Starting phenix.real_space_refine on Sun Dec 10 14:45:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l42_0828/12_2023/6l42_0828.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l42_0828/12_2023/6l42_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_0828/12_2023/6l42_0828.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l42_0828/12_2023/6l42_0828.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l42_0828/12_2023/6l42_0828.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l42_0828/12_2023/6l42_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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 7.98, per 1000 atoms: 0.54 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: 5.53 Conformation dependent library (CDL) restraints added in 2.7 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: 5.89 Time building geometry restraints manager: 6.10 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: 0.460 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: 3.080 Check model and map are aligned: 0.220 Set scattering table: 0.120 Process input model: 41.710 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.060 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.030 ------------------------------------------------------------------------------- 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 : 1.681 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 outliers start: 108 outliers final: 53 residues processed: 415 average time/residue: 0.3460 time to fit residues: 196.5967 Evaluate side-chains 272 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 219 time to evaluate : 1.735 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 3 residues processed: 53 average time/residue: 0.2135 time to fit residues: 20.0172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 78 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 95 optimal weight: 0.4980 chunk 75 optimal weight: 0.8980 chunk 145 optimal weight: 0.7980 chunk 56 optimal weight: 8.9990 chunk 88 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 168 optimal weight: 10.0000 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN A 376 ASN A 841 ASN ** A 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 HIS A 964 ASN A1035 HIS A1190 HIS A1204 GLN ** A1239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1255 HIS A1776 ASN A1930 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15117 Z= 0.260 Angle : 0.883 10.570 20379 Z= 0.462 Chirality : 0.050 0.228 2256 Planarity : 0.007 0.105 2599 Dihedral : 7.777 65.481 2020 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.66 % Allowed : 11.14 % Favored : 88.21 % Rotamer: Outliers : 2.81 % Allowed : 18.23 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 3.03 % Twisted General : 0.67 % 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: -4.37 (0.17), residues: 1832 helix: -2.27 (0.17), residues: 709 sheet: -1.87 (0.42), residues: 140 loop : -3.68 (0.17), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1521 HIS 0.014 0.001 HIS A 916 PHE 0.025 0.002 PHE A1545 TYR 0.024 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 296 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 250 time to evaluate : 1.745 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 outliers start: 46 outliers final: 24 residues processed: 275 average time/residue: 0.2978 time to fit residues: 118.8512 Evaluate side-chains 229 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 205 time to evaluate : 1.642 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1549 time to fit residues: 9.0224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 140 optimal weight: 0.6980 chunk 115 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 169 optimal weight: 7.9990 chunk 182 optimal weight: 8.9990 chunk 150 optimal weight: 6.9990 chunk 167 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 480 GLN A 513 ASN A 865 GLN ** A 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 959 ASN A1292 ASN A1391 HIS A1620 GLN A1776 ASN ** A1846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15117 Z= 0.253 Angle : 0.784 10.621 20379 Z= 0.403 Chirality : 0.046 0.242 2256 Planarity : 0.006 0.096 2599 Dihedral : 7.145 60.876 2020 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.44 % Allowed : 11.24 % Favored : 88.32 % Rotamer: Outliers : 3.06 % Allowed : 20.73 % Favored : 76.21 % 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: -3.76 (0.18), residues: 1832 helix: -1.77 (0.18), residues: 705 sheet: -1.34 (0.42), residues: 143 loop : -3.36 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 888 HIS 0.003 0.001 HIS A 706 PHE 0.026 0.002 PHE A1561 TYR 0.021 0.002 TYR A1348 ARG 0.011 0.001 ARG A 226 *********************** 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 278 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 228 time to evaluate : 1.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 20 residues processed: 259 average time/residue: 0.2968 time to fit residues: 111.8486 Evaluate side-chains 213 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 193 time to evaluate : 1.836 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1413 time to fit residues: 7.8005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 0.9980 chunk 127 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 80 optimal weight: 7.9990 chunk 113 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 chunk 179 optimal weight: 8.9990 chunk 88 optimal weight: 5.9990 chunk 160 optimal weight: 9.9990 chunk 48 optimal weight: 8.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1292 ASN ** A1846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15117 Z= 0.335 Angle : 0.785 10.215 20379 Z= 0.404 Chirality : 0.047 0.250 2256 Planarity : 0.006 0.098 2599 Dihedral : 6.965 61.280 2020 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.49 % Allowed : 12.50 % Favored : 87.01 % Rotamer: Outliers : 2.51 % Allowed : 23.55 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 4.55 % Twisted General : 0.51 % 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: -1.58 (0.18), residues: 712 sheet: -1.15 (0.44), residues: 135 loop : -3.22 (0.18), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A1746 HIS 0.006 0.001 HIS A1564 PHE 0.025 0.002 PHE A1561 TYR 0.017 0.002 TYR A1071 ARG 0.005 0.000 ARG A 726 *********************** 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 233 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 192 time to evaluate : 1.543 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 outliers start: 41 outliers final: 23 residues processed: 219 average time/residue: 0.2749 time to fit residues: 89.0994 Evaluate side-chains 202 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 179 time to evaluate : 1.824 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1368 time to fit residues: 8.3761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 133 optimal weight: 9.9990 chunk 74 optimal weight: 0.9980 chunk 153 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 799 HIS ** A 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 HIS A 954 ASN A1255 HIS ** A1707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15117 Z= 0.287 Angle : 0.760 9.784 20379 Z= 0.389 Chirality : 0.046 0.241 2256 Planarity : 0.005 0.095 2599 Dihedral : 6.812 62.162 2020 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.44 % Allowed : 11.90 % Favored : 87.66 % Rotamer: Outliers : 1.83 % Allowed : 24.65 % Favored : 73.52 % 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: -3.28 (0.18), residues: 1832 helix: -1.33 (0.19), residues: 711 sheet: -1.07 (0.44), residues: 137 loop : -3.11 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A1746 HIS 0.004 0.001 HIS A 80 PHE 0.027 0.002 PHE A 352 TYR 0.014 0.001 TYR A1864 ARG 0.010 0.000 ARG A1800 *********************** 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 228 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 198 time to evaluate : 1.753 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 outliers start: 30 outliers final: 15 residues processed: 219 average time/residue: 0.2926 time to fit residues: 94.4678 Evaluate side-chains 199 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 184 time to evaluate : 1.695 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1475 time to fit residues: 6.3794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 2.9990 chunk 161 optimal weight: 6.9990 chunk 35 optimal weight: 0.0570 chunk 105 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 179 optimal weight: 9.9990 chunk 149 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 overall best weight: 1.3502 ------------------------------------------------------------------------------- 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 A1255 HIS A1403 HIS ** A1707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.4181 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= 0.203 Angle : 0.740 11.403 20379 Z= 0.374 Chirality : 0.045 0.223 2256 Planarity : 0.005 0.095 2599 Dihedral : 6.612 61.476 2020 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.33 % Allowed : 11.24 % Favored : 88.43 % Rotamer: Outliers : 1.28 % Allowed : 26.18 % Favored : 72.54 % 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: -3.07 (0.19), residues: 1832 helix: -1.13 (0.19), residues: 714 sheet: -0.92 (0.44), residues: 137 loop : -3.03 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP A1746 HIS 0.004 0.001 HIS A1573 PHE 0.028 0.001 PHE A1793 TYR 0.015 0.001 TYR A 193 ARG 0.010 0.000 ARG A1800 *********************** 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 224 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 203 time to evaluate : 1.595 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 outliers start: 21 outliers final: 10 residues processed: 214 average time/residue: 0.2861 time to fit residues: 90.7567 Evaluate side-chains 195 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 185 time to evaluate : 1.735 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1430 time to fit residues: 5.0962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 102 optimal weight: 0.6980 chunk 131 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 151 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 179 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 A1255 HIS A1292 ASN ** A1707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15117 Z= 0.241 Angle : 0.741 10.716 20379 Z= 0.374 Chirality : 0.045 0.231 2256 Planarity : 0.005 0.097 2599 Dihedral : 6.508 61.614 2020 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.33 % Allowed : 11.24 % Favored : 88.43 % Rotamer: Outliers : 2.08 % Allowed : 26.30 % Favored : 71.62 % 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: -2.98 (0.19), residues: 1832 helix: -1.04 (0.19), residues: 725 sheet: -0.77 (0.44), residues: 137 loop : -3.02 (0.19), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP A1746 HIS 0.003 0.001 HIS A1573 PHE 0.021 0.001 PHE A1793 TYR 0.017 0.001 TYR A 193 ARG 0.008 0.000 ARG A1800 *********************** 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 225 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 191 time to evaluate : 1.734 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 outliers start: 34 outliers final: 19 residues processed: 216 average time/residue: 0.2864 time to fit residues: 92.1232 Evaluate side-chains 203 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 184 time to evaluate : 1.820 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1472 time to fit residues: 7.7862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 35 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 113 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 chunk 16 optimal weight: 0.0470 chunk 140 optimal weight: 0.7980 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 757 ASN ** A 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 959 ASN A1255 HIS ** A1707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.4497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15117 Z= 0.183 Angle : 0.726 9.261 20379 Z= 0.364 Chirality : 0.044 0.221 2256 Planarity : 0.005 0.093 2599 Dihedral : 6.259 60.337 2020 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.33 % Allowed : 10.59 % Favored : 89.08 % Rotamer: Outliers : 0.86 % Allowed : 26.97 % Favored : 72.17 % 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: -2.82 (0.19), residues: 1832 helix: -0.86 (0.19), residues: 727 sheet: -0.66 (0.45), residues: 136 loop : -2.98 (0.19), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP A1746 HIS 0.003 0.001 HIS A1564 PHE 0.018 0.001 PHE A1793 TYR 0.016 0.001 TYR A 193 ARG 0.007 0.000 ARG A1800 *********************** 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 216 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 202 time to evaluate : 1.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 4 residues processed: 211 average time/residue: 0.2896 time to fit residues: 90.7222 Evaluate side-chains 188 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 184 time to evaluate : 1.753 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1461 time to fit residues: 3.5194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 156 optimal weight: 10.0000 chunk 167 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 131 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 150 optimal weight: 0.0770 chunk 158 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 overall best weight: 1.7944 ------------------------------------------------------------------------------- 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 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 959 ASN ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1255 HIS ** A1707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.4609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15117 Z= 0.225 Angle : 0.745 10.022 20379 Z= 0.376 Chirality : 0.045 0.225 2256 Planarity : 0.005 0.095 2599 Dihedral : 6.215 60.415 2020 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.33 % Allowed : 11.08 % Favored : 88.59 % Rotamer: Outliers : 0.98 % Allowed : 27.77 % Favored : 71.25 % 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: -2.75 (0.19), residues: 1832 helix: -0.78 (0.19), residues: 731 sheet: -0.65 (0.43), residues: 142 loop : -2.97 (0.19), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP A1746 HIS 0.003 0.001 HIS A1564 PHE 0.026 0.001 PHE A 166 TYR 0.023 0.001 TYR A1308 ARG 0.007 0.000 ARG A1800 *********************** 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 205 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 189 time to evaluate : 1.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 11 residues processed: 195 average time/residue: 0.3094 time to fit residues: 89.2735 Evaluate side-chains 189 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 178 time to evaluate : 1.677 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2261 time to fit residues: 7.7715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 3.9990 chunk 176 optimal weight: 5.9990 chunk 107 optimal weight: 0.4980 chunk 83 optimal weight: 8.9990 chunk 122 optimal weight: 7.9990 chunk 185 optimal weight: 20.0000 chunk 170 optimal weight: 6.9990 chunk 147 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 113 optimal weight: 8.9990 chunk 90 optimal weight: 0.9980 overall best weight: 3.0986 ------------------------------------------------------------------------------- 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 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 959 ASN ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.4712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 15117 Z= 0.315 Angle : 0.805 11.303 20379 Z= 0.404 Chirality : 0.047 0.243 2256 Planarity : 0.005 0.097 2599 Dihedral : 6.413 62.237 2020 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.38 % Allowed : 11.84 % Favored : 87.77 % Rotamer: Outliers : 0.43 % Allowed : 28.26 % Favored : 71.31 % 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: -2.72 (0.19), residues: 1832 helix: -0.76 (0.19), residues: 724 sheet: -0.70 (0.41), residues: 146 loop : -2.94 (0.19), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP A1746 HIS 0.004 0.001 HIS A 706 PHE 0.024 0.002 PHE A 166 TYR 0.021 0.002 TYR A 923 ARG 0.007 0.000 ARG A 30 ********************** 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 184 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 177 time to evaluate : 1.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 181 average time/residue: 0.3028 time to fit residues: 80.7315 Evaluate side-chains 172 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 167 time to evaluate : 1.764 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1464 time to fit residues: 3.8492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 3.9990 chunk 157 optimal weight: 20.0000 chunk 45 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 21 optimal weight: 0.4980 chunk 41 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 151 optimal weight: 0.9990 chunk 18 optimal weight: 7.9990 chunk 27 optimal weight: 8.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- 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 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 959 ASN ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.109048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.083491 restraints weight = 35738.319| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 4.07 r_work: 0.3142 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.4798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15117 Z= 0.231 Angle : 0.777 13.071 20379 Z= 0.390 Chirality : 0.045 0.231 2256 Planarity : 0.005 0.096 2599 Dihedral : 6.268 61.551 2020 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.30 % Favored : 88.43 % Rotamer: Outliers : 0.43 % Allowed : 28.99 % Favored : 70.58 % 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: -2.67 (0.19), residues: 1832 helix: -0.70 (0.19), residues: 730 sheet: -0.77 (0.42), residues: 138 loop : -2.90 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP A1746 HIS 0.002 0.001 HIS A 706 PHE 0.024 0.001 PHE A 411 TYR 0.028 0.001 TYR A 923 ARG 0.012 0.000 ARG A1800 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3168.66 seconds wall clock time: 58 minutes 39.85 seconds (3519.85 seconds total)