0.1653 (mp0) REVERT: A 2259 PHE cc_start: 0.2005 (OUTLIER) cc_final: 0.0563 (t80) REVERT: A 2272 MET cc_start: 0.2434 (ttm) cc_final: 0.2015 (ttm) outliers start: 351 outliers final: 233 residues processed: 466 average time/residue: 0.1302 time to fit residues: 95.8499 Evaluate side-chains 359 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 256 poor density : 103 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 63 TYR Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 74 LYS Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 242 ASN Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 396 CYS Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 521 TRP Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 554 GLN Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 621 TYR Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 715 LYS Chi-restraints excluded: chain A residue 721 LYS Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 749 SER Chi-restraints excluded: chain A residue 777 GLU Chi-restraints excluded: chain A residue 782 ASN Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 814 ILE Chi-restraints excluded: chain A residue 818 GLU Chi-restraints excluded: chain A residue 819 LYS Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 824 GLU Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 852 SER Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 858 ASN Chi-restraints excluded: chain A residue 860 PHE Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 880 GLU Chi-restraints excluded: chain A residue 881 GLU Chi-restraints excluded: chain A residue 883 HIS Chi-restraints excluded: chain A residue 889 ASP Chi-restraints excluded: chain A residue 897 PHE Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 908 GLU Chi-restraints excluded: chain A residue 926 ILE Chi-restraints excluded: chain A residue 939 ASP Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 955 HIS Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 964 PHE Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 970 ILE Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 983 SER Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 997 THR Chi-restraints excluded: chain A residue 1000 ASN Chi-restraints excluded: chain A residue 1014 THR Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1018 GLU Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1054 ASP Chi-restraints excluded: chain A residue 1092 ILE Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1139 LEU Chi-restraints excluded: chain A residue 1143 LYS Chi-restraints excluded: chain A residue 1152 VAL Chi-restraints excluded: chain A residue 1194 THR Chi-restraints excluded: chain A residue 1196 TYR Chi-restraints excluded: chain A residue 1216 LEU Chi-restraints excluded: chain A residue 1221 MET Chi-restraints excluded: chain A residue 1245 GLU Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1252 LEU Chi-restraints excluded: chain A residue 1265 TRP Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1276 ILE Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1323 THR Chi-restraints excluded: chain A residue 1344 THR Chi-restraints excluded: chain A residue 1349 VAL Chi-restraints excluded: chain A residue 1352 VAL Chi-restraints excluded: chain A residue 1353 VAL Chi-restraints excluded: chain A residue 1361 ASP Chi-restraints excluded: chain A residue 1367 ASP Chi-restraints excluded: chain A residue 1377 SER Chi-restraints excluded: chain A residue 1409 ILE Chi-restraints excluded: chain A residue 1410 LEU Chi-restraints excluded: chain A residue 1411 GLU Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1426 TYR Chi-restraints excluded: chain A residue 1444 VAL Chi-restraints excluded: chain A residue 1448 ILE Chi-restraints excluded: chain A residue 1457 LEU Chi-restraints excluded: chain A residue 1458 GLN Chi-restraints excluded: chain A residue 1460 ASN Chi-restraints excluded: chain A residue 1469 GLU Chi-restraints excluded: chain A residue 1480 THR Chi-restraints excluded: chain A residue 1500 MET Chi-restraints excluded: chain A residue 1507 PHE Chi-restraints excluded: chain A residue 1509 TYR Chi-restraints excluded: chain A residue 1513 ASP Chi-restraints excluded: chain A residue 1532 TYR Chi-restraints excluded: chain A residue 1534 LYS Chi-restraints excluded: chain A residue 1537 ILE Chi-restraints excluded: chain A residue 1541 LEU Chi-restraints excluded: chain A residue 1543 PHE Chi-restraints excluded: chain A residue 1545 ILE Chi-restraints excluded: chain A residue 1546 GLN Chi-restraints excluded: chain A residue 1549 ASN Chi-restraints excluded: chain A residue 1550 THR Chi-restraints excluded: chain A residue 1558 LEU Chi-restraints excluded: chain A residue 1560 GLU Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1576 THR Chi-restraints excluded: chain A residue 1584 SER Chi-restraints excluded: chain A residue 1594 ILE Chi-restraints excluded: chain A residue 1596 ILE Chi-restraints excluded: chain A residue 1598 SER Chi-restraints excluded: chain A residue 1605 LEU Chi-restraints excluded: chain A residue 1607 LEU Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 1616 THR Chi-restraints excluded: chain A residue 1617 THR Chi-restraints excluded: chain A residue 1638 LYS Chi-restraints excluded: chain A residue 1639 PHE Chi-restraints excluded: chain A residue 1640 ASN Chi-restraints excluded: chain A residue 1642 LEU Chi-restraints excluded: chain A residue 1652 ASN Chi-restraints excluded: chain A residue 1662 TYR Chi-restraints excluded: chain A residue 1665 ASP Chi-restraints excluded: chain A residue 1672 SER Chi-restraints excluded: chain A residue 1674 VAL Chi-restraints excluded: chain A residue 1678 SER Chi-restraints excluded: chain A residue 1687 SER Chi-restraints excluded: chain A residue 1691 LYS Chi-restraints excluded: chain A residue 1705 ILE Chi-restraints excluded: chain A residue 1712 ASN Chi-restraints excluded: chain A residue 1726 ILE Chi-restraints excluded: chain A residue 1738 SER Chi-restraints excluded: chain A residue 1742 VAL Chi-restraints excluded: chain A residue 1745 ASN Chi-restraints excluded: chain A residue 1771 VAL Chi-restraints excluded: chain A residue 1773 LYS Chi-restraints excluded: chain A residue 1781 ILE Chi-restraints excluded: chain A residue 1798 SER Chi-restraints excluded: chain A residue 1812 TYR Chi-restraints excluded: chain A residue 1817 ILE Chi-restraints excluded: chain A residue 1834 SER Chi-restraints excluded: chain A residue 1836 LEU Chi-restraints excluded: chain A residue 1837 VAL Chi-restraints excluded: chain A residue 1843 LEU Chi-restraints excluded: chain A residue 1871 ASN Chi-restraints excluded: chain A residue 1876 SER Chi-restraints excluded: chain A residue 1890 SER Chi-restraints excluded: chain A residue 1927 THR Chi-restraints excluded: chain A residue 1960 SER Chi-restraints excluded: chain A residue 2078 VAL Chi-restraints excluded: chain A residue 2087 SER Chi-restraints excluded: chain A residue 2100 ILE Chi-restraints excluded: chain A residue 2104 ILE Chi-restraints excluded: chain A residue 2130 PHE Chi-restraints excluded: chain A residue 2143 GLN Chi-restraints excluded: chain A residue 2153 SER Chi-restraints excluded: chain A residue 2154 GLU Chi-restraints excluded: chain A residue 2157 LEU Chi-restraints excluded: chain A residue 2165 THR Chi-restraints excluded: chain A residue 2181 ASN Chi-restraints excluded: chain A residue 2195 VAL Chi-restraints excluded: chain A residue 2205 SER Chi-restraints excluded: chain A residue 2231 LYS Chi-restraints excluded: chain A residue 2259 PHE Chi-restraints excluded: chain A residue 2263 HIS Chi-restraints excluded: chain A residue 2329 LEU Chi-restraints excluded: chain A residue 2363 LEU Chi-restraints excluded: chain K residue 124 PHE Chi-restraints excluded: chain K residue 127 LEU Chi-restraints excluded: chain K residue 142 PHE Chi-restraints excluded: chain K residue 167 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 20.0000 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.0980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.5980 chunk 235 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 53 ASN A 90 ASN A 97 ASN A 106 GLN A 134 ASN A 139 ASN A 160 ASN A 162 ASN A 167 ASN A 257 GLN A 344 GLN A 403 GLN A 412 ASN A 426 ASN A 518 ASN A 522 GLN A 538 ASN A 741 ASN A 782 ASN A 803 GLN ** A 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1160 ASN A1381 ASN A1446 GLN A1502 ASN A1621 GLN A1828 ASN A1886 ASN A1935 ASN A2176 ASN ** A2181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2298 ASN ** A2308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2310 ASN K 146 GLN A K 146 GLN B K 164 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.211392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.175607 restraints weight = 43638.766| |-----------------------------------------------------------------------------| r_work (start): 0.4178 rms_B_bonded: 3.02 r_work: 0.3766 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3763 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3763 r_free = 0.3763 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3763 r_free = 0.3763 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3763 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19532 Z= 0.148 Angle : 0.697 8.859 26433 Z= 0.372 Chirality : 0.048 0.175 2914 Planarity : 0.005 0.076 3443 Dihedral : 12.779 80.502 3071 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.06 % Favored : 88.78 % Rotamer: Outliers : 8.40 % Allowed : 25.28 % Favored : 66.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.64 (0.14), residues: 2398 helix: -2.68 (0.18), residues: 573 sheet: -2.93 (0.25), residues: 348 loop : -3.46 (0.13), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1354 TYR 0.068 0.002 TYR A1463 PHE 0.021 0.002 PHE A 246 TRP 0.013 0.002 TRP A2326 HIS 0.005 0.001 HIS A1179 Details of bonding type rmsd covalent geometry : bond 0.00330 (19529) covalent geometry : angle 0.69726 (26427) SS BOND : bond 0.00225 ( 3) SS BOND : angle 1.03670 ( 6) hydrogen bonds : bond 0.04224 ( 447) hydrogen bonds : angle 6.43392 ( 1251) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 133 time to evaluate : 0.516 Fit side-chains revert: symmetry clash REVERT: A 604 TYR cc_start: 0.7370 (m-80) cc_final: 0.7104 (m-10) REVERT: A 615 ASP cc_start: 0.6673 (OUTLIER) cc_final: 0.6359 (p0) REVERT: A 617 GLU cc_start: 0.6936 (mm-30) cc_final: 0.5723 (tt0) REVERT: A 860 PHE cc_start: 0.8388 (OUTLIER) cc_final: 0.7618 (m-10) REVERT: A 1058 ARG cc_start: 0.3225 (OUTLIER) cc_final: 0.2423 (ptt90) REVERT: A 1109 ASN cc_start: 0.2369 (OUTLIER) cc_final: 0.2016 (t0) REVERT: A 1225 ASN cc_start: 0.8627 (p0) cc_final: 0.8052 (m-40) REVERT: A 1482 GLU cc_start: 0.5068 (OUTLIER) cc_final: 0.2896 (tm-30) REVERT: A 1526 ILE cc_start: 0.6998 (OUTLIER) cc_final: 0.6702 (mm) REVERT: A 1532 TYR cc_start: 0.7270 (OUTLIER) cc_final: 0.5744 (t80) REVERT: A 1560 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6444 (tp30) REVERT: A 1568 LYS cc_start: 0.6967 (ttpp) cc_final: 0.6723 (ttmt) REVERT: A 1708 VAL cc_start: 0.7792 (t) cc_final: 0.7458 (m) REVERT: A 1841 ASP cc_start: 0.6963 (t0) cc_final: 0.6539 (t0) REVERT: A 2143 GLN cc_start: 0.5364 (OUTLIER) cc_final: 0.3620 (pp30) REVERT: A 2259 PHE cc_start: 0.1485 (OUTLIER) cc_final: 0.0619 (t80) REVERT: A 2272 MET cc_start: 0.2309 (ttm) cc_final: 0.1872 (ttm) outliers start: 176 outliers final: 93 residues processed: 301 average time/residue: 0.1226 time to fit residues: 58.9211 Evaluate side-chains 206 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 103 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 396 CYS Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 554 GLN Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 819 LYS Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 824 GLU Chi-restraints excluded: chain A residue 834 GLU Chi-restraints excluded: chain A residue 858 ASN Chi-restraints excluded: chain A residue 860 PHE Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 881 GLU Chi-restraints excluded: chain A residue 883 HIS Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 908 GLU Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 955 HIS Chi-restraints excluded: chain A residue 964 PHE Chi-restraints excluded: chain A residue 983 SER Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 997 THR Chi-restraints excluded: chain A residue 1014 THR Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1058 ARG Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1104 ILE Chi-restraints excluded: chain A residue 1109 ASN Chi-restraints excluded: chain A residue 1139 LEU Chi-restraints excluded: chain A residue 1152 VAL Chi-restraints excluded: chain A residue 1252 LEU Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1276 ILE Chi-restraints excluded: chain A residue 1348 ASP Chi-restraints excluded: chain A residue 1352 VAL Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1409 ILE Chi-restraints excluded: chain A residue 1410 LEU Chi-restraints excluded: chain A residue 1411 GLU Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1426 TYR Chi-restraints excluded: chain A residue 1458 GLN Chi-restraints excluded: chain A residue 1460 ASN Chi-restraints excluded: chain A residue 1480 THR Chi-restraints excluded: chain A residue 1482 GLU Chi-restraints excluded: chain A residue 1507 PHE Chi-restraints excluded: chain A residue 1526 ILE Chi-restraints excluded: chain A residue 1532 TYR Chi-restraints excluded: chain A residue 1545 ILE Chi-restraints excluded: chain A residue 1550 THR Chi-restraints excluded: chain A residue 1558 LEU Chi-restraints excluded: chain A residue 1560 GLU Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1596 ILE Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 1616 THR Chi-restraints excluded: chain A residue 1639 PHE Chi-restraints excluded: chain A residue 1652 ASN Chi-restraints excluded: chain A residue 1662 TYR Chi-restraints excluded: chain A residue 1665 ASP Chi-restraints excluded: chain A residue 1670 ILE Chi-restraints excluded: chain A residue 1674 VAL Chi-restraints excluded: chain A residue 1706 THR Chi-restraints excluded: chain A residue 1739 ILE Chi-restraints excluded: chain A residue 1800 PHE Chi-restraints excluded: chain A residue 1826 ILE Chi-restraints excluded: chain A residue 1854 ILE Chi-restraints excluded: chain A residue 1876 SER Chi-restraints excluded: chain A residue 1975 ASP Chi-restraints excluded: chain A residue 2078 VAL Chi-restraints excluded: chain A residue 2094 ASN Chi-restraints excluded: chain A residue 2143 GLN Chi-restraints excluded: chain A residue 2154 GLU Chi-restraints excluded: chain A residue 2165 THR Chi-restraints excluded: chain A residue 2193 VAL Chi-restraints excluded: chain A residue 2195 VAL Chi-restraints excluded: chain A residue 2259 PHE Chi-restraints excluded: chain A residue 2359 ASP Chi-restraints excluded: chain A residue 2363 LEU Chi-restraints excluded: chain K residue 124 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 118 optimal weight: 7.9990 chunk 29 optimal weight: 0.0040 chunk 213 optimal weight: 7.9990 chunk 103 optimal weight: 20.0000 chunk 46 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 chunk 182 optimal weight: 0.5980 chunk 203 optimal weight: 20.0000 chunk 99 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 overall best weight: 1.0794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 ASN A 758 HIS A1160 ASN A1828 ASN A1935 ASN ** A1950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2308 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.210133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.174446 restraints weight = 46590.812| |-----------------------------------------------------------------------------| r_work (start): 0.4171 rms_B_bonded: 2.93 r_work: 0.3771 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3786 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3786 r_free = 0.3786 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3786 r_free = 0.3786 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3786 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19532 Z= 0.142 Angle : 0.642 8.587 26433 Z= 0.341 Chirality : 0.047 0.178 2914 Planarity : 0.004 0.063 3443 Dihedral : 9.864 82.857 2737 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.56 % Favored : 87.32 % Rotamer: Outliers : 7.59 % Allowed : 25.85 % Favored : 66.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.98 (0.15), residues: 2398 helix: -1.88 (0.20), residues: 575 sheet: -2.54 (0.26), residues: 350 loop : -3.15 (0.14), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1197 TYR 0.059 0.002 TYR A1463 PHE 0.018 0.001 PHE A1639 TRP 0.009 0.001 TRP A 102 HIS 0.004 0.001 HIS A 654 Details of bonding type rmsd covalent geometry : bond 0.00320 (19529) covalent geometry : angle 0.64141 (26427) SS BOND : bond 0.00124 ( 3) SS BOND : angle 1.12529 ( 6) hydrogen bonds : bond 0.04128 ( 447) hydrogen bonds : angle 5.91609 ( 1251) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 125 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 604 TYR cc_start: 0.7450 (m-80) cc_final: 0.7241 (m-80) REVERT: A 617 GLU cc_start: 0.6884 (mm-30) cc_final: 0.5736 (tt0) REVERT: A 860 PHE cc_start: 0.8430 (OUTLIER) cc_final: 0.7584 (m-10) REVERT: A 910 ILE cc_start: 0.6277 (mm) cc_final: 0.5967 (mt) REVERT: A 942 ASN cc_start: 0.5477 (OUTLIER) cc_final: 0.5006 (p0) REVERT: A 946 VAL cc_start: 0.3763 (OUTLIER) cc_final: 0.3525 (p) REVERT: A 1058 ARG cc_start: 0.3165 (OUTLIER) cc_final: 0.2184 (ptt90) REVERT: A 1157 ASP cc_start: 0.6674 (t0) cc_final: 0.6470 (t0) REVERT: A 1160 ASN cc_start: 0.6028 (OUTLIER) cc_final: 0.5799 (t0) REVERT: A 1225 ASN cc_start: 0.8526 (p0) cc_final: 0.8068 (m-40) REVERT: A 1343 ASP cc_start: 0.5523 (p0) cc_final: 0.5216 (p0) REVERT: A 1382 LYS cc_start: 0.4093 (OUTLIER) cc_final: 0.3853 (mptt) REVERT: A 1438 MET cc_start: 0.6734 (mtt) cc_final: 0.6495 (mtt) REVERT: A 1526 ILE cc_start: 0.6946 (OUTLIER) cc_final: 0.6729 (mm) REVERT: A 1532 TYR cc_start: 0.6875 (OUTLIER) cc_final: 0.5472 (t80) REVERT: A 1560 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6423 (tp30) REVERT: A 1568 LYS cc_start: 0.6432 (ttpp) cc_final: 0.6184 (ttmt) REVERT: A 1632 ILE cc_start: 0.6372 (OUTLIER) cc_final: 0.6143 (mt) REVERT: A 1656 MET cc_start: 0.6670 (ttm) cc_final: 0.6206 (ttm) REVERT: A 1708 VAL cc_start: 0.7874 (t) cc_final: 0.7622 (m) REVERT: A 1841 ASP cc_start: 0.6885 (t0) cc_final: 0.6571 (t0) REVERT: A 2143 GLN cc_start: 0.5288 (OUTLIER) cc_final: 0.3512 (pp30) REVERT: A 2212 TRP cc_start: 0.3815 (OUTLIER) cc_final: 0.3169 (t60) REVERT: A 2259 PHE cc_start: 0.1924 (OUTLIER) cc_final: 0.0961 (t80) REVERT: A 2272 MET cc_start: 0.2252 (ttm) cc_final: 0.1839 (ttm) outliers start: 159 outliers final: 104 residues processed: 275 average time/residue: 0.1216 time to fit residues: 54.0237 Evaluate side-chains 227 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 110 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 554 GLN Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 814 ILE Chi-restraints excluded: chain A residue 819 LYS Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 824 GLU Chi-restraints excluded: chain A residue 834 GLU Chi-restraints excluded: chain A residue 858 ASN Chi-restraints excluded: chain A residue 860 PHE Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 881 GLU Chi-restraints excluded: chain A residue 883 HIS Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 908 GLU Chi-restraints excluded: chain A residue 942 ASN Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 955 HIS Chi-restraints excluded: chain A residue 964 PHE Chi-restraints excluded: chain A residue 983 SER Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 997 THR Chi-restraints excluded: chain A residue 1014 THR Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1058 ARG Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1139 LEU Chi-restraints excluded: chain A residue 1160 ASN Chi-restraints excluded: chain A residue 1163 ILE Chi-restraints excluded: chain A residue 1209 VAL Chi-restraints excluded: chain A residue 1252 LEU Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1323 THR Chi-restraints excluded: chain A residue 1352 VAL Chi-restraints excluded: chain A residue 1353 VAL Chi-restraints excluded: chain A residue 1359 GLU Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1382 LYS Chi-restraints excluded: chain A residue 1409 ILE Chi-restraints excluded: chain A residue 1411 GLU Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1426 TYR Chi-restraints excluded: chain A residue 1458 GLN Chi-restraints excluded: chain A residue 1460 ASN Chi-restraints excluded: chain A residue 1480 THR Chi-restraints excluded: chain A residue 1526 ILE Chi-restraints excluded: chain A residue 1532 TYR Chi-restraints excluded: chain A residue 1543 PHE Chi-restraints excluded: chain A residue 1545 ILE Chi-restraints excluded: chain A residue 1550 THR Chi-restraints excluded: chain A residue 1551 ILE Chi-restraints excluded: chain A residue 1558 LEU Chi-restraints excluded: chain A residue 1560 GLU Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1596 ILE Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 1616 THR Chi-restraints excluded: chain A residue 1632 ILE Chi-restraints excluded: chain A residue 1652 ASN Chi-restraints excluded: chain A residue 1662 TYR Chi-restraints excluded: chain A residue 1665 ASP Chi-restraints excluded: chain A residue 1670 ILE Chi-restraints excluded: chain A residue 1706 THR Chi-restraints excluded: chain A residue 1714 THR Chi-restraints excluded: chain A residue 1739 ILE Chi-restraints excluded: chain A residue 1771 VAL Chi-restraints excluded: chain A residue 1800 PHE Chi-restraints excluded: chain A residue 1812 TYR Chi-restraints excluded: chain A residue 1826 ILE Chi-restraints excluded: chain A residue 1828 ASN Chi-restraints excluded: chain A residue 1831 MET Chi-restraints excluded: chain A residue 1854 ILE Chi-restraints excluded: chain A residue 1857 PHE Chi-restraints excluded: chain A residue 1876 SER Chi-restraints excluded: chain A residue 1975 ASP Chi-restraints excluded: chain A residue 1997 THR Chi-restraints excluded: chain A residue 2078 VAL Chi-restraints excluded: chain A residue 2094 ASN Chi-restraints excluded: chain A residue 2143 GLN Chi-restraints excluded: chain A residue 2154 GLU Chi-restraints excluded: chain A residue 2165 THR Chi-restraints excluded: chain A residue 2193 VAL Chi-restraints excluded: chain A residue 2195 VAL Chi-restraints excluded: chain A residue 2212 TRP Chi-restraints excluded: chain A residue 2259 PHE Chi-restraints excluded: chain A residue 2359 ASP Chi-restraints excluded: chain A residue 2363 LEU Chi-restraints excluded: chain K residue 124 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 184 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 175 optimal weight: 9.9990 chunk 157 optimal weight: 0.0010 chunk 77 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 187 optimal weight: 9.9990 chunk 231 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 chunk 51 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 overall best weight: 0.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 GLN A1460 ASN ** A1918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.211358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.180269 restraints weight = 35396.529| |-----------------------------------------------------------------------------| r_work (start): 0.4239 rms_B_bonded: 2.00 r_work: 0.3871 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3881 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3881 r_free = 0.3881 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3881 r_free = 0.3881 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3881 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19532 Z= 0.124 Angle : 0.610 8.292 26433 Z= 0.323 Chirality : 0.047 0.369 2914 Planarity : 0.004 0.057 3443 Dihedral : 9.090 86.941 2716 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.81 % Favored : 89.03 % Rotamer: Outliers : 7.45 % Allowed : 25.62 % Favored : 66.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.60 (0.16), residues: 2398 helix: -1.45 (0.21), residues: 574 sheet: -2.31 (0.26), residues: 369 loop : -2.95 (0.15), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1197 TYR 0.060 0.001 TYR A1463 PHE 0.016 0.001 PHE A 243 TRP 0.008 0.001 TRP A 102 HIS 0.003 0.001 HIS A1127 Details of bonding type rmsd covalent geometry : bond 0.00280 (19529) covalent geometry : angle 0.61028 (26427) SS BOND : bond 0.00201 ( 3) SS BOND : angle 0.97564 ( 6) hydrogen bonds : bond 0.03699 ( 447) hydrogen bonds : angle 5.57405 ( 1251) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 123 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7448 (mt) REVERT: A 411 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8618 (tp) REVERT: A 466 THR cc_start: 0.8862 (OUTLIER) cc_final: 0.8581 (m) REVERT: A 617 GLU cc_start: 0.6746 (mm-30) cc_final: 0.6084 (tt0) REVERT: A 784 LYS cc_start: 0.7463 (OUTLIER) cc_final: 0.7188 (ptmm) REVERT: A 860 PHE cc_start: 0.8410 (OUTLIER) cc_final: 0.7651 (m-10) REVERT: A 881 GLU cc_start: 0.5852 (OUTLIER) cc_final: 0.5021 (tt0) REVERT: A 942 ASN cc_start: 0.5632 (OUTLIER) cc_final: 0.5375 (p0) REVERT: A 1058 ARG cc_start: 0.3132 (OUTLIER) cc_final: 0.2088 (ptt90) REVERT: A 1109 ASN cc_start: 0.2325 (OUTLIER) cc_final: 0.1973 (t0) REVERT: A 1225 ASN cc_start: 0.8455 (p0) cc_final: 0.8058 (m-40) REVERT: A 1438 MET cc_start: 0.6456 (mtt) cc_final: 0.6149 (mtt) REVERT: A 1482 GLU cc_start: 0.4527 (OUTLIER) cc_final: 0.2644 (tm-30) REVERT: A 1526 ILE cc_start: 0.6892 (OUTLIER) cc_final: 0.6620 (mm) REVERT: A 1532 TYR cc_start: 0.6885 (OUTLIER) cc_final: 0.5650 (t80) REVERT: A 1632 ILE cc_start: 0.6144 (OUTLIER) cc_final: 0.5903 (mt) REVERT: A 1841 ASP cc_start: 0.6698 (t0) cc_final: 0.6382 (t0) REVERT: A 2143 GLN cc_start: 0.5205 (OUTLIER) cc_final: 0.3563 (pp30) REVERT: A 2212 TRP cc_start: 0.3905 (OUTLIER) cc_final: 0.3128 (t60) REVERT: A 2236 ILE cc_start: -0.1495 (OUTLIER) cc_final: -0.1759 (pt) REVERT: A 2259 PHE cc_start: 0.1877 (OUTLIER) cc_final: 0.0934 (t80) REVERT: A 2268 GLU cc_start: 0.2387 (OUTLIER) cc_final: 0.1675 (tm-30) REVERT: A 2272 MET cc_start: 0.2197 (ttm) cc_final: 0.1735 (ttm) REVERT: K 137 TYR cc_start: 0.4831 (t80) cc_final: 0.4556 (t80) outliers start: 156 outliers final: 95 residues processed: 268 average time/residue: 0.1227 time to fit residues: 53.2710 Evaluate side-chains 224 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 111 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 554 GLN Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 784 LYS Chi-restraints excluded: chain A residue 814 ILE Chi-restraints excluded: chain A residue 819 LYS Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 824 GLU Chi-restraints excluded: chain A residue 834 GLU Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 860 PHE Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 864 GLU Chi-restraints excluded: chain A residue 881 GLU Chi-restraints excluded: chain A residue 883 HIS Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 908 GLU Chi-restraints excluded: chain A residue 942 ASN Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 955 HIS Chi-restraints excluded: chain A residue 959 THR Chi-restraints excluded: chain A residue 964 PHE Chi-restraints excluded: chain A residue 983 SER Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 997 THR Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1014 THR Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1058 ARG Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1104 ILE Chi-restraints excluded: chain A residue 1109 ASN Chi-restraints excluded: chain A residue 1139 LEU Chi-restraints excluded: chain A residue 1152 VAL Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1252 LEU Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1323 THR Chi-restraints excluded: chain A residue 1352 VAL Chi-restraints excluded: chain A residue 1353 VAL Chi-restraints excluded: chain A residue 1359 GLU Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1426 TYR Chi-restraints excluded: chain A residue 1458 GLN Chi-restraints excluded: chain A residue 1460 ASN Chi-restraints excluded: chain A residue 1480 THR Chi-restraints excluded: chain A residue 1482 GLU Chi-restraints excluded: chain A residue 1526 ILE Chi-restraints excluded: chain A residue 1532 TYR Chi-restraints excluded: chain A residue 1543 PHE Chi-restraints excluded: chain A residue 1545 ILE Chi-restraints excluded: chain A residue 1550 THR Chi-restraints excluded: chain A residue 1558 LEU Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1566 ILE Chi-restraints excluded: chain A residue 1596 ILE Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 1616 THR Chi-restraints excluded: chain A residue 1624 PHE Chi-restraints excluded: chain A residue 1632 ILE Chi-restraints excluded: chain A residue 1662 TYR Chi-restraints excluded: chain A residue 1665 ASP Chi-restraints excluded: chain A residue 1670 ILE Chi-restraints excluded: chain A residue 1706 THR Chi-restraints excluded: chain A residue 1771 VAL Chi-restraints excluded: chain A residue 1780 LYS Chi-restraints excluded: chain A residue 1800 PHE Chi-restraints excluded: chain A residue 1831 MET Chi-restraints excluded: chain A residue 1854 ILE Chi-restraints excluded: chain A residue 1857 PHE Chi-restraints excluded: chain A residue 1997 THR Chi-restraints excluded: chain A residue 2094 ASN Chi-restraints excluded: chain A residue 2143 GLN Chi-restraints excluded: chain A residue 2154 GLU Chi-restraints excluded: chain A residue 2165 THR Chi-restraints excluded: chain A residue 2195 VAL Chi-restraints excluded: chain A residue 2202 PHE Chi-restraints excluded: chain A residue 2212 TRP Chi-restraints excluded: chain A residue 2236 ILE Chi-restraints excluded: chain A residue 2259 PHE Chi-restraints excluded: chain A residue 2268 GLU Chi-restraints excluded: chain A residue 2359 ASP Chi-restraints excluded: chain K residue 124 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 97 optimal weight: 0.7980 chunk 170 optimal weight: 6.9990 chunk 180 optimal weight: 2.9990 chunk 198 optimal weight: 30.0000 chunk 207 optimal weight: 6.9990 chunk 78 optimal weight: 0.1980 chunk 219 optimal weight: 0.2980 chunk 224 optimal weight: 8.9990 chunk 124 optimal weight: 9.9990 chunk 93 optimal weight: 0.0570 chunk 44 optimal weight: 1.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1059 GLN A1633 GLN ** A1918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.212437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.181067 restraints weight = 35550.934| |-----------------------------------------------------------------------------| r_work (start): 0.4250 rms_B_bonded: 2.07 r_work: 0.3889 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3894 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3894 r_free = 0.3894 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3894 r_free = 0.3894 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3894 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 19532 Z= 0.115 Angle : 0.595 8.284 26433 Z= 0.315 Chirality : 0.046 0.222 2914 Planarity : 0.004 0.054 3443 Dihedral : 8.466 89.844 2692 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.05 % Favored : 89.78 % Rotamer: Outliers : 7.35 % Allowed : 25.62 % Favored : 67.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.35 (0.16), residues: 2398 helix: -1.20 (0.21), residues: 578 sheet: -2.10 (0.26), residues: 368 loop : -2.83 (0.15), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1197 TYR 0.060 0.001 TYR A1463 PHE 0.016 0.001 PHE A 243 TRP 0.006 0.001 TRP A 102 HIS 0.003 0.001 HIS A1127 Details of bonding type rmsd covalent geometry : bond 0.00264 (19529) covalent geometry : angle 0.59478 (26427) SS BOND : bond 0.00196 ( 3) SS BOND : angle 0.83048 ( 6) hydrogen bonds : bond 0.03442 ( 447) hydrogen bonds : angle 5.34508 ( 1251) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 128 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 319 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7320 (mt-10) REVERT: A 411 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8612 (tp) REVERT: A 466 THR cc_start: 0.8835 (OUTLIER) cc_final: 0.8562 (m) REVERT: A 617 GLU cc_start: 0.6705 (mm-30) cc_final: 0.5906 (tt0) REVERT: A 784 LYS cc_start: 0.7477 (OUTLIER) cc_final: 0.7205 (ptmm) REVERT: A 860 PHE cc_start: 0.8417 (OUTLIER) cc_final: 0.7609 (m-10) REVERT: A 922 TYR cc_start: 0.7288 (t80) cc_final: 0.6944 (t80) REVERT: A 942 ASN cc_start: 0.5707 (OUTLIER) cc_final: 0.5386 (p0) REVERT: A 1058 ARG cc_start: 0.2999 (OUTLIER) cc_final: 0.2028 (ptt90) REVERT: A 1109 ASN cc_start: 0.2436 (OUTLIER) cc_final: 0.2151 (t0) REVERT: A 1225 ASN cc_start: 0.8342 (p0) cc_final: 0.7995 (m-40) REVERT: A 1333 MET cc_start: 0.5383 (ptp) cc_final: 0.4735 (ptp) REVERT: A 1337 ILE cc_start: 0.7394 (mp) cc_final: 0.6993 (mt) REVERT: A 1438 MET cc_start: 0.6234 (mtt) cc_final: 0.5962 (mtt) REVERT: A 1482 GLU cc_start: 0.4591 (OUTLIER) cc_final: 0.2556 (tm-30) REVERT: A 1526 ILE cc_start: 0.6627 (OUTLIER) cc_final: 0.6391 (mm) REVERT: A 1532 TYR cc_start: 0.6906 (OUTLIER) cc_final: 0.5805 (t80) REVERT: A 1632 ILE cc_start: 0.6234 (OUTLIER) cc_final: 0.5944 (mt) REVERT: A 1841 ASP cc_start: 0.6636 (t0) cc_final: 0.6343 (t0) REVERT: A 2143 GLN cc_start: 0.4826 (OUTLIER) cc_final: 0.3379 (pp30) REVERT: A 2236 ILE cc_start: -0.1660 (OUTLIER) cc_final: -0.1935 (pt) REVERT: A 2259 PHE cc_start: 0.1790 (OUTLIER) cc_final: 0.0898 (t80) REVERT: A 2268 GLU cc_start: 0.2588 (OUTLIER) cc_final: 0.1886 (tm-30) REVERT: A 2272 MET cc_start: 0.1837 (ttm) cc_final: 0.1386 (ttm) REVERT: A 2331 GLU cc_start: -0.1798 (OUTLIER) cc_final: -0.2375 (tm-30) REVERT: K 137 TYR cc_start: 0.4796 (t80) cc_final: 0.4580 (t80) outliers start: 154 outliers final: 101 residues processed: 269 average time/residue: 0.1186 time to fit residues: 51.9240 Evaluate side-chains 235 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 117 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 554 GLN Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 784 LYS Chi-restraints excluded: chain A residue 814 ILE Chi-restraints excluded: chain A residue 819 LYS Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 824 GLU Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 860 PHE Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 864 GLU Chi-restraints excluded: chain A residue 882 SER Chi-restraints excluded: chain A residue 883 HIS Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 908 GLU Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 942 ASN Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 955 HIS Chi-restraints excluded: chain A residue 959 THR Chi-restraints excluded: chain A residue 964 PHE Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 997 THR Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1058 ARG Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1104 ILE Chi-restraints excluded: chain A residue 1109 ASN Chi-restraints excluded: chain A residue 1139 LEU Chi-restraints excluded: chain A residue 1152 VAL Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1209 VAL Chi-restraints excluded: chain A residue 1252 LEU Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1285 ASP Chi-restraints excluded: chain A residue 1323 THR Chi-restraints excluded: chain A residue 1336 ASN Chi-restraints excluded: chain A residue 1339 LEU Chi-restraints excluded: chain A residue 1352 VAL Chi-restraints excluded: chain A residue 1353 VAL Chi-restraints excluded: chain A residue 1359 GLU Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1411 GLU Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1426 TYR Chi-restraints excluded: chain A residue 1458 GLN Chi-restraints excluded: chain A residue 1460 ASN Chi-restraints excluded: chain A residue 1480 THR Chi-restraints excluded: chain A residue 1482 GLU Chi-restraints excluded: chain A residue 1521 THR Chi-restraints excluded: chain A residue 1526 ILE Chi-restraints excluded: chain A residue 1532 TYR Chi-restraints excluded: chain A residue 1543 PHE Chi-restraints excluded: chain A residue 1545 ILE Chi-restraints excluded: chain A residue 1550 THR Chi-restraints excluded: chain A residue 1558 LEU Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1566 ILE Chi-restraints excluded: chain A residue 1596 ILE Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 1616 THR Chi-restraints excluded: chain A residue 1632 ILE Chi-restraints excluded: chain A residue 1662 TYR Chi-restraints excluded: chain A residue 1670 ILE Chi-restraints excluded: chain A residue 1706 THR Chi-restraints excluded: chain A residue 1718 VAL Chi-restraints excluded: chain A residue 1771 VAL Chi-restraints excluded: chain A residue 1780 LYS Chi-restraints excluded: chain A residue 1800 PHE Chi-restraints excluded: chain A residue 1817 ILE Chi-restraints excluded: chain A residue 1831 MET Chi-restraints excluded: chain A residue 1837 VAL Chi-restraints excluded: chain A residue 1854 ILE Chi-restraints excluded: chain A residue 1857 PHE Chi-restraints excluded: chain A residue 1879 GLU Chi-restraints excluded: chain A residue 1880 THR Chi-restraints excluded: chain A residue 1975 ASP Chi-restraints excluded: chain A residue 1997 THR Chi-restraints excluded: chain A residue 2094 ASN Chi-restraints excluded: chain A residue 2143 GLN Chi-restraints excluded: chain A residue 2193 VAL Chi-restraints excluded: chain A residue 2195 VAL Chi-restraints excluded: chain A residue 2202 PHE Chi-restraints excluded: chain A residue 2236 ILE Chi-restraints excluded: chain A residue 2259 PHE Chi-restraints excluded: chain A residue 2268 GLU Chi-restraints excluded: chain A residue 2331 GLU Chi-restraints excluded: chain A residue 2359 ASP Chi-restraints excluded: chain A residue 2363 LEU Chi-restraints excluded: chain K residue 124 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 205 optimal weight: 30.0000 chunk 19 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 158 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 174 optimal weight: 3.9990 chunk 33 optimal weight: 0.2980 chunk 181 optimal weight: 3.9990 chunk 170 optimal weight: 6.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN A 421 GLN ** A1918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.211325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.180383 restraints weight = 35989.754| |-----------------------------------------------------------------------------| r_work (start): 0.4246 rms_B_bonded: 1.97 r_work: 0.3909 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3897 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3897 r_free = 0.3897 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3897 r_free = 0.3897 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3897 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19532 Z= 0.139 Angle : 0.612 10.620 26433 Z= 0.322 Chirality : 0.047 0.226 2914 Planarity : 0.004 0.055 3443 Dihedral : 7.801 68.911 2675 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.93 % Favored : 88.90 % Rotamer: Outliers : 7.50 % Allowed : 25.62 % Favored : 66.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.22 (0.16), residues: 2398 helix: -1.12 (0.21), residues: 583 sheet: -2.02 (0.26), residues: 369 loop : -2.74 (0.15), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1197 TYR 0.056 0.001 TYR A1463 PHE 0.025 0.001 PHE A 243 TRP 0.009 0.001 TRP A 102 HIS 0.003 0.001 HIS A1127 Details of bonding type rmsd covalent geometry : bond 0.00321 (19529) covalent geometry : angle 0.61217 (26427) SS BOND : bond 0.00167 ( 3) SS BOND : angle 0.74054 ( 6) hydrogen bonds : bond 0.03622 ( 447) hydrogen bonds : angle 5.34097 ( 1251) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 122 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 288 ASP cc_start: 0.8054 (OUTLIER) cc_final: 0.7804 (p0) REVERT: A 411 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8624 (tp) REVERT: A 466 THR cc_start: 0.8905 (OUTLIER) cc_final: 0.8618 (m) REVERT: A 617 GLU cc_start: 0.6780 (mm-30) cc_final: 0.5936 (tt0) REVERT: A 742 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.7914 (mt0) REVERT: A 784 LYS cc_start: 0.7439 (OUTLIER) cc_final: 0.7236 (ptmm) REVERT: A 860 PHE cc_start: 0.8477 (OUTLIER) cc_final: 0.7637 (m-10) REVERT: A 1058 ARG cc_start: 0.2901 (OUTLIER) cc_final: 0.1992 (ptt90) REVERT: A 1109 ASN cc_start: 0.2327 (OUTLIER) cc_final: 0.1964 (t0) REVERT: A 1333 MET cc_start: 0.5386 (ptp) cc_final: 0.4814 (ptp) REVERT: A 1438 MET cc_start: 0.5845 (mtt) cc_final: 0.5568 (mtt) REVERT: A 1522 LYS cc_start: 0.4094 (OUTLIER) cc_final: 0.3661 (mmmt) REVERT: A 1526 ILE cc_start: 0.6828 (OUTLIER) cc_final: 0.6569 (mm) REVERT: A 1532 TYR cc_start: 0.6729 (OUTLIER) cc_final: 0.5422 (t80) REVERT: A 1841 ASP cc_start: 0.6557 (t0) cc_final: 0.6229 (t0) REVERT: A 2212 TRP cc_start: 0.3647 (OUTLIER) cc_final: 0.2483 (t60) REVERT: A 2236 ILE cc_start: -0.1736 (OUTLIER) cc_final: -0.1986 (pt) REVERT: A 2259 PHE cc_start: 0.1766 (OUTLIER) cc_final: 0.0949 (t80) REVERT: A 2268 GLU cc_start: 0.2471 (OUTLIER) cc_final: 0.2114 (tp30) REVERT: A 2272 MET cc_start: 0.1671 (ttm) cc_final: 0.1250 (ttm) REVERT: A 2331 GLU cc_start: -0.1782 (OUTLIER) cc_final: -0.2366 (tm-30) REVERT: K 137 TYR cc_start: 0.4818 (t80) cc_final: 0.4586 (t80) outliers start: 157 outliers final: 105 residues processed: 266 average time/residue: 0.1211 time to fit residues: 52.4354 Evaluate side-chains 236 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 115 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 554 GLN Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 742 GLN Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 784 LYS Chi-restraints excluded: chain A residue 814 ILE Chi-restraints excluded: chain A residue 819 LYS Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 824 GLU Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 858 ASN Chi-restraints excluded: chain A residue 860 PHE Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 864 GLU Chi-restraints excluded: chain A residue 882 SER Chi-restraints excluded: chain A residue 883 HIS Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 955 HIS Chi-restraints excluded: chain A residue 959 THR Chi-restraints excluded: chain A residue 964 PHE Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 997 THR Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1058 ARG Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1104 ILE Chi-restraints excluded: chain A residue 1109 ASN Chi-restraints excluded: chain A residue 1139 LEU Chi-restraints excluded: chain A residue 1152 VAL Chi-restraints excluded: chain A residue 1163 ILE Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1209 VAL Chi-restraints excluded: chain A residue 1252 LEU Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1285 ASP Chi-restraints excluded: chain A residue 1323 THR Chi-restraints excluded: chain A residue 1339 LEU Chi-restraints excluded: chain A residue 1352 VAL Chi-restraints excluded: chain A residue 1353 VAL Chi-restraints excluded: chain A residue 1359 GLU Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1411 GLU Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1426 TYR Chi-restraints excluded: chain A residue 1429 LEU Chi-restraints excluded: chain A residue 1458 GLN Chi-restraints excluded: chain A residue 1460 ASN Chi-restraints excluded: chain A residue 1480 THR Chi-restraints excluded: chain A residue 1521 THR Chi-restraints excluded: chain A residue 1522 LYS Chi-restraints excluded: chain A residue 1526 ILE Chi-restraints excluded: chain A residue 1532 TYR Chi-restraints excluded: chain A residue 1543 PHE Chi-restraints excluded: chain A residue 1545 ILE Chi-restraints excluded: chain A residue 1550 THR Chi-restraints excluded: chain A residue 1558 LEU Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1566 ILE Chi-restraints excluded: chain A residue 1596 ILE Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 1616 THR Chi-restraints excluded: chain A residue 1617 THR Chi-restraints excluded: chain A residue 1662 TYR Chi-restraints excluded: chain A residue 1670 ILE Chi-restraints excluded: chain A residue 1706 THR Chi-restraints excluded: chain A residue 1714 THR Chi-restraints excluded: chain A residue 1718 VAL Chi-restraints excluded: chain A residue 1771 VAL Chi-restraints excluded: chain A residue 1794 ASN Chi-restraints excluded: chain A residue 1800 PHE Chi-restraints excluded: chain A residue 1817 ILE Chi-restraints excluded: chain A residue 1826 ILE Chi-restraints excluded: chain A residue 1831 MET Chi-restraints excluded: chain A residue 1837 VAL Chi-restraints excluded: chain A residue 1854 ILE Chi-restraints excluded: chain A residue 1880 THR Chi-restraints excluded: chain A residue 2078 VAL Chi-restraints excluded: chain A residue 2094 ASN Chi-restraints excluded: chain A residue 2193 VAL Chi-restraints excluded: chain A residue 2195 VAL Chi-restraints excluded: chain A residue 2202 PHE Chi-restraints excluded: chain A residue 2212 TRP Chi-restraints excluded: chain A residue 2236 ILE Chi-restraints excluded: chain A residue 2259 PHE Chi-restraints excluded: chain A residue 2268 GLU Chi-restraints excluded: chain A residue 2331 GLU Chi-restraints excluded: chain A residue 2359 ASP Chi-restraints excluded: chain A residue 2363 LEU Chi-restraints excluded: chain K residue 124 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 39 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 200 optimal weight: 5.9990 chunk 103 optimal weight: 20.0000 chunk 117 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 19 optimal weight: 0.0670 chunk 126 optimal weight: 0.9990 chunk 115 optimal weight: 0.0070 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2049 ASN A2181 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.213700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.182672 restraints weight = 36130.195| |-----------------------------------------------------------------------------| r_work (start): 0.4255 rms_B_bonded: 2.01 r_work: 0.3881 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3731 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3711 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3711 r_free = 0.3711 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3711 r_free = 0.3711 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3711 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19532 Z= 0.116 Angle : 0.590 9.961 26433 Z= 0.310 Chirality : 0.046 0.213 2914 Planarity : 0.003 0.053 3443 Dihedral : 7.447 65.914 2668 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.05 % Favored : 89.78 % Rotamer: Outliers : 6.74 % Allowed : 26.57 % Favored : 66.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.03 (0.16), residues: 2398 helix: -0.88 (0.22), residues: 581 sheet: -1.92 (0.26), residues: 376 loop : -2.64 (0.15), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1197 TYR 0.065 0.001 TYR A1463 PHE 0.020 0.001 PHE A 243 TRP 0.007 0.001 TRP A 118 HIS 0.003 0.001 HIS A1127 Details of bonding type rmsd covalent geometry : bond 0.00262 (19529) covalent geometry : angle 0.59041 (26427) SS BOND : bond 0.00189 ( 3) SS BOND : angle 0.67207 ( 6) hydrogen bonds : bond 0.03339 ( 447) hydrogen bonds : angle 5.19406 ( 1251) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 120 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8661 (tp) REVERT: A 466 THR cc_start: 0.8939 (OUTLIER) cc_final: 0.8662 (m) REVERT: A 617 GLU cc_start: 0.6972 (mm-30) cc_final: 0.6112 (tt0) REVERT: A 742 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.7855 (mt0) REVERT: A 860 PHE cc_start: 0.8521 (OUTLIER) cc_final: 0.7914 (m-80) REVERT: A 1058 ARG cc_start: 0.3249 (OUTLIER) cc_final: 0.2224 (ptt90) REVERT: A 1109 ASN cc_start: 0.2643 (OUTLIER) cc_final: 0.2292 (t0) REVERT: A 1145 MET cc_start: 0.6061 (ttt) cc_final: 0.5286 (ptp) REVERT: A 1146 MET cc_start: 0.7210 (mpp) cc_final: 0.6743 (mpp) REVERT: A 1318 TYR cc_start: 0.6493 (t80) cc_final: 0.6226 (t80) REVERT: A 1333 MET cc_start: 0.5578 (ptp) cc_final: 0.5024 (ptp) REVERT: A 1337 ILE cc_start: 0.7395 (mp) cc_final: 0.6973 (mt) REVERT: A 1438 MET cc_start: 0.5858 (mtt) cc_final: 0.5642 (mtt) REVERT: A 1522 LYS cc_start: 0.4035 (OUTLIER) cc_final: 0.3582 (mmmt) REVERT: A 1532 TYR cc_start: 0.6722 (OUTLIER) cc_final: 0.5797 (t80) REVERT: A 1841 ASP cc_start: 0.6962 (t0) cc_final: 0.6647 (t0) REVERT: A 2143 GLN cc_start: 0.4922 (OUTLIER) cc_final: 0.3170 (pp30) REVERT: A 2212 TRP cc_start: 0.3093 (OUTLIER) cc_final: 0.2170 (t60) REVERT: A 2252 MET cc_start: -0.0819 (mtp) cc_final: -0.2192 (ppp) REVERT: A 2259 PHE cc_start: 0.1433 (OUTLIER) cc_final: 0.0862 (t80) REVERT: A 2268 GLU cc_start: 0.2125 (OUTLIER) cc_final: 0.1841 (tp30) REVERT: A 2272 MET cc_start: 0.1416 (ttm) cc_final: 0.1003 (ttm) REVERT: A 2331 GLU cc_start: -0.1484 (OUTLIER) cc_final: -0.2040 (tm-30) REVERT: K 137 TYR cc_start: 0.5036 (t80) cc_final: 0.4812 (t80) outliers start: 141 outliers final: 101 residues processed: 249 average time/residue: 0.1156 time to fit residues: 46.8331 Evaluate side-chains 232 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 118 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 742 GLN Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 814 ILE Chi-restraints excluded: chain A residue 819 LYS Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 824 GLU Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 860 PHE Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 864 GLU Chi-restraints excluded: chain A residue 883 HIS Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 913 GLU Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 955 HIS Chi-restraints excluded: chain A residue 959 THR Chi-restraints excluded: chain A residue 964 PHE Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 997 THR Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1058 ARG Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1104 ILE Chi-restraints excluded: chain A residue 1109 ASN Chi-restraints excluded: chain A residue 1139 LEU Chi-restraints excluded: chain A residue 1152 VAL Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1209 VAL Chi-restraints excluded: chain A residue 1252 LEU Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1285 ASP Chi-restraints excluded: chain A residue 1339 LEU Chi-restraints excluded: chain A residue 1352 VAL Chi-restraints excluded: chain A residue 1353 VAL Chi-restraints excluded: chain A residue 1359 GLU Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1411 GLU Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1426 TYR Chi-restraints excluded: chain A residue 1429 LEU Chi-restraints excluded: chain A residue 1460 ASN Chi-restraints excluded: chain A residue 1480 THR Chi-restraints excluded: chain A residue 1521 THR Chi-restraints excluded: chain A residue 1522 LYS Chi-restraints excluded: chain A residue 1532 TYR Chi-restraints excluded: chain A residue 1543 PHE Chi-restraints excluded: chain A residue 1545 ILE Chi-restraints excluded: chain A residue 1550 THR Chi-restraints excluded: chain A residue 1558 LEU Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1566 ILE Chi-restraints excluded: chain A residue 1596 ILE Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 1616 THR Chi-restraints excluded: chain A residue 1617 THR Chi-restraints excluded: chain A residue 1662 TYR Chi-restraints excluded: chain A residue 1706 THR Chi-restraints excluded: chain A residue 1714 THR Chi-restraints excluded: chain A residue 1718 VAL Chi-restraints excluded: chain A residue 1753 MET Chi-restraints excluded: chain A residue 1771 VAL Chi-restraints excluded: chain A residue 1800 PHE Chi-restraints excluded: chain A residue 1806 VAL Chi-restraints excluded: chain A residue 1817 ILE Chi-restraints excluded: chain A residue 1826 ILE Chi-restraints excluded: chain A residue 1831 MET Chi-restraints excluded: chain A residue 1837 VAL Chi-restraints excluded: chain A residue 1854 ILE Chi-restraints excluded: chain A residue 1880 THR Chi-restraints excluded: chain A residue 1975 ASP Chi-restraints excluded: chain A residue 2078 VAL Chi-restraints excluded: chain A residue 2094 ASN Chi-restraints excluded: chain A residue 2140 SER Chi-restraints excluded: chain A residue 2142 MET Chi-restraints excluded: chain A residue 2143 GLN Chi-restraints excluded: chain A residue 2181 ASN Chi-restraints excluded: chain A residue 2193 VAL Chi-restraints excluded: chain A residue 2195 VAL Chi-restraints excluded: chain A residue 2202 PHE Chi-restraints excluded: chain A residue 2212 TRP Chi-restraints excluded: chain A residue 2259 PHE Chi-restraints excluded: chain A residue 2268 GLU Chi-restraints excluded: chain A residue 2331 GLU Chi-restraints excluded: chain A residue 2359 ASP Chi-restraints excluded: chain K residue 124 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 134 optimal weight: 0.3980 chunk 20 optimal weight: 0.9990 chunk 101 optimal weight: 8.9990 chunk 148 optimal weight: 3.9990 chunk 198 optimal weight: 20.0000 chunk 139 optimal weight: 3.9990 chunk 126 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 chunk 165 optimal weight: 0.6980 chunk 170 optimal weight: 6.9990 chunk 208 optimal weight: 0.0770 overall best weight: 0.6342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 HIS A1458 GLN A1610 ASN ** A1918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2181 ASN ** 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 = 0.4606 r_free = 0.4606 target = 0.213457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.183119 restraints weight = 32755.323| |-----------------------------------------------------------------------------| r_work (start): 0.4270 rms_B_bonded: 1.88 r_work: 0.3907 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3756 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3744 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3744 r_free = 0.3744 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3744 r_free = 0.3744 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3744 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 19532 Z= 0.111 Angle : 0.581 9.723 26433 Z= 0.306 Chirality : 0.046 0.204 2914 Planarity : 0.003 0.052 3443 Dihedral : 6.926 59.468 2662 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.89 % Favored : 89.95 % Rotamer: Outliers : 6.02 % Allowed : 27.13 % Favored : 66.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.86 (0.16), residues: 2398 helix: -0.68 (0.22), residues: 580 sheet: -1.78 (0.26), residues: 373 loop : -2.57 (0.15), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1197 TYR 0.068 0.001 TYR A1463 PHE 0.017 0.001 PHE A 243 TRP 0.011 0.001 TRP A1345 HIS 0.002 0.001 HIS A1127 Details of bonding type rmsd covalent geometry : bond 0.00245 (19529) covalent geometry : angle 0.58127 (26427) SS BOND : bond 0.00197 ( 3) SS BOND : angle 0.64751 ( 6) hydrogen bonds : bond 0.03238 ( 447) hydrogen bonds : angle 5.06625 ( 1251) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 125 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8379 (pt) REVERT: A 411 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8660 (tp) REVERT: A 466 THR cc_start: 0.8896 (OUTLIER) cc_final: 0.8654 (m) REVERT: A 617 GLU cc_start: 0.7072 (mm-30) cc_final: 0.6290 (tt0) REVERT: A 742 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.7900 (mt0) REVERT: A 870 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8071 (mp) REVERT: A 922 TYR cc_start: 0.7509 (t80) cc_final: 0.6765 (t80) REVERT: A 1058 ARG cc_start: 0.3303 (OUTLIER) cc_final: 0.2235 (ptt90) REVERT: A 1109 ASN cc_start: 0.2597 (OUTLIER) cc_final: 0.2287 (t0) REVERT: A 1145 MET cc_start: 0.6056 (ttt) cc_final: 0.5144 (ptp) REVERT: A 1146 MET cc_start: 0.7151 (mpp) cc_final: 0.6663 (mpp) REVERT: A 1333 MET cc_start: 0.5501 (ptp) cc_final: 0.4993 (ptp) REVERT: A 1337 ILE cc_start: 0.7267 (mp) cc_final: 0.6916 (mt) REVERT: A 1438 MET cc_start: 0.5540 (mtt) cc_final: 0.5334 (mtt) REVERT: A 1532 TYR cc_start: 0.6659 (OUTLIER) cc_final: 0.5935 (t80) REVERT: A 1841 ASP cc_start: 0.6893 (t0) cc_final: 0.6571 (t0) REVERT: A 2212 TRP cc_start: 0.2875 (OUTLIER) cc_final: 0.1965 (t60) REVERT: A 2252 MET cc_start: -0.0959 (mtp) cc_final: -0.2257 (ppp) REVERT: A 2259 PHE cc_start: 0.1376 (OUTLIER) cc_final: 0.0838 (t80) REVERT: A 2272 MET cc_start: 0.1299 (ttm) cc_final: 0.0957 (ttm) REVERT: A 2331 GLU cc_start: -0.1283 (OUTLIER) cc_final: -0.1814 (tm-30) REVERT: K 137 TYR cc_start: 0.4929 (t80) cc_final: 0.4705 (t80) outliers start: 126 outliers final: 95 residues processed: 239 average time/residue: 0.1171 time to fit residues: 45.9438 Evaluate side-chains 226 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 120 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 742 GLN Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 814 ILE Chi-restraints excluded: chain A residue 819 LYS Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 864 GLU Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 883 HIS Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 913 GLU Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 955 HIS Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 997 THR Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1058 ARG Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1104 ILE Chi-restraints excluded: chain A residue 1109 ASN Chi-restraints excluded: chain A residue 1152 VAL Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1209 VAL Chi-restraints excluded: chain A residue 1252 LEU Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1285 ASP Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1339 LEU Chi-restraints excluded: chain A residue 1352 VAL Chi-restraints excluded: chain A residue 1353 VAL Chi-restraints excluded: chain A residue 1359 GLU Chi-restraints excluded: chain A residue 1411 GLU Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1426 TYR Chi-restraints excluded: chain A residue 1429 LEU Chi-restraints excluded: chain A residue 1460 ASN Chi-restraints excluded: chain A residue 1480 THR Chi-restraints excluded: chain A residue 1521 THR Chi-restraints excluded: chain A residue 1532 TYR Chi-restraints excluded: chain A residue 1543 PHE Chi-restraints excluded: chain A residue 1545 ILE Chi-restraints excluded: chain A residue 1550 THR Chi-restraints excluded: chain A residue 1558 LEU Chi-restraints excluded: chain A residue 1566 ILE Chi-restraints excluded: chain A residue 1596 ILE Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 1616 THR Chi-restraints excluded: chain A residue 1617 THR Chi-restraints excluded: chain A residue 1662 TYR Chi-restraints excluded: chain A residue 1670 ILE Chi-restraints excluded: chain A residue 1706 THR Chi-restraints excluded: chain A residue 1714 THR Chi-restraints excluded: chain A residue 1718 VAL Chi-restraints excluded: chain A residue 1753 MET Chi-restraints excluded: chain A residue 1771 VAL Chi-restraints excluded: chain A residue 1800 PHE Chi-restraints excluded: chain A residue 1806 VAL Chi-restraints excluded: chain A residue 1817 ILE Chi-restraints excluded: chain A residue 1826 ILE Chi-restraints excluded: chain A residue 1831 MET Chi-restraints excluded: chain A residue 1854 ILE Chi-restraints excluded: chain A residue 1879 GLU Chi-restraints excluded: chain A residue 1880 THR Chi-restraints excluded: chain A residue 1975 ASP Chi-restraints excluded: chain A residue 2078 VAL Chi-restraints excluded: chain A residue 2094 ASN Chi-restraints excluded: chain A residue 2140 SER Chi-restraints excluded: chain A residue 2142 MET Chi-restraints excluded: chain A residue 2193 VAL Chi-restraints excluded: chain A residue 2195 VAL Chi-restraints excluded: chain A residue 2202 PHE Chi-restraints excluded: chain A residue 2212 TRP Chi-restraints excluded: chain A residue 2259 PHE Chi-restraints excluded: chain A residue 2331 GLU Chi-restraints excluded: chain A residue 2359 ASP Chi-restraints excluded: chain K residue 124 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 62 optimal weight: 0.0970 chunk 223 optimal weight: 5.9990 chunk 165 optimal weight: 0.4980 chunk 69 optimal weight: 0.9990 chunk 121 optimal weight: 10.0000 chunk 118 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 200 optimal weight: 9.9990 chunk 167 optimal weight: 0.8980 chunk 152 optimal weight: 4.9990 chunk 150 optimal weight: 0.9980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 HIS ** A1918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2315 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.213414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.181410 restraints weight = 46384.635| |-----------------------------------------------------------------------------| r_work (start): 0.4265 rms_B_bonded: 2.91 r_work: 0.3834 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3843 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3843 r_free = 0.3843 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3843 r_free = 0.3843 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3843 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19532 Z= 0.111 Angle : 0.573 8.967 26433 Z= 0.302 Chirality : 0.046 0.204 2914 Planarity : 0.003 0.050 3443 Dihedral : 6.519 59.015 2651 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.80 % Favored : 90.03 % Rotamer: Outliers : 5.41 % Allowed : 28.08 % Favored : 66.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.69 (0.16), residues: 2398 helix: -0.53 (0.22), residues: 581 sheet: -1.61 (0.27), residues: 363 loop : -2.49 (0.15), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 576 TYR 0.059 0.001 TYR A1463 PHE 0.017 0.001 PHE A 243 TRP 0.009 0.001 TRP A1345 HIS 0.002 0.001 HIS A1127 Details of bonding type rmsd covalent geometry : bond 0.00249 (19529) covalent geometry : angle 0.57279 (26427) SS BOND : bond 0.00207 ( 3) SS BOND : angle 0.61474 ( 6) hydrogen bonds : bond 0.03196 ( 447) hydrogen bonds : angle 5.01978 ( 1251) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 121 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 411 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8645 (tp) REVERT: A 466 THR cc_start: 0.8888 (OUTLIER) cc_final: 0.8637 (m) REVERT: A 617 GLU cc_start: 0.7002 (mm-30) cc_final: 0.6259 (tt0) REVERT: A 672 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8302 (tm) REVERT: A 725 SER cc_start: 0.7576 (t) cc_final: 0.7209 (p) REVERT: A 860 PHE cc_start: 0.8482 (OUTLIER) cc_final: 0.7939 (m-80) REVERT: A 870 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8105 (mp) REVERT: A 922 TYR cc_start: 0.7530 (t80) cc_final: 0.6834 (t80) REVERT: A 1104 ILE cc_start: 0.1498 (OUTLIER) cc_final: 0.0715 (pt) REVERT: A 1109 ASN cc_start: 0.2800 (OUTLIER) cc_final: 0.2450 (t0) REVERT: A 1145 MET cc_start: 0.5970 (ttt) cc_final: 0.5126 (ptp) REVERT: A 1146 MET cc_start: 0.7028 (mpp) cc_final: 0.6525 (mpp) REVERT: A 1333 MET cc_start: 0.5312 (ptp) cc_final: 0.4791 (ptp) REVERT: A 1337 ILE cc_start: 0.7337 (mp) cc_final: 0.6935 (mt) REVERT: A 1438 MET cc_start: 0.5415 (mtt) cc_final: 0.5189 (mtt) REVERT: A 1522 LYS cc_start: 0.3898 (OUTLIER) cc_final: 0.3479 (mmmt) REVERT: A 1532 TYR cc_start: 0.6608 (OUTLIER) cc_final: 0.6145 (t80) REVERT: A 1841 ASP cc_start: 0.6803 (t0) cc_final: 0.6500 (t0) REVERT: A 2143 GLN cc_start: 0.4717 (OUTLIER) cc_final: 0.3337 (pp30) REVERT: A 2212 TRP cc_start: 0.3209 (OUTLIER) cc_final: 0.2034 (t60) REVERT: A 2252 MET cc_start: -0.0987 (mtp) cc_final: -0.2429 (ppp) REVERT: A 2259 PHE cc_start: 0.1257 (OUTLIER) cc_final: 0.0613 (t80) REVERT: A 2272 MET cc_start: 0.1453 (ttm) cc_final: 0.0954 (ttm) REVERT: A 2331 GLU cc_start: -0.0938 (OUTLIER) cc_final: -0.1645 (tm-30) REVERT: K 137 TYR cc_start: 0.4771 (t80) cc_final: 0.4567 (t80) outliers start: 113 outliers final: 84 residues processed: 222 average time/residue: 0.1116 time to fit residues: 40.7117 Evaluate side-chains 209 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 112 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 814 ILE Chi-restraints excluded: chain A residue 819 LYS Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 858 ASN Chi-restraints excluded: chain A residue 860 PHE Chi-restraints excluded: chain A residue 864 GLU Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 883 HIS Chi-restraints excluded: chain A residue 913 GLU Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 955 HIS Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 997 THR Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1104 ILE Chi-restraints excluded: chain A residue 1109 ASN Chi-restraints excluded: chain A residue 1152 VAL Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1209 VAL Chi-restraints excluded: chain A residue 1252 LEU Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1285 ASP Chi-restraints excluded: chain A residue 1352 VAL Chi-restraints excluded: chain A residue 1353 VAL Chi-restraints excluded: chain A residue 1411 GLU Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1426 TYR Chi-restraints excluded: chain A residue 1429 LEU Chi-restraints excluded: chain A residue 1460 ASN Chi-restraints excluded: chain A residue 1480 THR Chi-restraints excluded: chain A residue 1521 THR Chi-restraints excluded: chain A residue 1522 LYS Chi-restraints excluded: chain A residue 1532 TYR Chi-restraints excluded: chain A residue 1543 PHE Chi-restraints excluded: chain A residue 1545 ILE Chi-restraints excluded: chain A residue 1550 THR Chi-restraints excluded: chain A residue 1558 LEU Chi-restraints excluded: chain A residue 1566 ILE Chi-restraints excluded: chain A residue 1596 ILE Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 1617 THR Chi-restraints excluded: chain A residue 1662 TYR Chi-restraints excluded: chain A residue 1706 THR Chi-restraints excluded: chain A residue 1714 THR Chi-restraints excluded: chain A residue 1718 VAL Chi-restraints excluded: chain A residue 1753 MET Chi-restraints excluded: chain A residue 1771 VAL Chi-restraints excluded: chain A residue 1800 PHE Chi-restraints excluded: chain A residue 1806 VAL Chi-restraints excluded: chain A residue 1817 ILE Chi-restraints excluded: chain A residue 1854 ILE Chi-restraints excluded: chain A residue 1879 GLU Chi-restraints excluded: chain A residue 1880 THR Chi-restraints excluded: chain A residue 1975 ASP Chi-restraints excluded: chain A residue 2078 VAL Chi-restraints excluded: chain A residue 2094 ASN Chi-restraints excluded: chain A residue 2142 MET Chi-restraints excluded: chain A residue 2143 GLN Chi-restraints excluded: chain A residue 2193 VAL Chi-restraints excluded: chain A residue 2195 VAL Chi-restraints excluded: chain A residue 2202 PHE Chi-restraints excluded: chain A residue 2212 TRP Chi-restraints excluded: chain A residue 2259 PHE Chi-restraints excluded: chain A residue 2331 GLU Chi-restraints excluded: chain A residue 2359 ASP Chi-restraints excluded: chain K residue 124 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 121 optimal weight: 10.0000 chunk 235 optimal weight: 0.8980 chunk 164 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 233 optimal weight: 9.9990 chunk 145 optimal weight: 0.0770 chunk 108 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 157 optimal weight: 0.1980 chunk 79 optimal weight: 0.8980 chunk 89 optimal weight: 0.3980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 ASN ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1621 GLN ** A1918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2181 ASN A2315 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.215428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.184602 restraints weight = 46860.182| |-----------------------------------------------------------------------------| r_work (start): 0.4287 rms_B_bonded: 2.93 r_work: 0.3865 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3861 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3861 r_free = 0.3861 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3861 r_free = 0.3861 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3861 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 19532 Z= 0.103 Angle : 0.563 9.159 26433 Z= 0.296 Chirality : 0.045 0.195 2914 Planarity : 0.003 0.049 3443 Dihedral : 6.263 59.432 2643 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.55 % Favored : 90.28 % Rotamer: Outliers : 4.60 % Allowed : 28.94 % Favored : 66.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.16), residues: 2398 helix: -0.41 (0.22), residues: 584 sheet: -1.45 (0.27), residues: 356 loop : -2.44 (0.15), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1197 TYR 0.058 0.001 TYR A1463 PHE 0.017 0.001 PHE A2286 TRP 0.010 0.001 TRP A1345 HIS 0.004 0.001 HIS A 925 Details of bonding type rmsd covalent geometry : bond 0.00227 (19529) covalent geometry : angle 0.56255 (26427) SS BOND : bond 0.00200 ( 3) SS BOND : angle 0.64398 ( 6) hydrogen bonds : bond 0.03053 ( 447) hydrogen bonds : angle 4.93204 ( 1251) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 120 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8633 (tp) REVERT: A 466 THR cc_start: 0.8857 (OUTLIER) cc_final: 0.8615 (m) REVERT: A 508 ASN cc_start: 0.8216 (OUTLIER) cc_final: 0.7876 (m110) REVERT: A 617 GLU cc_start: 0.6982 (mm-30) cc_final: 0.6249 (tt0) REVERT: A 672 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8280 (tm) REVERT: A 860 PHE cc_start: 0.8437 (OUTLIER) cc_final: 0.7912 (m-80) REVERT: A 870 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8046 (mp) REVERT: A 922 TYR cc_start: 0.7416 (t80) cc_final: 0.6740 (t80) REVERT: A 948 LYS cc_start: 0.2653 (OUTLIER) cc_final: 0.2389 (tptm) REVERT: A 1104 ILE cc_start: 0.1676 (OUTLIER) cc_final: 0.0779 (pt) REVERT: A 1109 ASN cc_start: 0.3008 (OUTLIER) cc_final: 0.2675 (t0) REVERT: A 1145 MET cc_start: 0.5796 (ttt) cc_final: 0.4994 (ptp) REVERT: A 1146 MET cc_start: 0.7018 (mpp) cc_final: 0.6117 (mpp) REVERT: A 1333 MET cc_start: 0.5212 (ptp) cc_final: 0.4705 (ptp) REVERT: A 1337 ILE cc_start: 0.7340 (mp) cc_final: 0.6899 (mt) REVERT: A 1522 LYS cc_start: 0.3894 (OUTLIER) cc_final: 0.3488 (mmmt) REVERT: A 1550 THR cc_start: 0.6501 (OUTLIER) cc_final: 0.6235 (t) REVERT: A 1841 ASP cc_start: 0.6794 (t0) cc_final: 0.6489 (t0) REVERT: A 2143 GLN cc_start: 0.4663 (OUTLIER) cc_final: 0.3359 (pp30) REVERT: A 2212 TRP cc_start: 0.3027 (OUTLIER) cc_final: 0.1893 (t60) REVERT: A 2252 MET cc_start: -0.0966 (mtp) cc_final: -0.2479 (ppp) REVERT: A 2259 PHE cc_start: 0.1266 (OUTLIER) cc_final: 0.0627 (t80) REVERT: A 2331 GLU cc_start: -0.0700 (OUTLIER) cc_final: -0.1488 (tm-30) REVERT: K 137 TYR cc_start: 0.4659 (t80) cc_final: 0.4450 (t80) outliers start: 96 outliers final: 72 residues processed: 205 average time/residue: 0.1216 time to fit residues: 40.9372 Evaluate side-chains 203 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 116 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 819 LYS Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 858 ASN Chi-restraints excluded: chain A residue 860 PHE Chi-restraints excluded: chain A residue 864 GLU Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 883 HIS Chi-restraints excluded: chain A residue 913 GLU Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 948 LYS Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 955 HIS Chi-restraints excluded: chain A residue 959 THR Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1104 ILE Chi-restraints excluded: chain A residue 1109 ASN Chi-restraints excluded: chain A residue 1152 VAL Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1209 VAL Chi-restraints excluded: chain A residue 1252 LEU Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1285 ASP Chi-restraints excluded: chain A residue 1411 GLU Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1426 TYR Chi-restraints excluded: chain A residue 1429 LEU Chi-restraints excluded: chain A residue 1460 ASN Chi-restraints excluded: chain A residue 1480 THR Chi-restraints excluded: chain A residue 1521 THR Chi-restraints excluded: chain A residue 1522 LYS Chi-restraints excluded: chain A residue 1543 PHE Chi-restraints excluded: chain A residue 1545 ILE Chi-restraints excluded: chain A residue 1550 THR Chi-restraints excluded: chain A residue 1558 LEU Chi-restraints excluded: chain A residue 1566 ILE Chi-restraints excluded: chain A residue 1596 ILE Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 1617 THR Chi-restraints excluded: chain A residue 1662 TYR Chi-restraints excluded: chain A residue 1670 ILE Chi-restraints excluded: chain A residue 1706 THR Chi-restraints excluded: chain A residue 1714 THR Chi-restraints excluded: chain A residue 1718 VAL Chi-restraints excluded: chain A residue 1753 MET Chi-restraints excluded: chain A residue 1800 PHE Chi-restraints excluded: chain A residue 1806 VAL Chi-restraints excluded: chain A residue 1817 ILE Chi-restraints excluded: chain A residue 1854 ILE Chi-restraints excluded: chain A residue 1879 GLU Chi-restraints excluded: chain A residue 1880 THR Chi-restraints excluded: chain A residue 1975 ASP Chi-restraints excluded: chain A residue 2078 VAL Chi-restraints excluded: chain A residue 2094 ASN Chi-restraints excluded: chain A residue 2142 MET Chi-restraints excluded: chain A residue 2143 GLN Chi-restraints excluded: chain A residue 2181 ASN Chi-restraints excluded: chain A residue 2193 VAL Chi-restraints excluded: chain A residue 2195 VAL Chi-restraints excluded: chain A residue 2202 PHE Chi-restraints excluded: chain A residue 2212 TRP Chi-restraints excluded: chain A residue 2259 PHE Chi-restraints excluded: chain A residue 2331 GLU Chi-restraints excluded: chain A residue 2359 ASP Chi-restraints excluded: chain K residue 124 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 18 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 94 optimal weight: 6.9990 chunk 157 optimal weight: 1.9990 chunk 214 optimal weight: 10.0000 chunk 121 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 173 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 221 optimal weight: 7.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2181 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.214653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.182372 restraints weight = 39015.448| |-----------------------------------------------------------------------------| r_work (start): 0.4262 rms_B_bonded: 2.22 r_work: 0.3885 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3893 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3893 r_free = 0.3893 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3893 r_free = 0.3893 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3893 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.240 19532 Z= 0.236 Angle : 0.824 59.199 26433 Z= 0.468 Chirality : 0.056 1.262 2914 Planarity : 0.005 0.178 3443 Dihedral : 6.126 59.452 2633 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.43 % Favored : 90.32 % Rotamer: Outliers : 4.55 % Allowed : 29.13 % Favored : 66.32 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.56 (0.16), residues: 2398 helix: -0.42 (0.22), residues: 584 sheet: -1.44 (0.28), residues: 356 loop : -2.44 (0.15), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1653 TYR 0.052 0.001 TYR A1463 PHE 0.016 0.001 PHE A 243 TRP 0.009 0.001 TRP A1345 HIS 0.004 0.001 HIS A 925 Details of bonding type rmsd covalent geometry : bond 0.00471 (19529) covalent geometry : angle 0.82379 (26427) SS BOND : bond 0.00233 ( 3) SS BOND : angle 0.66029 ( 6) hydrogen bonds : bond 0.03123 ( 447) hydrogen bonds : angle 4.93865 ( 1251) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6501.42 seconds wall clock time: 111 minutes 45.94 seconds (6705.94 seconds total)