Starting phenix.real_space_refine on Fri Feb 16 08:04:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l42_0828/02_2024/6l42_0828.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l42_0828/02_2024/6l42_0828.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l42_0828/02_2024/6l42_0828.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l42_0828/02_2024/6l42_0828.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l42_0828/02_2024/6l42_0828.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l42_0828/02_2024/6l42_0828.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mg 1 5.21 5 S 91 5.16 5 C 9388 2.51 5 N 2574 2.21 5 O 2773 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 13": "OE1" <-> "OE2" Residue "A ARG 93": "NH1" <-> "NH2" Residue "A GLU 139": "OE1" <-> "OE2" Residue "A GLU 161": "OE1" <-> "OE2" Residue "A GLU 189": "OE1" <-> "OE2" Residue "A GLU 200": "OE1" <-> "OE2" Residue "A GLU 274": "OE1" <-> "OE2" Residue "A GLU 276": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A GLU 363": "OE1" <-> "OE2" Residue "A GLU 488": "OE1" <-> "OE2" Residue "A ARG 582": "NH1" <-> "NH2" Residue "A GLU 643": "OE1" <-> "OE2" Residue "A GLU 672": "OE1" <-> "OE2" Residue "A ARG 712": "NH1" <-> "NH2" Residue "A ARG 726": "NH1" <-> "NH2" Residue "A ARG 739": "NH1" <-> "NH2" Residue "A GLU 769": "OE1" <-> "OE2" Residue "A GLU 814": "OE1" <-> "OE2" Residue "A GLU 831": "OE1" <-> "OE2" Residue "A GLU 876": "OE1" <-> "OE2" Residue "A GLU 945": "OE1" <-> "OE2" Residue "A GLU 950": "OE1" <-> "OE2" Residue "A ARG 971": "NH1" <-> "NH2" Residue "A GLU 1061": "OE1" <-> "OE2" Residue "A GLU 1180": "OE1" <-> "OE2" Residue "A GLU 1216": "OE1" <-> "OE2" Residue "A GLU 1367": "OE1" <-> "OE2" Residue "A TYR 1414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1526": "NH1" <-> "NH2" Residue "A ARG 1542": "NH1" <-> "NH2" Residue "A GLU 1624": "OE1" <-> "OE2" Residue "A GLU 1644": "OE1" <-> "OE2" Residue "A GLU 1648": "OE1" <-> "OE2" Residue "A ARG 1712": "NH1" <-> "NH2" Residue "A ARG 1751": "NH1" <-> "NH2" Residue "A ARG 1757": "NH1" <-> "NH2" Residue "A ARG 1767": "NH1" <-> "NH2" Residue "A ARG 1777": "NH1" <-> "NH2" Residue "A ARG 1783": "NH1" <-> "NH2" Residue "A ARG 1789": "NH1" <-> "NH2" Residue "A ARG 1800": "NH1" <-> "NH2" Residue "A ARG 1807": "NH1" <-> "NH2" Residue "A GLU 1817": "OE1" <-> "OE2" Residue "A GLU 1841": "OE1" <-> "OE2" Residue "A GLU 1952": "OE1" <-> "OE2" Residue "A GLU 1958": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14827 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 14827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1865, 14827 Unusual residues: {' MG': 1} Classifications: {'peptide': 1864, 'undetermined': 1} Link IDs: {'CIS': 2, 'PTRANS': 66, 'TRANS': 1795, None: 1} Not linked: pdbres="ARG A2049 " pdbres=" MG A2101 " Chain breaks: 15 Time building chain proxies: 7.93, per 1000 atoms: 0.53 Number of scatterers: 14827 At special positions: 0 Unit cell: (90.72, 112.32, 138.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 91 16.00 Mg 1 11.99 O 2773 8.00 N 2574 7.00 C 9388 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 5.56 Conformation dependent library (CDL) restraints added in 2.6 seconds 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3488 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 14 sheets defined 42.2% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'A' and resid 3 through 10 removed outlier: 4.038A pdb=" N ILE A 10 " --> pdb=" O LEU A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 83 removed outlier: 4.484A pdb=" N THR A 83 " --> pdb=" O ASN A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 158 removed outlier: 3.780A pdb=" N ILE A 146 " --> pdb=" O TYR A 142 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS A 148 " --> pdb=" O THR A 144 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR A 149 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ASP A 151 " --> pdb=" O GLU A 147 " (cutoff:3.500A) Proline residue: A 152 - end of helix removed outlier: 3.515A pdb=" N ASP A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 206 removed outlier: 3.798A pdb=" N ALA A 188 " --> pdb=" O THR A 184 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU A 189 " --> pdb=" O GLN A 185 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N MET A 192 " --> pdb=" O ALA A 188 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS A 204 " --> pdb=" O GLU A 200 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 232 removed outlier: 4.224A pdb=" N ARG A 226 " --> pdb=" O GLU A 222 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 245 Processing helix chain 'A' and resid 251 through 258 removed outlier: 3.630A pdb=" N GLN A 255 " --> pdb=" O GLU A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 285 removed outlier: 3.852A pdb=" N LYS A 271 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU A 276 " --> pdb=" O ALA A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 318 removed outlier: 3.739A pdb=" N GLU A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE A 299 " --> pdb=" O GLU A 295 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASN A 300 " --> pdb=" O ARG A 296 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG A 301 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG A 318 " --> pdb=" O GLY A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 375 removed outlier: 3.637A pdb=" N TRP A 365 " --> pdb=" O TYR A 361 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU A 374 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLY A 375 " --> pdb=" O ASP A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 406 removed outlier: 3.571A pdb=" N ILE A 406 " --> pdb=" O GLU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 427 removed outlier: 4.037A pdb=" N LEU A 425 " --> pdb=" O GLN A 421 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN A 426 " --> pdb=" O GLU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 465 removed outlier: 4.044A pdb=" N GLY A 460 " --> pdb=" O VAL A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 482 removed outlier: 3.992A pdb=" N ALA A 482 " --> pdb=" O SER A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 492 removed outlier: 3.725A pdb=" N LEU A 486 " --> pdb=" O ALA A 482 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 503 Processing helix chain 'A' and resid 506 through 511 Processing helix chain 'A' and resid 514 through 531 removed outlier: 4.138A pdb=" N TRP A 520 " --> pdb=" O GLN A 516 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL A 521 " --> pdb=" O TRP A 517 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER A 530 " --> pdb=" O GLN A 526 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 611 removed outlier: 4.379A pdb=" N LEU A 609 " --> pdb=" O LYS A 605 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ASN A 611 " --> pdb=" O THR A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 615 Processing helix chain 'A' and resid 616 through 621 Processing helix chain 'A' and resid 621 through 627 Processing helix chain 'A' and resid 638 through 652 removed outlier: 3.846A pdb=" N GLU A 643 " --> pdb=" O SER A 639 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLN A 644 " --> pdb=" O GLU A 640 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR A 648 " --> pdb=" O GLN A 644 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A 650 " --> pdb=" O GLY A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 661 removed outlier: 3.951A pdb=" N GLU A 660 " --> pdb=" O LYS A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 667 Processing helix chain 'A' and resid 670 through 675 removed outlier: 3.623A pdb=" N VAL A 675 " --> pdb=" O GLU A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 690 removed outlier: 3.567A pdb=" N LEU A 687 " --> pdb=" O GLN A 684 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLY A 688 " --> pdb=" O LYS A 685 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS A 689 " --> pdb=" O MET A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 713 removed outlier: 3.581A pdb=" N TYR A 701 " --> pdb=" O LYS A 697 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ASP A 708 " --> pdb=" O ARG A 704 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N CYS A 709 " --> pdb=" O LYS A 705 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N MET A 710 " --> pdb=" O HIS A 706 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N VAL A 711 " --> pdb=" O LEU A 707 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE A 713 " --> pdb=" O CYS A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 750 removed outlier: 4.419A pdb=" N ASN A 748 " --> pdb=" O GLU A 744 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER A 749 " --> pdb=" O ASN A 745 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TRP A 750 " --> pdb=" O MET A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 776 removed outlier: 3.521A pdb=" N LEU A 767 " --> pdb=" O GLU A 763 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU A 769 " --> pdb=" O ASN A 765 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE A 774 " --> pdb=" O MET A 770 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A 775 " --> pdb=" O TYR A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 819 removed outlier: 3.546A pdb=" N LEU A 806 " --> pdb=" O SER A 802 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER A 812 " --> pdb=" O ALA A 808 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU A 813 " --> pdb=" O ALA A 809 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU A 814 " --> pdb=" O CYS A 810 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ARG A 815 " --> pdb=" O SER A 811 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA A 818 " --> pdb=" O GLU A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 838 removed outlier: 4.610A pdb=" N GLU A 831 " --> pdb=" O GLN A 827 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG A 835 " --> pdb=" O GLU A 831 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLY A 838 " --> pdb=" O LEU A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 859 removed outlier: 3.536A pdb=" N GLU A 859 " --> pdb=" O LYS A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 883 removed outlier: 3.579A pdb=" N LEU A 881 " --> pdb=" O LYS A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 902 Processing helix chain 'A' and resid 929 through 945 removed outlier: 3.959A pdb=" N VAL A 936 " --> pdb=" O VAL A 932 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR A 938 " --> pdb=" O PHE A 934 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N MET A 939 " --> pdb=" O GLY A 935 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL A 943 " --> pdb=" O MET A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 960 Processing helix chain 'A' and resid 961 through 969 removed outlier: 4.294A pdb=" N GLY A 966 " --> pdb=" O ILE A 962 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N LEU A 967 " --> pdb=" O GLU A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1006 removed outlier: 4.357A pdb=" N LEU A 998 " --> pdb=" O TYR A 994 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A 999 " --> pdb=" O THR A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1019 removed outlier: 4.181A pdb=" N ALA A1016 " --> pdb=" O ARG A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1037 removed outlier: 3.667A pdb=" N LEU A1033 " --> pdb=" O ASP A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1047 through 1058 Processing helix chain 'A' and resid 1086 through 1107 removed outlier: 3.562A pdb=" N LEU A1090 " --> pdb=" O THR A1086 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER A1104 " --> pdb=" O SER A1100 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1155 removed outlier: 3.583A pdb=" N PHE A1147 " --> pdb=" O VAL A1143 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N PHE A1148 " --> pdb=" O ARG A1144 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A1152 " --> pdb=" O PHE A1148 " (cutoff:3.500A) Processing helix chain 'A' and resid 1156 through 1158 No H-bonds generated for 'chain 'A' and resid 1156 through 1158' Processing helix chain 'A' and resid 1195 through 1200 removed outlier: 3.742A pdb=" N ALA A1200 " --> pdb=" O LEU A1196 " (cutoff:3.500A) Processing helix chain 'A' and resid 1212 through 1228 removed outlier: 3.767A pdb=" N GLU A1216 " --> pdb=" O ALA A1212 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN A1224 " --> pdb=" O ASN A1220 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N CYS A1225 " --> pdb=" O LEU A1221 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU A1226 " --> pdb=" O LEU A1222 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLU A1227 " --> pdb=" O THR A1223 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1252 removed outlier: 3.610A pdb=" N LEU A1244 " --> pdb=" O CYS A1240 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU A1249 " --> pdb=" O HIS A1245 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU A1250 " --> pdb=" O HIS A1246 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY A1251 " --> pdb=" O TYR A1247 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU A1252 " --> pdb=" O MET A1248 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1266 removed outlier: 3.802A pdb=" N LEU A1265 " --> pdb=" O PHE A1261 " (cutoff:3.500A) Processing helix chain 'A' and resid 1288 through 1299 removed outlier: 3.721A pdb=" N ASN A1292 " --> pdb=" O GLY A1288 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR A1299 " --> pdb=" O ARG A1295 " (cutoff:3.500A) Processing helix chain 'A' and resid 1306 through 1311 Processing helix chain 'A' and resid 1345 through 1350 Processing helix chain 'A' and resid 1360 through 1367 Processing helix chain 'A' and resid 1369 through 1373 removed outlier: 3.570A pdb=" N TYR A1373 " --> pdb=" O GLY A1370 " (cutoff:3.500A) Processing helix chain 'A' and resid 1378 through 1392 removed outlier: 3.683A pdb=" N HIS A1391 " --> pdb=" O ALA A1387 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N SER A1392 " --> pdb=" O GLU A1388 " (cutoff:3.500A) Processing helix chain 'A' and resid 1403 through 1418 removed outlier: 3.766A pdb=" N ARG A1407 " --> pdb=" O HIS A1403 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL A1409 " --> pdb=" O VAL A1405 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA A1411 " --> pdb=" O ARG A1407 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU A1415 " --> pdb=" O ALA A1411 " (cutoff:3.500A) Processing helix chain 'A' and resid 1435 through 1443 removed outlier: 3.513A pdb=" N ILE A1439 " --> pdb=" O LYS A1435 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS A1440 " --> pdb=" O ALA A1436 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU A1441 " --> pdb=" O SER A1437 " (cutoff:3.500A) Processing helix chain 'A' and resid 1451 through 1457 Processing helix chain 'A' and resid 1514 through 1522 removed outlier: 4.108A pdb=" N SER A1518 " --> pdb=" O GLU A1514 " (cutoff:3.500A) Processing helix chain 'A' and resid 1536 through 1544 removed outlier: 3.695A pdb=" N LYS A1540 " --> pdb=" O GLU A1536 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER A1544 " --> pdb=" O LYS A1540 " (cutoff:3.500A) Processing helix chain 'A' and resid 1553 through 1558 removed outlier: 3.614A pdb=" N ARG A1557 " --> pdb=" O SER A1553 " (cutoff:3.500A) Processing helix chain 'A' and resid 1563 through 1572 removed outlier: 3.616A pdb=" N PHE A1567 " --> pdb=" O SER A1563 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASN A1569 " --> pdb=" O VAL A1565 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N PHE A1570 " --> pdb=" O GLN A1566 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE A1571 " --> pdb=" O PHE A1567 " (cutoff:3.500A) Processing helix chain 'A' and resid 1617 through 1628 Processing helix chain 'A' and resid 1635 through 1638 Processing helix chain 'A' and resid 1639 through 1647 removed outlier: 3.744A pdb=" N GLU A1643 " --> pdb=" O GLY A1639 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU A1644 " --> pdb=" O PRO A1640 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N TYR A1645 " --> pdb=" O TYR A1641 " (cutoff:3.500A) Processing helix chain 'A' and resid 1671 through 1676 Processing helix chain 'A' and resid 1688 through 1694 removed outlier: 3.883A pdb=" N ILE A1692 " --> pdb=" O ILE A1688 " (cutoff:3.500A) Processing helix chain 'A' and resid 1758 through 1773 removed outlier: 3.956A pdb=" N GLU A1763 " --> pdb=" O TYR A1759 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU A1768 " --> pdb=" O SER A1764 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP A1770 " --> pdb=" O ARG A1766 " (cutoff:3.500A) Processing helix chain 'A' and resid 1797 through 1801 Processing helix chain 'A' and resid 1859 through 1866 removed outlier: 3.631A pdb=" N ALA A1863 " --> pdb=" O GLU A1859 " (cutoff:3.500A) Processing helix chain 'A' and resid 1871 through 1875 Processing helix chain 'A' and resid 1900 through 1909 removed outlier: 3.614A pdb=" N ASP A1904 " --> pdb=" O LEU A1900 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG A1905 " --> pdb=" O LEU A1901 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LYS A1906 " --> pdb=" O ALA A1902 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN A1908 " --> pdb=" O ASP A1904 " (cutoff:3.500A) Processing helix chain 'A' and resid 1922 through 1924 No H-bonds generated for 'chain 'A' and resid 1922 through 1924' Processing helix chain 'A' and resid 1925 through 1933 removed outlier: 4.243A pdb=" N LYS A1929 " --> pdb=" O GLY A1925 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU A1932 " --> pdb=" O ARG A1928 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N MET A1933 " --> pdb=" O LYS A1929 " (cutoff:3.500A) Processing helix chain 'A' and resid 1936 through 1941 removed outlier: 3.666A pdb=" N MET A1940 " --> pdb=" O LYS A1936 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL A1941 " --> pdb=" O LEU A1937 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1936 through 1941' Processing helix chain 'A' and resid 2012 through 2019 removed outlier: 3.663A pdb=" N ASP A2016 " --> pdb=" O LEU A2012 " (cutoff:3.500A) Processing helix chain 'A' and resid 2029 through 2034 Processing helix chain 'A' and resid 2041 through 2049 removed outlier: 3.880A pdb=" N GLN A2047 " --> pdb=" O ALA A2043 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 17 removed outlier: 6.076A pdb=" N GLY A 15 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N PHE A 167 " --> pdb=" O GLY A 15 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N SER A 17 " --> pdb=" O PHE A 167 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N VAL A 169 " --> pdb=" O SER A 17 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 17 removed outlier: 6.076A pdb=" N GLY A 15 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N PHE A 167 " --> pdb=" O GLY A 15 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N SER A 17 " --> pdb=" O PHE A 167 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N VAL A 169 " --> pdb=" O SER A 17 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE A 122 " --> pdb=" O PHE A 166 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N GLY A 168 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL A 124 " --> pdb=" O GLY A 168 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N ILE A 170 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLU A 126 " --> pdb=" O ILE A 170 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N VAL A 172 " --> pdb=" O GLU A 126 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N THR A 128 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 113 " --> pdb=" O VAL A 125 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 336 through 337 Processing sheet with id=AA4, first strand: chain 'A' and resid 544 through 545 removed outlier: 3.502A pdb=" N ILE A 570 " --> pdb=" O GLU A 594 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU A 594 " --> pdb=" O ILE A 570 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 595 " --> pdb=" O ILE A 588 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 563 through 566 Processing sheet with id=AA6, first strand: chain 'A' and resid 720 through 721 removed outlier: 3.510A pdb=" N ILE A 721 " --> pdb=" O GLU A 728 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU A 728 " --> pdb=" O ILE A 721 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 921 through 923 removed outlier: 4.393A pdb=" N LEU A 910 " --> pdb=" O MET A1027 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS A1024 " --> pdb=" O THR A1074 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 980 through 981 Processing sheet with id=AA9, first strand: chain 'A' and resid 1179 through 1180 Processing sheet with id=AB1, first strand: chain 'A' and resid 1328 through 1330 removed outlier: 3.816A pdb=" N ALA A1328 " --> pdb=" O SER A1335 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1699 through 1700 removed outlier: 3.709A pdb=" N LEU A1700 " --> pdb=" O VAL A1728 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1709 through 1712 removed outlier: 3.912A pdb=" N GLY A1716 " --> pdb=" O ARG A1712 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1723 through 1726 removed outlier: 6.589A pdb=" N GLN A1735 " --> pdb=" O ILE A1750 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE A1750 " --> pdb=" O GLN A1735 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU A1737 " --> pdb=" O GLU A1748 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1825 through 1829 removed outlier: 3.860A pdb=" N ARG A1829 " --> pdb=" O ILE A1832 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE A1832 " --> pdb=" O ARG A1829 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LEU A1833 " --> pdb=" O SER A1849 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N SER A1849 " --> pdb=" O LEU A1833 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU A1835 " --> pdb=" O ILE A1847 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A1847 " --> pdb=" O LEU A1835 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ARG A1843 " --> pdb=" O ILE A1839 " (cutoff:3.500A) 405 hydrogen bonds defined for protein. 1122 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: 5.49 Time building geometry restraints manager: 6.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.00 - 1.16: 4 1.16 - 1.33: 2757 1.33 - 1.49: 5739 1.49 - 1.65: 6461 1.65 - 1.81: 156 Bond restraints: 15117 Sorted by residual: bond pdb=" CA VAL A1520 " pdb=" C VAL A1520 " ideal model delta sigma weight residual 1.522 1.174 0.348 1.50e-02 4.44e+03 5.39e+02 bond pdb=" C ALA A 892 " pdb=" N VAL A 893 " ideal model delta sigma weight residual 1.336 1.591 -0.255 1.17e-02 7.31e+03 4.75e+02 bond pdb=" C THR A 348 " pdb=" N ASP A 349 " ideal model delta sigma weight residual 1.333 1.596 -0.262 1.34e-02 5.57e+03 3.83e+02 bond pdb=" CA THR A 348 " pdb=" C THR A 348 " ideal model delta sigma weight residual 1.533 1.638 -0.104 5.60e-03 3.19e+04 3.48e+02 bond pdb=" C MET A 1 " pdb=" N ASN A 2 " ideal model delta sigma weight residual 1.332 1.576 -0.243 1.40e-02 5.10e+03 3.02e+02 ... (remaining 15112 not shown) Histogram of bond angle deviations from ideal: 69.95 - 89.54: 52 89.54 - 109.13: 1477 109.13 - 128.72: 18581 128.72 - 148.31: 250 148.31 - 167.90: 19 Bond angle restraints: 20379 Sorted by residual: angle pdb=" O THR A 348 " pdb=" C THR A 348 " pdb=" N ASP A 349 " ideal model delta sigma weight residual 121.47 79.92 41.55 7.50e-01 1.78e+00 3.07e+03 angle pdb=" CA THR A 348 " pdb=" C THR A 348 " pdb=" N ASP A 349 " ideal model delta sigma weight residual 120.47 157.47 -37.00 1.03e+00 9.43e-01 1.29e+03 angle pdb=" O SER A1580 " pdb=" C SER A1580 " pdb=" N VAL A1581 " ideal model delta sigma weight residual 122.97 78.20 44.77 1.39e+00 5.18e-01 1.04e+03 angle pdb=" O LEU A1584 " pdb=" C LEU A1584 " pdb=" N GLY A1585 " ideal model delta sigma weight residual 123.13 89.16 33.97 1.07e+00 8.73e-01 1.01e+03 angle pdb=" O VAL A1581 " pdb=" C VAL A1581 " pdb=" N ARG A1582 " ideal model delta sigma weight residual 122.57 161.28 -38.71 1.25e+00 6.40e-01 9.59e+02 ... (remaining 20374 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.74: 8465 25.74 - 51.48: 611 51.48 - 77.23: 65 77.23 - 102.97: 10 102.97 - 128.71: 2 Dihedral angle restraints: 9153 sinusoidal: 3763 harmonic: 5390 Sorted by residual: dihedral pdb=" CA THR A 348 " pdb=" C THR A 348 " pdb=" N ASP A 349 " pdb=" CA ASP A 349 " ideal model delta harmonic sigma weight residual -180.00 -51.29 -128.71 0 5.00e+00 4.00e-02 6.63e+02 dihedral pdb=" CA VAL A1574 " pdb=" C VAL A1574 " pdb=" N ASP A1575 " pdb=" CA ASP A1575 " ideal model delta harmonic sigma weight residual 180.00 65.64 114.36 0 5.00e+00 4.00e-02 5.23e+02 dihedral pdb=" CA LEU A 95 " pdb=" C LEU A 95 " pdb=" N SER A 96 " pdb=" CA SER A 96 " ideal model delta harmonic sigma weight residual 180.00 87.25 92.75 0 5.00e+00 4.00e-02 3.44e+02 ... (remaining 9150 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.310: 2134 0.310 - 0.620: 92 0.620 - 0.930: 16 0.930 - 1.240: 4 1.240 - 1.550: 10 Chirality restraints: 2256 Sorted by residual: chirality pdb=" CA PHE A1793 " pdb=" N PHE A1793 " pdb=" C PHE A1793 " pdb=" CB PHE A1793 " both_signs ideal model delta sigma weight residual False 2.51 0.96 1.55 2.00e-01 2.50e+01 6.01e+01 chirality pdb=" CA TRP A 790 " pdb=" N TRP A 790 " pdb=" C TRP A 790 " pdb=" CB TRP A 790 " both_signs ideal model delta sigma weight residual False 2.51 0.98 1.53 2.00e-01 2.50e+01 5.83e+01 chirality pdb=" CA GLN A 824 " pdb=" N GLN A 824 " pdb=" C GLN A 824 " pdb=" CB GLN A 824 " both_signs ideal model delta sigma weight residual False 2.51 0.99 1.52 2.00e-01 2.50e+01 5.80e+01 ... (remaining 2253 not shown) Planarity restraints: 2599 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A1393 " -0.153 2.00e-02 2.50e+03 3.09e-01 9.54e+02 pdb=" C PRO A1393 " 0.522 2.00e-02 2.50e+03 pdb=" O PRO A1393 " -0.280 2.00e-02 2.50e+03 pdb=" N GLY A1394 " -0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A1687 " -0.158 2.00e-02 2.50e+03 2.47e-01 6.11e+02 pdb=" C SER A1687 " 0.422 2.00e-02 2.50e+03 pdb=" O SER A1687 " -0.187 2.00e-02 2.50e+03 pdb=" N ILE A1688 " -0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1584 " -0.141 2.00e-02 2.50e+03 2.43e-01 5.92e+02 pdb=" C LEU A1584 " 0.418 2.00e-02 2.50e+03 pdb=" O LEU A1584 " -0.180 2.00e-02 2.50e+03 pdb=" N GLY A1585 " -0.097 2.00e-02 2.50e+03 ... (remaining 2596 not shown) Histogram of nonbonded interaction distances: 1.22 - 1.96: 55 1.96 - 2.69: 1041 2.69 - 3.43: 21036 3.43 - 4.16: 32655 4.16 - 4.90: 56204 Nonbonded interactions: 110991 Sorted by model distance: nonbonded pdb=" CZ PHE A1567 " pdb=" CD1 ILE A1571 " model vdw 1.223 3.760 nonbonded pdb=" O ASP A1515 " pdb=" OE1 GLU A1519 " model vdw 1.260 3.040 nonbonded pdb=" O PHE A 84 " pdb=" OG SER A 88 " model vdw 1.354 2.440 nonbonded pdb=" CB ALA A1296 " pdb=" OD2 ASP A1301 " model vdw 1.363 3.460 nonbonded pdb=" CE2 TYR A1348 " pdb=" CB SER A1397 " model vdw 1.393 3.740 ... (remaining 110986 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.590 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: 3.100 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 40.350 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 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 0.348 15117 Z= 0.808 Angle : 3.318 50.587 20379 Z= 2.152 Chirality : 0.171 1.550 2256 Planarity : 0.021 0.309 2599 Dihedral : 16.555 128.708 5665 Min Nonbonded Distance : 1.223 Molprobity Statistics. All-atom Clashscore : 41.56 Ramachandran Plot: Outliers : 2.02 % Allowed : 11.41 % Favored : 86.57 % Rotamer: Outliers : 6.61 % Allowed : 7.40 % Favored : 85.99 % Cbeta Deviations : 6.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 1.80 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.16 (0.15), residues: 1832 helix: -3.17 (0.14), residues: 663 sheet: -2.42 (0.41), residues: 136 loop : -3.92 (0.16), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 520 HIS 0.004 0.001 HIS A 916 PHE 0.127 0.002 PHE A 352 TYR 0.010 0.001 TYR A1101 ARG 0.013 0.000 ARG A1568 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 334 time to evaluate : 1.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 GLU cc_start: 0.7288 (tt0) cc_final: 0.7047 (mt-10) REVERT: A 420 ARG cc_start: 0.7990 (mtp-110) cc_final: 0.7575 (mtp-110) REVERT: A 672 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7301 (mt-10) REVERT: A 773 LYS cc_start: 0.9095 (tttt) cc_final: 0.8802 (ttmm) REVERT: A 777 MET cc_start: 0.8179 (ttm) cc_final: 0.7872 (ttm) REVERT: A 778 GLU cc_start: 0.8119 (tp30) cc_final: 0.7882 (tp30) REVERT: A 913 LYS cc_start: 0.7383 (OUTLIER) cc_final: 0.7176 (ptmt) REVERT: A 933 GLN cc_start: 0.8743 (tm-30) cc_final: 0.8491 (tm-30) REVERT: A 1020 MET cc_start: 0.8014 (mtp) cc_final: 0.7746 (mtm) REVERT: A 1067 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8154 (tppt) REVERT: A 1131 MET cc_start: 0.7983 (mtm) cc_final: 0.7644 (mtt) REVERT: A 1527 THR cc_start: 0.6439 (OUTLIER) cc_final: 0.5840 (m) REVERT: A 1544 SER cc_start: 0.5449 (OUTLIER) cc_final: 0.5127 (p) REVERT: A 1637 LEU cc_start: 0.9154 (pp) cc_final: 0.8943 (pp) REVERT: A 1791 SER cc_start: 0.8188 (OUTLIER) cc_final: 0.7722 (p) REVERT: A 1800 ARG cc_start: 0.8133 (ttm-80) cc_final: 0.7671 (ttm-80) REVERT: A 2015 MET cc_start: 0.8374 (tpp) cc_final: 0.8097 (tpt) outliers start: 108 outliers final: 53 residues processed: 415 average time/residue: 0.3512 time to fit residues: 199.2978 Evaluate side-chains 281 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 223 time to evaluate : 1.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 CYS Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 30 ARG Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 161 GLU Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 699 GLN Chi-restraints excluded: chain A residue 888 TRP Chi-restraints excluded: chain A residue 913 LYS Chi-restraints excluded: chain A residue 921 GLU Chi-restraints excluded: chain A residue 949 HIS Chi-restraints excluded: chain A residue 971 ARG Chi-restraints excluded: chain A residue 1024 LYS Chi-restraints excluded: chain A residue 1064 TRP Chi-restraints excluded: chain A residue 1067 LYS Chi-restraints excluded: chain A residue 1071 TYR Chi-restraints excluded: chain A residue 1107 LYS Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1428 HIS Chi-restraints excluded: chain A residue 1460 GLN Chi-restraints excluded: chain A residue 1477 LEU Chi-restraints excluded: chain A residue 1514 GLU Chi-restraints excluded: chain A residue 1521 TRP Chi-restraints excluded: chain A residue 1527 THR Chi-restraints excluded: chain A residue 1534 LEU Chi-restraints excluded: chain A residue 1537 GLU Chi-restraints excluded: chain A residue 1538 TRP Chi-restraints excluded: chain A residue 1541 LEU Chi-restraints excluded: chain A residue 1542 ARG Chi-restraints excluded: chain A residue 1544 SER Chi-restraints excluded: chain A residue 1545 PHE Chi-restraints excluded: chain A residue 1589 LYS Chi-restraints excluded: chain A residue 1649 MET Chi-restraints excluded: chain A residue 1652 GLU Chi-restraints excluded: chain A residue 1657 LEU Chi-restraints excluded: chain A residue 1790 LEU Chi-restraints excluded: chain A residue 1791 SER Chi-restraints excluded: chain A residue 1796 LYS Chi-restraints excluded: chain A residue 1810 GLU Chi-restraints excluded: chain A residue 1911 ASP Chi-restraints excluded: chain A residue 1976 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 9.9990 chunk 140 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 75 optimal weight: 0.0970 chunk 145 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 88 optimal weight: 0.0870 chunk 108 optimal weight: 2.9990 chunk 168 optimal weight: 9.9990 overall best weight: 1.4362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 ASN A 247 ASN A 376 ASN A 513 ASN A 841 ASN A 964 ASN A1035 HIS A1190 HIS A1204 GLN ** A1239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1255 HIS A1930 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15117 Z= 0.259 Angle : 0.877 13.531 20379 Z= 0.456 Chirality : 0.050 0.225 2256 Planarity : 0.007 0.091 2599 Dihedral : 10.896 81.590 2165 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.76 % Allowed : 11.08 % Favored : 88.16 % Rotamer: Outliers : 4.53 % Allowed : 17.68 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 3.03 % Twisted General : 0.56 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.29 (0.17), residues: 1832 helix: -2.20 (0.17), residues: 703 sheet: -1.79 (0.42), residues: 140 loop : -3.64 (0.17), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 520 HIS 0.012 0.001 HIS A 916 PHE 0.018 0.002 PHE A 352 TYR 0.025 0.002 TYR A 193 ARG 0.009 0.001 ARG A 871 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 256 time to evaluate : 1.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 LYS cc_start: 0.8952 (tmmt) cc_final: 0.8623 (ptmm) REVERT: A 406 ILE cc_start: 0.7555 (OUTLIER) cc_final: 0.7022 (pt) REVERT: A 773 LYS cc_start: 0.9133 (tttt) cc_final: 0.8871 (ttmm) REVERT: A 777 MET cc_start: 0.8054 (ttm) cc_final: 0.7753 (ttm) REVERT: A 971 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.8460 (ttm110) REVERT: A 1020 MET cc_start: 0.8157 (mtp) cc_final: 0.7894 (mtm) REVERT: A 1111 MET cc_start: 0.8744 (mpp) cc_final: 0.8116 (ppp) REVERT: A 1131 MET cc_start: 0.7986 (mtm) cc_final: 0.7655 (mtt) REVERT: A 1305 LYS cc_start: 0.8471 (mtpt) cc_final: 0.8251 (mtpp) REVERT: A 1532 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.8261 (mmm-85) REVERT: A 1620 GLN cc_start: 0.9523 (tp40) cc_final: 0.9271 (tp-100) REVERT: A 1746 TRP cc_start: 0.8693 (p90) cc_final: 0.7985 (p90) REVERT: A 1800 ARG cc_start: 0.8222 (ttm-80) cc_final: 0.7891 (ttm-80) REVERT: A 1829 ARG cc_start: 0.7097 (mtm180) cc_final: 0.6858 (mtm-85) REVERT: A 1950 THR cc_start: 0.3479 (OUTLIER) cc_final: 0.3141 (p) REVERT: A 1965 ASP cc_start: 0.8536 (OUTLIER) cc_final: 0.7958 (p0) REVERT: A 2015 MET cc_start: 0.8263 (tpp) cc_final: 0.7897 (tpt) outliers start: 74 outliers final: 38 residues processed: 301 average time/residue: 0.3077 time to fit residues: 131.9402 Evaluate side-chains 249 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 206 time to evaluate : 1.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 572 LYS Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 921 GLU Chi-restraints excluded: chain A residue 971 ARG Chi-restraints excluded: chain A residue 1064 TRP Chi-restraints excluded: chain A residue 1071 TYR Chi-restraints excluded: chain A residue 1160 ASN Chi-restraints excluded: chain A residue 1178 CYS Chi-restraints excluded: chain A residue 1255 HIS Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1444 MET Chi-restraints excluded: chain A residue 1514 GLU Chi-restraints excluded: chain A residue 1532 ARG Chi-restraints excluded: chain A residue 1534 LEU Chi-restraints excluded: chain A residue 1537 GLU Chi-restraints excluded: chain A residue 1541 LEU Chi-restraints excluded: chain A residue 1573 HIS Chi-restraints excluded: chain A residue 1595 THR Chi-restraints excluded: chain A residue 1672 MET Chi-restraints excluded: chain A residue 1738 ILE Chi-restraints excluded: chain A residue 1769 CYS Chi-restraints excluded: chain A residue 1790 LEU Chi-restraints excluded: chain A residue 1796 LYS Chi-restraints excluded: chain A residue 1868 ASN Chi-restraints excluded: chain A residue 1910 ILE Chi-restraints excluded: chain A residue 1950 THR Chi-restraints excluded: chain A residue 1957 LEU Chi-restraints excluded: chain A residue 1965 ASP Chi-restraints excluded: chain A residue 2007 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 140 optimal weight: 0.0040 chunk 115 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 169 optimal weight: 10.0000 chunk 182 optimal weight: 9.9990 chunk 150 optimal weight: 6.9990 chunk 167 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 135 optimal weight: 0.7980 overall best weight: 1.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 865 GLN ** A 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1255 HIS A1391 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15117 Z= 0.213 Angle : 0.771 11.189 20379 Z= 0.395 Chirality : 0.046 0.216 2256 Planarity : 0.006 0.094 2599 Dihedral : 8.401 60.848 2060 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.44 % Allowed : 11.14 % Favored : 88.43 % Rotamer: Outliers : 4.16 % Allowed : 20.67 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 4.55 % Twisted General : 0.45 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.81 (0.18), residues: 1832 helix: -1.81 (0.18), residues: 709 sheet: -1.34 (0.42), residues: 142 loop : -3.40 (0.18), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 888 HIS 0.011 0.001 HIS A1255 PHE 0.022 0.001 PHE A1561 TYR 0.017 0.001 TYR A1071 ARG 0.011 0.000 ARG A1814 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 224 time to evaluate : 1.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6890 (mt-10) REVERT: A 160 MET cc_start: 0.7413 (mmm) cc_final: 0.6870 (mmm) REVERT: A 237 ASN cc_start: 0.8141 (OUTLIER) cc_final: 0.7595 (t0) REVERT: A 406 ILE cc_start: 0.7442 (OUTLIER) cc_final: 0.6895 (pt) REVERT: A 616 MET cc_start: 0.9121 (mmm) cc_final: 0.8914 (mmm) REVERT: A 679 MET cc_start: 0.8908 (mmt) cc_final: 0.8628 (mmt) REVERT: A 773 LYS cc_start: 0.9151 (tttt) cc_final: 0.8884 (ttmm) REVERT: A 848 MET cc_start: 0.7397 (tpp) cc_final: 0.6364 (tpt) REVERT: A 1079 MET cc_start: 0.7976 (mmp) cc_final: 0.6736 (mmp) REVERT: A 1131 MET cc_start: 0.7968 (mtm) cc_final: 0.7631 (mtt) REVERT: A 1381 GLU cc_start: 0.8676 (pm20) cc_final: 0.8151 (pm20) REVERT: A 1554 GLU cc_start: 0.5735 (tp30) cc_final: 0.5322 (tp30) REVERT: A 1620 GLN cc_start: 0.9554 (tp40) cc_final: 0.9351 (tp-100) REVERT: A 1637 LEU cc_start: 0.9358 (pp) cc_final: 0.8826 (pp) REVERT: A 1729 MET cc_start: 0.6641 (ptp) cc_final: 0.6311 (ptt) REVERT: A 1746 TRP cc_start: 0.8501 (p90) cc_final: 0.8196 (p90) REVERT: A 1829 ARG cc_start: 0.6816 (mtm180) cc_final: 0.6588 (mtm-85) REVERT: A 1845 MET cc_start: 0.8896 (ttm) cc_final: 0.8691 (ptp) REVERT: A 1965 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.7811 (p0) REVERT: A 2015 MET cc_start: 0.8290 (tpp) cc_final: 0.7926 (tpt) outliers start: 68 outliers final: 44 residues processed: 266 average time/residue: 0.3085 time to fit residues: 119.8609 Evaluate side-chains 246 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 198 time to evaluate : 1.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 699 GLN Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 1064 TRP Chi-restraints excluded: chain A residue 1071 TYR Chi-restraints excluded: chain A residue 1160 ASN Chi-restraints excluded: chain A residue 1178 CYS Chi-restraints excluded: chain A residue 1189 ARG Chi-restraints excluded: chain A residue 1255 HIS Chi-restraints excluded: chain A residue 1300 THR Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1433 THR Chi-restraints excluded: chain A residue 1442 LEU Chi-restraints excluded: chain A residue 1444 MET Chi-restraints excluded: chain A residue 1534 LEU Chi-restraints excluded: chain A residue 1541 LEU Chi-restraints excluded: chain A residue 1573 HIS Chi-restraints excluded: chain A residue 1595 THR Chi-restraints excluded: chain A residue 1672 MET Chi-restraints excluded: chain A residue 1769 CYS Chi-restraints excluded: chain A residue 1790 LEU Chi-restraints excluded: chain A residue 1796 LYS Chi-restraints excluded: chain A residue 1806 VAL Chi-restraints excluded: chain A residue 1868 ASN Chi-restraints excluded: chain A residue 1957 LEU Chi-restraints excluded: chain A residue 1965 ASP Chi-restraints excluded: chain A residue 1977 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 10.0000 chunk 127 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 18 optimal weight: 9.9990 chunk 80 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 169 optimal weight: 5.9990 chunk 179 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 chunk 160 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN A 199 ASN A 237 ASN ** A 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 15117 Z= 0.319 Angle : 0.780 11.125 20379 Z= 0.399 Chirality : 0.047 0.242 2256 Planarity : 0.005 0.099 2599 Dihedral : 7.528 60.851 2042 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.44 % Allowed : 12.61 % Favored : 86.95 % Rotamer: Outliers : 4.77 % Allowed : 21.22 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 4.55 % Twisted General : 0.45 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (0.18), residues: 1832 helix: -1.55 (0.18), residues: 715 sheet: -1.33 (0.42), residues: 152 loop : -3.23 (0.18), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 888 HIS 0.023 0.001 HIS A1255 PHE 0.023 0.002 PHE A1561 TYR 0.020 0.002 TYR A1071 ARG 0.004 0.000 ARG A1622 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 201 time to evaluate : 1.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 TYR cc_start: 0.8001 (m-80) cc_final: 0.7766 (m-10) REVERT: A 160 MET cc_start: 0.7390 (mmm) cc_final: 0.7044 (mmm) REVERT: A 193 TYR cc_start: 0.8324 (t80) cc_final: 0.8077 (t80) REVERT: A 237 ASN cc_start: 0.8002 (OUTLIER) cc_final: 0.7451 (t0) REVERT: A 773 LYS cc_start: 0.9122 (tttt) cc_final: 0.8918 (ttmm) REVERT: A 831 GLU cc_start: 0.8712 (mp0) cc_final: 0.8489 (mp0) REVERT: A 836 GLU cc_start: 0.9073 (tm-30) cc_final: 0.8849 (tm-30) REVERT: A 848 MET cc_start: 0.7665 (tpp) cc_final: 0.7157 (tpt) REVERT: A 925 MET cc_start: 0.8250 (mmm) cc_final: 0.7792 (tmm) REVERT: A 933 GLN cc_start: 0.8695 (tm-30) cc_final: 0.8325 (tm-30) REVERT: A 950 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7295 (mt-10) REVERT: A 1111 MET cc_start: 0.8793 (mpp) cc_final: 0.8160 (ppp) REVERT: A 1126 ASP cc_start: 0.8412 (t0) cc_final: 0.8169 (t0) REVERT: A 1381 GLU cc_start: 0.8680 (pm20) cc_final: 0.8157 (pm20) REVERT: A 1442 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8615 (tp) REVERT: A 1477 LEU cc_start: 0.4943 (OUTLIER) cc_final: 0.4679 (tp) REVERT: A 1729 MET cc_start: 0.6689 (ptp) cc_final: 0.6330 (ptt) REVERT: A 1746 TRP cc_start: 0.8479 (p90) cc_final: 0.8257 (p90) REVERT: A 1790 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8796 (pp) REVERT: A 1845 MET cc_start: 0.8965 (ttm) cc_final: 0.8750 (ptp) REVERT: A 1950 THR cc_start: 0.2774 (OUTLIER) cc_final: 0.2421 (p) REVERT: A 2015 MET cc_start: 0.8217 (tpp) cc_final: 0.7906 (tpt) outliers start: 78 outliers final: 56 residues processed: 254 average time/residue: 0.2855 time to fit residues: 107.1887 Evaluate side-chains 240 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 179 time to evaluate : 1.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 954 ASN Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1064 TRP Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1160 ASN Chi-restraints excluded: chain A residue 1178 CYS Chi-restraints excluded: chain A residue 1255 HIS Chi-restraints excluded: chain A residue 1300 THR Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1433 THR Chi-restraints excluded: chain A residue 1442 LEU Chi-restraints excluded: chain A residue 1444 MET Chi-restraints excluded: chain A residue 1474 VAL Chi-restraints excluded: chain A residue 1477 LEU Chi-restraints excluded: chain A residue 1534 LEU Chi-restraints excluded: chain A residue 1541 LEU Chi-restraints excluded: chain A residue 1573 HIS Chi-restraints excluded: chain A residue 1574 VAL Chi-restraints excluded: chain A residue 1595 THR Chi-restraints excluded: chain A residue 1672 MET Chi-restraints excluded: chain A residue 1709 THR Chi-restraints excluded: chain A residue 1739 ASP Chi-restraints excluded: chain A residue 1769 CYS Chi-restraints excluded: chain A residue 1790 LEU Chi-restraints excluded: chain A residue 1806 VAL Chi-restraints excluded: chain A residue 1868 ASN Chi-restraints excluded: chain A residue 1886 LEU Chi-restraints excluded: chain A residue 1910 ILE Chi-restraints excluded: chain A residue 1950 THR Chi-restraints excluded: chain A residue 1954 VAL Chi-restraints excluded: chain A residue 1957 LEU Chi-restraints excluded: chain A residue 1977 ASP Chi-restraints excluded: chain A residue 2007 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 0.8980 chunk 161 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 865 GLN ** A 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1255 HIS ** A1846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15117 Z= 0.235 Angle : 0.739 10.864 20379 Z= 0.375 Chirality : 0.045 0.229 2256 Planarity : 0.005 0.096 2599 Dihedral : 7.114 60.525 2036 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.38 % Allowed : 11.24 % Favored : 88.37 % Rotamer: Outliers : 4.34 % Allowed : 23.00 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 4.55 % Twisted General : 0.45 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.18 (0.18), residues: 1832 helix: -1.27 (0.19), residues: 710 sheet: -0.84 (0.45), residues: 135 loop : -3.07 (0.18), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1989 HIS 0.004 0.001 HIS A1255 PHE 0.019 0.001 PHE A 352 TYR 0.015 0.001 TYR A1071 ARG 0.003 0.000 ARG A 30 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 204 time to evaluate : 1.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 LYS cc_start: 0.9279 (ttpt) cc_final: 0.9024 (tttt) REVERT: A 149 TYR cc_start: 0.7481 (m-80) cc_final: 0.7202 (m-10) REVERT: A 160 MET cc_start: 0.7328 (mmm) cc_final: 0.6840 (mmm) REVERT: A 193 TYR cc_start: 0.8331 (t80) cc_final: 0.8082 (t80) REVERT: A 406 ILE cc_start: 0.7714 (OUTLIER) cc_final: 0.7147 (pt) REVERT: A 513 ASN cc_start: 0.8693 (OUTLIER) cc_final: 0.8067 (t0) REVERT: A 625 GLU cc_start: 0.8707 (tm-30) cc_final: 0.8469 (tm-30) REVERT: A 773 LYS cc_start: 0.9140 (tttt) cc_final: 0.8893 (ttmm) REVERT: A 836 GLU cc_start: 0.9065 (tm-30) cc_final: 0.8809 (tm-30) REVERT: A 848 MET cc_start: 0.7637 (tpp) cc_final: 0.7379 (tpt) REVERT: A 925 MET cc_start: 0.8273 (mmm) cc_final: 0.7830 (mmm) REVERT: A 1027 MET cc_start: 0.8438 (ttp) cc_final: 0.7976 (mtp) REVERT: A 1079 MET cc_start: 0.7956 (mmp) cc_final: 0.7748 (mmp) REVERT: A 1111 MET cc_start: 0.8716 (mpp) cc_final: 0.8139 (ppp) REVERT: A 1381 GLU cc_start: 0.8633 (pm20) cc_final: 0.8165 (pm20) REVERT: A 1463 MET cc_start: 0.4413 (tmm) cc_final: 0.4141 (tmm) REVERT: A 1635 MET cc_start: 0.8441 (ppp) cc_final: 0.7955 (ppp) REVERT: A 1729 MET cc_start: 0.6603 (ptp) cc_final: 0.6205 (ptt) REVERT: A 1746 TRP cc_start: 0.8636 (p90) cc_final: 0.8163 (p90) REVERT: A 1845 MET cc_start: 0.8959 (ttm) cc_final: 0.8757 (ptp) REVERT: A 1950 THR cc_start: 0.2687 (OUTLIER) cc_final: 0.2296 (p) REVERT: A 2015 MET cc_start: 0.8249 (tpp) cc_final: 0.7958 (tpt) outliers start: 71 outliers final: 47 residues processed: 253 average time/residue: 0.2732 time to fit residues: 103.1295 Evaluate side-chains 239 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 189 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain A residue 954 ASN Chi-restraints excluded: chain A residue 1160 ASN Chi-restraints excluded: chain A residue 1178 CYS Chi-restraints excluded: chain A residue 1191 LEU Chi-restraints excluded: chain A residue 1300 THR Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1444 MET Chi-restraints excluded: chain A residue 1534 LEU Chi-restraints excluded: chain A residue 1556 LEU Chi-restraints excluded: chain A residue 1573 HIS Chi-restraints excluded: chain A residue 1595 THR Chi-restraints excluded: chain A residue 1672 MET Chi-restraints excluded: chain A residue 1676 LEU Chi-restraints excluded: chain A residue 1739 ASP Chi-restraints excluded: chain A residue 1769 CYS Chi-restraints excluded: chain A residue 1806 VAL Chi-restraints excluded: chain A residue 1868 ASN Chi-restraints excluded: chain A residue 1886 LEU Chi-restraints excluded: chain A residue 1910 ILE Chi-restraints excluded: chain A residue 1950 THR Chi-restraints excluded: chain A residue 1954 VAL Chi-restraints excluded: chain A residue 1955 ASP Chi-restraints excluded: chain A residue 1957 LEU Chi-restraints excluded: chain A residue 1969 VAL Chi-restraints excluded: chain A residue 1977 ASP Chi-restraints excluded: chain A residue 2007 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 0.3980 chunk 161 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 179 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 59 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 799 HIS ** A 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 959 ASN A1255 HIS A1292 ASN A1403 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15117 Z= 0.185 Angle : 0.713 10.877 20379 Z= 0.358 Chirality : 0.044 0.215 2256 Planarity : 0.005 0.094 2599 Dihedral : 6.502 59.767 2028 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.38 % Allowed : 11.30 % Favored : 88.32 % Rotamer: Outliers : 4.16 % Allowed : 23.49 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 3.03 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.19), residues: 1832 helix: -1.04 (0.19), residues: 718 sheet: -0.75 (0.45), residues: 136 loop : -2.95 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.001 TRP A1064 HIS 0.006 0.001 HIS A1190 PHE 0.019 0.001 PHE A 352 TYR 0.013 0.001 TYR A1864 ARG 0.007 0.000 ARG A1060 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 212 time to evaluate : 1.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 LYS cc_start: 0.9181 (ttpt) cc_final: 0.8906 (tttt) REVERT: A 149 TYR cc_start: 0.7375 (m-80) cc_final: 0.7136 (m-10) REVERT: A 160 MET cc_start: 0.7192 (mmm) cc_final: 0.6960 (mmm) REVERT: A 193 TYR cc_start: 0.8304 (t80) cc_final: 0.8066 (t80) REVERT: A 347 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8688 (tttm) REVERT: A 406 ILE cc_start: 0.7632 (OUTLIER) cc_final: 0.7129 (pt) REVERT: A 513 ASN cc_start: 0.8680 (OUTLIER) cc_final: 0.8046 (t0) REVERT: A 625 GLU cc_start: 0.8746 (tm-30) cc_final: 0.8539 (tm-30) REVERT: A 773 LYS cc_start: 0.9134 (tttt) cc_final: 0.8887 (ttmm) REVERT: A 836 GLU cc_start: 0.8992 (tm-30) cc_final: 0.8768 (tp30) REVERT: A 848 MET cc_start: 0.7565 (tpp) cc_final: 0.7267 (tpt) REVERT: A 925 MET cc_start: 0.8226 (mmm) cc_final: 0.7784 (mmm) REVERT: A 933 GLN cc_start: 0.8621 (tm-30) cc_final: 0.8296 (tm-30) REVERT: A 1027 MET cc_start: 0.8329 (ttp) cc_final: 0.8053 (mtp) REVERT: A 1079 MET cc_start: 0.8155 (mmp) cc_final: 0.7864 (mmp) REVERT: A 1111 MET cc_start: 0.8651 (mpp) cc_final: 0.8125 (ppp) REVERT: A 1381 GLU cc_start: 0.8671 (pm20) cc_final: 0.8197 (pm20) REVERT: A 1463 MET cc_start: 0.4548 (tmm) cc_final: 0.4273 (tmm) REVERT: A 1529 LEU cc_start: 0.6698 (OUTLIER) cc_final: 0.6482 (mp) REVERT: A 1729 MET cc_start: 0.6472 (ptp) cc_final: 0.6074 (ptt) REVERT: A 1739 ASP cc_start: 0.8605 (OUTLIER) cc_final: 0.8068 (t70) REVERT: A 1746 TRP cc_start: 0.8622 (p90) cc_final: 0.8140 (p90) REVERT: A 1950 THR cc_start: 0.2729 (OUTLIER) cc_final: 0.2405 (p) REVERT: A 1981 ILE cc_start: 0.8847 (OUTLIER) cc_final: 0.8600 (tt) REVERT: A 2012 LEU cc_start: 0.8598 (pp) cc_final: 0.8259 (tp) REVERT: A 2015 MET cc_start: 0.8178 (tpp) cc_final: 0.7913 (tpt) outliers start: 68 outliers final: 45 residues processed: 260 average time/residue: 0.2688 time to fit residues: 104.1443 Evaluate side-chains 247 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 195 time to evaluate : 1.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 322 GLN Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 799 HIS Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain A residue 954 ASN Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 1160 ASN Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1444 MET Chi-restraints excluded: chain A residue 1529 LEU Chi-restraints excluded: chain A residue 1556 LEU Chi-restraints excluded: chain A residue 1595 THR Chi-restraints excluded: chain A residue 1672 MET Chi-restraints excluded: chain A residue 1709 THR Chi-restraints excluded: chain A residue 1738 ILE Chi-restraints excluded: chain A residue 1739 ASP Chi-restraints excluded: chain A residue 1769 CYS Chi-restraints excluded: chain A residue 1806 VAL Chi-restraints excluded: chain A residue 1868 ASN Chi-restraints excluded: chain A residue 1886 LEU Chi-restraints excluded: chain A residue 1910 ILE Chi-restraints excluded: chain A residue 1950 THR Chi-restraints excluded: chain A residue 1954 VAL Chi-restraints excluded: chain A residue 1957 LEU Chi-restraints excluded: chain A residue 1965 ASP Chi-restraints excluded: chain A residue 1977 ASP Chi-restraints excluded: chain A residue 1981 ILE Chi-restraints excluded: chain A residue 1990 SER Chi-restraints excluded: chain A residue 2007 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 102 optimal weight: 0.0670 chunk 131 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 151 optimal weight: 10.0000 chunk 100 optimal weight: 8.9990 chunk 179 optimal weight: 0.0670 chunk 112 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 overall best weight: 1.4262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 959 ASN A1245 HIS A1255 HIS ** A1846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15117 Z= 0.203 Angle : 0.724 11.102 20379 Z= 0.363 Chirality : 0.045 0.295 2256 Planarity : 0.005 0.095 2599 Dihedral : 6.379 59.788 2026 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.33 % Allowed : 10.64 % Favored : 89.03 % Rotamer: Outliers : 4.59 % Allowed : 24.16 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 4.55 % Twisted General : 0.34 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.19), residues: 1832 helix: -0.88 (0.19), residues: 714 sheet: -0.46 (0.44), residues: 140 loop : -2.93 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1883 HIS 0.004 0.001 HIS A 799 PHE 0.022 0.001 PHE A 166 TYR 0.017 0.001 TYR A1308 ARG 0.004 0.000 ARG A1189 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 200 time to evaluate : 1.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 TYR cc_start: 0.8319 (t80) cc_final: 0.8077 (t80) REVERT: A 406 ILE cc_start: 0.7493 (OUTLIER) cc_final: 0.6870 (pt) REVERT: A 513 ASN cc_start: 0.8685 (OUTLIER) cc_final: 0.8045 (t0) REVERT: A 626 LYS cc_start: 0.9010 (tppt) cc_final: 0.8785 (tppt) REVERT: A 773 LYS cc_start: 0.9138 (tttt) cc_final: 0.8831 (ttmm) REVERT: A 777 MET cc_start: 0.8657 (mtp) cc_final: 0.8381 (mtp) REVERT: A 836 GLU cc_start: 0.9014 (tm-30) cc_final: 0.8800 (tp30) REVERT: A 848 MET cc_start: 0.7656 (tpp) cc_final: 0.7430 (tpt) REVERT: A 933 GLN cc_start: 0.8614 (tm-30) cc_final: 0.8287 (tm-30) REVERT: A 1126 ASP cc_start: 0.8272 (t0) cc_final: 0.8055 (t0) REVERT: A 1140 MET cc_start: 0.8407 (ttp) cc_final: 0.8084 (tmm) REVERT: A 1381 GLU cc_start: 0.8664 (pm20) cc_final: 0.8183 (pm20) REVERT: A 1635 MET cc_start: 0.8323 (ppp) cc_final: 0.7993 (ppp) REVERT: A 1729 MET cc_start: 0.6451 (ptp) cc_final: 0.6064 (ptt) REVERT: A 1739 ASP cc_start: 0.8641 (OUTLIER) cc_final: 0.8065 (t70) REVERT: A 1746 TRP cc_start: 0.8598 (p90) cc_final: 0.8121 (p90) REVERT: A 1981 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8624 (tt) REVERT: A 2012 LEU cc_start: 0.8586 (pp) cc_final: 0.8236 (tp) REVERT: A 2015 MET cc_start: 0.8192 (tpp) cc_final: 0.7931 (tpt) outliers start: 75 outliers final: 48 residues processed: 257 average time/residue: 0.2574 time to fit residues: 98.9276 Evaluate side-chains 240 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 188 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 322 GLN Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 810 CYS Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain A residue 954 ASN Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1160 ASN Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1300 THR Chi-restraints excluded: chain A residue 1372 LEU Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1444 MET Chi-restraints excluded: chain A residue 1556 LEU Chi-restraints excluded: chain A residue 1595 THR Chi-restraints excluded: chain A residue 1672 MET Chi-restraints excluded: chain A residue 1709 THR Chi-restraints excluded: chain A residue 1739 ASP Chi-restraints excluded: chain A residue 1769 CYS Chi-restraints excluded: chain A residue 1806 VAL Chi-restraints excluded: chain A residue 1868 ASN Chi-restraints excluded: chain A residue 1886 LEU Chi-restraints excluded: chain A residue 1910 ILE Chi-restraints excluded: chain A residue 1954 VAL Chi-restraints excluded: chain A residue 1957 LEU Chi-restraints excluded: chain A residue 1965 ASP Chi-restraints excluded: chain A residue 1969 VAL Chi-restraints excluded: chain A residue 1977 ASP Chi-restraints excluded: chain A residue 1981 ILE Chi-restraints excluded: chain A residue 2007 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 35 optimal weight: 0.0070 chunk 34 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 chunk 122 optimal weight: 0.5980 chunk 88 optimal weight: 0.6980 chunk 16 optimal weight: 7.9990 chunk 140 optimal weight: 0.9980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 799 HIS ** A 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 959 ASN A1255 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15117 Z= 0.183 Angle : 0.726 11.504 20379 Z= 0.362 Chirality : 0.045 0.289 2256 Planarity : 0.005 0.094 2599 Dihedral : 6.237 59.314 2026 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.33 % Allowed : 10.81 % Favored : 88.86 % Rotamer: Outliers : 3.61 % Allowed : 25.14 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 3.03 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.19), residues: 1832 helix: -0.79 (0.19), residues: 720 sheet: -0.47 (0.44), residues: 140 loop : -2.92 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1883 HIS 0.003 0.000 HIS A1631 PHE 0.021 0.001 PHE A 166 TYR 0.017 0.001 TYR A1850 ARG 0.017 0.000 ARG A1829 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 208 time to evaluate : 1.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 TYR cc_start: 0.8244 (t80) cc_final: 0.8024 (t80) REVERT: A 406 ILE cc_start: 0.7065 (OUTLIER) cc_final: 0.6680 (pt) REVERT: A 513 ASN cc_start: 0.8680 (OUTLIER) cc_final: 0.8043 (t0) REVERT: A 773 LYS cc_start: 0.9099 (tttt) cc_final: 0.8793 (ttmm) REVERT: A 777 MET cc_start: 0.8675 (mtp) cc_final: 0.8389 (mtp) REVERT: A 830 GLU cc_start: 0.8541 (tm-30) cc_final: 0.8339 (tm-30) REVERT: A 836 GLU cc_start: 0.8970 (tm-30) cc_final: 0.8766 (tp30) REVERT: A 848 MET cc_start: 0.7575 (tpp) cc_final: 0.7300 (tpt) REVERT: A 933 GLN cc_start: 0.8610 (tm-30) cc_final: 0.8260 (tm-30) REVERT: A 1140 MET cc_start: 0.8395 (ttp) cc_final: 0.8086 (tmm) REVERT: A 1279 ASP cc_start: 0.8416 (OUTLIER) cc_final: 0.8198 (m-30) REVERT: A 1324 ARG cc_start: 0.7743 (ttt180) cc_final: 0.7241 (ttm-80) REVERT: A 1381 GLU cc_start: 0.8664 (pm20) cc_final: 0.8177 (pm20) REVERT: A 1693 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8125 (tp30) REVERT: A 1729 MET cc_start: 0.6302 (ptp) cc_final: 0.5889 (ptt) REVERT: A 1739 ASP cc_start: 0.8646 (OUTLIER) cc_final: 0.8073 (t70) REVERT: A 1746 TRP cc_start: 0.8606 (p90) cc_final: 0.8111 (p90) REVERT: A 2012 LEU cc_start: 0.8573 (pp) cc_final: 0.8175 (tp) REVERT: A 2015 MET cc_start: 0.8170 (tpp) cc_final: 0.7912 (tpt) outliers start: 59 outliers final: 42 residues processed: 253 average time/residue: 0.2640 time to fit residues: 101.3253 Evaluate side-chains 240 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 194 time to evaluate : 1.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 799 HIS Chi-restraints excluded: chain A residue 810 CYS Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 954 ASN Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 1160 ASN Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1279 ASP Chi-restraints excluded: chain A residue 1300 THR Chi-restraints excluded: chain A residue 1372 LEU Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1444 MET Chi-restraints excluded: chain A residue 1556 LEU Chi-restraints excluded: chain A residue 1595 THR Chi-restraints excluded: chain A residue 1672 MET Chi-restraints excluded: chain A residue 1676 LEU Chi-restraints excluded: chain A residue 1709 THR Chi-restraints excluded: chain A residue 1739 ASP Chi-restraints excluded: chain A residue 1769 CYS Chi-restraints excluded: chain A residue 1806 VAL Chi-restraints excluded: chain A residue 1868 ASN Chi-restraints excluded: chain A residue 1886 LEU Chi-restraints excluded: chain A residue 1954 VAL Chi-restraints excluded: chain A residue 1957 LEU Chi-restraints excluded: chain A residue 1965 ASP Chi-restraints excluded: chain A residue 1969 VAL Chi-restraints excluded: chain A residue 1977 ASP Chi-restraints excluded: chain A residue 2007 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 3.9990 chunk 171 optimal weight: 10.0000 chunk 156 optimal weight: 0.7980 chunk 167 optimal weight: 7.9990 chunk 100 optimal weight: 10.0000 chunk 72 optimal weight: 0.0070 chunk 131 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 150 optimal weight: 0.0370 chunk 158 optimal weight: 20.0000 chunk 166 optimal weight: 5.9990 overall best weight: 1.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 748 ASN A 799 HIS ** A 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 959 ASN A1255 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.4589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15117 Z= 0.224 Angle : 0.738 10.876 20379 Z= 0.369 Chirality : 0.045 0.283 2256 Planarity : 0.005 0.096 2599 Dihedral : 6.221 59.353 2026 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.33 % Allowed : 10.86 % Favored : 88.81 % Rotamer: Outliers : 3.61 % Allowed : 25.32 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 4.55 % Twisted General : 0.45 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.19), residues: 1832 helix: -0.64 (0.19), residues: 722 sheet: -0.47 (0.43), residues: 141 loop : -2.91 (0.19), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 520 HIS 0.004 0.001 HIS A 799 PHE 0.026 0.001 PHE A 352 TYR 0.014 0.001 TYR A1308 ARG 0.005 0.000 ARG A1928 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 195 time to evaluate : 1.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 TYR cc_start: 0.8256 (t80) cc_final: 0.8034 (t80) REVERT: A 406 ILE cc_start: 0.7050 (OUTLIER) cc_final: 0.6574 (pt) REVERT: A 513 ASN cc_start: 0.8739 (OUTLIER) cc_final: 0.8096 (t0) REVERT: A 773 LYS cc_start: 0.9113 (tttt) cc_final: 0.8800 (ttmm) REVERT: A 777 MET cc_start: 0.8707 (mtp) cc_final: 0.8355 (mtp) REVERT: A 848 MET cc_start: 0.7602 (tpp) cc_final: 0.7395 (tpt) REVERT: A 878 MET cc_start: 0.8753 (pmm) cc_final: 0.8451 (pmm) REVERT: A 933 GLN cc_start: 0.8656 (tm-30) cc_final: 0.8291 (tm-30) REVERT: A 1126 ASP cc_start: 0.8236 (t0) cc_final: 0.8006 (t0) REVERT: A 1140 MET cc_start: 0.8435 (ttp) cc_final: 0.8096 (tmm) REVERT: A 1324 ARG cc_start: 0.7787 (ttt180) cc_final: 0.7234 (ttm-80) REVERT: A 1355 MET cc_start: 0.8806 (pmm) cc_final: 0.8433 (pmm) REVERT: A 1381 GLU cc_start: 0.8659 (pm20) cc_final: 0.8185 (pm20) REVERT: A 1693 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8154 (tp30) REVERT: A 1729 MET cc_start: 0.6312 (ptp) cc_final: 0.5915 (ptt) REVERT: A 1746 TRP cc_start: 0.8610 (p90) cc_final: 0.8097 (p90) REVERT: A 2012 LEU cc_start: 0.8556 (pp) cc_final: 0.8231 (tp) REVERT: A 2015 MET cc_start: 0.8161 (tpp) cc_final: 0.7892 (tpt) outliers start: 59 outliers final: 47 residues processed: 239 average time/residue: 0.2538 time to fit residues: 91.2533 Evaluate side-chains 241 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 192 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 810 CYS Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 954 ASN Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 1160 ASN Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1255 HIS Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1265 LEU Chi-restraints excluded: chain A residue 1300 THR Chi-restraints excluded: chain A residue 1372 LEU Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1444 MET Chi-restraints excluded: chain A residue 1556 LEU Chi-restraints excluded: chain A residue 1595 THR Chi-restraints excluded: chain A residue 1672 MET Chi-restraints excluded: chain A residue 1709 THR Chi-restraints excluded: chain A residue 1738 ILE Chi-restraints excluded: chain A residue 1743 THR Chi-restraints excluded: chain A residue 1769 CYS Chi-restraints excluded: chain A residue 1806 VAL Chi-restraints excluded: chain A residue 1868 ASN Chi-restraints excluded: chain A residue 1886 LEU Chi-restraints excluded: chain A residue 1954 VAL Chi-restraints excluded: chain A residue 1957 LEU Chi-restraints excluded: chain A residue 1965 ASP Chi-restraints excluded: chain A residue 1969 VAL Chi-restraints excluded: chain A residue 1977 ASP Chi-restraints excluded: chain A residue 2007 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 7.9990 chunk 176 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 83 optimal weight: 0.3980 chunk 122 optimal weight: 10.0000 chunk 185 optimal weight: 20.0000 chunk 170 optimal weight: 5.9990 chunk 147 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 757 ASN ** A 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 959 ASN A1255 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.4625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 15117 Z= 0.329 Angle : 0.800 10.716 20379 Z= 0.402 Chirality : 0.047 0.265 2256 Planarity : 0.005 0.098 2599 Dihedral : 6.393 60.253 2026 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.38 % Allowed : 11.52 % Favored : 88.10 % Rotamer: Outliers : 3.36 % Allowed : 25.57 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 4.55 % Twisted General : 0.39 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.19), residues: 1832 helix: -0.69 (0.19), residues: 724 sheet: -0.94 (0.41), residues: 153 loop : -2.92 (0.19), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 520 HIS 0.019 0.001 HIS A1255 PHE 0.023 0.002 PHE A 352 TYR 0.015 0.001 TYR A1864 ARG 0.004 0.000 ARG A1189 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 194 time to evaluate : 1.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 TYR cc_start: 0.8281 (t80) cc_final: 0.8035 (t80) REVERT: A 406 ILE cc_start: 0.7264 (OUTLIER) cc_final: 0.6767 (pt) REVERT: A 513 ASN cc_start: 0.8799 (OUTLIER) cc_final: 0.8129 (t0) REVERT: A 757 ASN cc_start: 0.8921 (OUTLIER) cc_final: 0.8568 (t0) REVERT: A 773 LYS cc_start: 0.9128 (tttt) cc_final: 0.8831 (ttmm) REVERT: A 777 MET cc_start: 0.8772 (mtp) cc_final: 0.8483 (mtp) REVERT: A 848 MET cc_start: 0.7935 (tpp) cc_final: 0.7691 (tpt) REVERT: A 878 MET cc_start: 0.8773 (pmm) cc_final: 0.8543 (pmm) REVERT: A 933 GLN cc_start: 0.8727 (tm-30) cc_final: 0.8367 (tm-30) REVERT: A 1126 ASP cc_start: 0.8326 (t0) cc_final: 0.8125 (t0) REVERT: A 1140 MET cc_start: 0.8478 (ttp) cc_final: 0.8049 (tmm) REVERT: A 1324 ARG cc_start: 0.7822 (ttt180) cc_final: 0.7256 (ttm-80) REVERT: A 1381 GLU cc_start: 0.8631 (pm20) cc_final: 0.8191 (pm20) REVERT: A 1693 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8176 (tp30) REVERT: A 1746 TRP cc_start: 0.8616 (p90) cc_final: 0.8089 (p90) REVERT: A 1749 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7607 (mm-30) REVERT: A 2015 MET cc_start: 0.8203 (tpp) cc_final: 0.7937 (tpt) outliers start: 55 outliers final: 47 residues processed: 234 average time/residue: 0.2726 time to fit residues: 95.7112 Evaluate side-chains 239 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 189 time to evaluate : 1.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 757 ASN Chi-restraints excluded: chain A residue 810 CYS Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 954 ASN Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 1160 ASN Chi-restraints excluded: chain A residue 1255 HIS Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1265 LEU Chi-restraints excluded: chain A residue 1300 THR Chi-restraints excluded: chain A residue 1372 LEU Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1444 MET Chi-restraints excluded: chain A residue 1556 LEU Chi-restraints excluded: chain A residue 1595 THR Chi-restraints excluded: chain A residue 1672 MET Chi-restraints excluded: chain A residue 1709 THR Chi-restraints excluded: chain A residue 1738 ILE Chi-restraints excluded: chain A residue 1769 CYS Chi-restraints excluded: chain A residue 1806 VAL Chi-restraints excluded: chain A residue 1835 LEU Chi-restraints excluded: chain A residue 1868 ASN Chi-restraints excluded: chain A residue 1886 LEU Chi-restraints excluded: chain A residue 1910 ILE Chi-restraints excluded: chain A residue 1954 VAL Chi-restraints excluded: chain A residue 1957 LEU Chi-restraints excluded: chain A residue 1965 ASP Chi-restraints excluded: chain A residue 1977 ASP Chi-restraints excluded: chain A residue 2007 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 1.9990 chunk 157 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 147 optimal weight: 0.0670 chunk 61 optimal weight: 0.4980 chunk 151 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 overall best weight: 1.3124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 757 ASN ** A 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 959 ASN ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1255 HIS A1566 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.110068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.084328 restraints weight = 35406.998| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 4.02 r_work: 0.3155 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.4697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15117 Z= 0.216 Angle : 0.772 12.506 20379 Z= 0.385 Chirality : 0.046 0.254 2256 Planarity : 0.005 0.095 2599 Dihedral : 6.322 59.860 2026 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.97 % Favored : 88.76 % Rotamer: Outliers : 3.30 % Allowed : 26.54 % Favored : 70.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 4.55 % Twisted General : 0.45 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.19), residues: 1832 helix: -0.56 (0.19), residues: 723 sheet: -0.57 (0.42), residues: 146 loop : -2.95 (0.18), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 520 HIS 0.020 0.001 HIS A1255 PHE 0.023 0.001 PHE A 352 TYR 0.032 0.001 TYR A1348 ARG 0.004 0.000 ARG A1928 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3314.89 seconds wall clock time: 61 minutes 9.75 seconds (3669.75 seconds total)