Starting phenix.real_space_refine on Sat Jul 4 07:24:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jpl_22415/07_2026/7jpl_22415_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jpl_22415/07_2026/7jpl_22415.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 { model { file = "/net/cci-nas-00/data/ceres_data/7jpl_22415/07_2026/7jpl_22415_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jpl_22415/07_2026/7jpl_22415_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jpl_22415/07_2026/7jpl_22415.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jpl_22415/07_2026/7jpl_22415.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 P 10 5.49 5 S 109 5.16 5 C 12113 2.51 5 N 2981 2.21 5 O 3348 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 153 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18565 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1114, 8998 Classifications: {'peptide': 1114} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 36, 'TRANS': 1077} Chain breaks: 9 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1326 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain breaks: 4 Chain: "F" Number of atoms: 7804 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 973, 7796 Classifications: {'peptide': 973} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 927} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 973, 7796 Classifications: {'peptide': 973} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 927} Chain breaks: 2 bond proxies already assigned to first conformer: 7954 Chain: "A" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 436 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'3PE': 9, 'C8U': 1, 'PC1': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain breaks: 1 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'3PE:plan-1': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 5.23, per 1000 atoms: 0.28 Number of scatterers: 18565 At special positions: 0 Unit cell: (143.706, 137.022, 155.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 1 19.99 S 109 16.00 P 10 15.00 F 3 9.00 O 3348 8.00 N 2981 7.00 C 12113 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 226 " - pdb=" SG CYS A 254 " distance=2.03 Simple disulfide: pdb=" SG CYS A 245 " - pdb=" SG CYS A 261 " distance=2.03 Simple disulfide: pdb=" SG CYS A 957 " - pdb=" SG CYS A 968 " distance=2.02 Simple disulfide: pdb=" SG CYS A1338 " - pdb=" SG CYS A1352 " distance=2.04 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 80 " distance=2.04 Simple disulfide: pdb=" SG CYS F 305 " - pdb=" SG CYS F1047 " distance=2.03 Simple disulfide: pdb=" SG CYS F 356 " - pdb=" SG CYS F1062 " distance=2.03 Simple disulfide: pdb=" SG CYS F 406 " - pdb=" SG CYS F1074 " distance=2.03 Simple disulfide: pdb=" SG CYS F 670 " - pdb=" SG CYS F 700 " distance=2.03 Simple disulfide: pdb=" SG CYS F 844 " - pdb=" SG CYS F 853 " distance=2.03 Simple disulfide: pdb=" SG CYS F 907 " - pdb=" SG CYS F 977 " distance=2.03 Simple disulfide: pdb=" SG CYS F 999 " - pdb=" SG CYS F1029 " distance=2.03 Simple disulfide: pdb=" SG CYS F1002 " - pdb=" SG CYS F1027 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.90 Conformation dependent library (CDL) restraints added in 1.1 seconds 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4270 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 16 sheets defined 52.3% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 52 through 59 removed outlier: 4.070A pdb=" N ILE A 56 " --> pdb=" O PRO A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 70 removed outlier: 3.617A pdb=" N LEU A 68 " --> pdb=" O ASN A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 88 removed outlier: 3.678A pdb=" N LYS A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 107 removed outlier: 3.963A pdb=" N PHE A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL A 96 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE A 97 " --> pdb=" O PHE A 93 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER A 98 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA A 101 " --> pdb=" O PHE A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 141 removed outlier: 3.667A pdb=" N GLN A 141 " --> pdb=" O ALA A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 170 removed outlier: 3.647A pdb=" N PHE A 167 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL A 169 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A 170 " --> pdb=" O PHE A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 179 removed outlier: 3.998A pdb=" N LEU A 175 " --> pdb=" O ARG A 171 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL A 176 " --> pdb=" O PRO A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 187 Processing helix chain 'A' and resid 196 through 218 removed outlier: 3.592A pdb=" N PHE A 205 " --> pdb=" O LEU A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 290 removed outlier: 3.517A pdb=" N TYR A 286 " --> pdb=" O MET A 282 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS A 288 " --> pdb=" O THR A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 305 removed outlier: 3.602A pdb=" N VAL A 297 " --> pdb=" O GLY A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 320 removed outlier: 3.572A pdb=" N PHE A 314 " --> pdb=" O PRO A 310 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 343 Processing helix chain 'A' and resid 433 through 436 removed outlier: 3.641A pdb=" N TRP A 436 " --> pdb=" O VAL A 433 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 433 through 436' Processing helix chain 'A' and resid 437 through 450 removed outlier: 3.681A pdb=" N ILE A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 477 removed outlier: 3.614A pdb=" N ASP A 465 " --> pdb=" O THR A 461 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN A 468 " --> pdb=" O GLN A 464 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ARG A 469 " --> pdb=" O ASP A 465 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 472 " --> pdb=" O ASN A 468 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N PHE A 475 " --> pdb=" O LEU A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 496 through 512 removed outlier: 4.009A pdb=" N ASP A 500 " --> pdb=" O PHE A 496 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N CYS A 501 " --> pdb=" O ASN A 497 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N PHE A 502 " --> pdb=" O ARG A 498 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 503 " --> pdb=" O PHE A 499 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL A 504 " --> pdb=" O ASP A 500 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LEU A 509 " --> pdb=" O CYS A 505 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU A 510 " --> pdb=" O SER A 506 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU A 511 " --> pdb=" O GLY A 507 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A 512 " --> pdb=" O ILE A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 530 removed outlier: 4.009A pdb=" N LEU A 527 " --> pdb=" O GLY A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 535 Processing helix chain 'A' and resid 536 through 541 removed outlier: 3.771A pdb=" N LYS A 540 " --> pdb=" O PHE A 536 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TYR A 541 " --> pdb=" O LYS A 537 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 536 through 541' Processing helix chain 'A' and resid 542 through 548 Processing helix chain 'A' and resid 548 through 556 removed outlier: 3.676A pdb=" N LEU A 552 " --> pdb=" O LEU A 548 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ASN A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 581 removed outlier: 3.736A pdb=" N PHE A 567 " --> pdb=" O LEU A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 612 removed outlier: 3.655A pdb=" N ILE A 605 " --> pdb=" O PRO A 601 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A 610 " --> pdb=" O SER A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 626 removed outlier: 3.644A pdb=" N VAL A 619 " --> pdb=" O ASP A 615 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR A 621 " --> pdb=" O ASN A 617 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY A 623 " --> pdb=" O VAL A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 636 Processing helix chain 'A' and resid 637 through 647 removed outlier: 4.005A pdb=" N PHE A 641 " --> pdb=" O VAL A 637 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE A 645 " --> pdb=" O PHE A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 656 removed outlier: 3.836A pdb=" N ILE A 651 " --> pdb=" O CYS A 647 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 656 " --> pdb=" O LEU A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 662 removed outlier: 3.601A pdb=" N ASP A 662 " --> pdb=" O ALA A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 673 removed outlier: 3.515A pdb=" N ALA A 667 " --> pdb=" O ASN A 663 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU A 668 " --> pdb=" O LEU A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 818 removed outlier: 3.668A pdb=" N THR A 802 " --> pdb=" O ALA A 798 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU A 807 " --> pdb=" O ASN A 803 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE A 808 " --> pdb=" O PHE A 804 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU A 810 " --> pdb=" O LEU A 806 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU A 816 " --> pdb=" O SER A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 853 removed outlier: 3.841A pdb=" N GLN A 830 " --> pdb=" O SER A 826 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE A 831 " --> pdb=" O VAL A 827 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL A 842 " --> pdb=" O ALA A 838 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL A 845 " --> pdb=" O SER A 841 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU A 846 " --> pdb=" O VAL A 842 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE A 847 " --> pdb=" O PHE A 843 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL A 848 " --> pdb=" O THR A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 881 removed outlier: 4.130A pdb=" N LEU A 874 " --> pdb=" O ILE A 870 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL A 875 " --> pdb=" O LEU A 871 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL A 876 " --> pdb=" O ASP A 872 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE A 881 " --> pdb=" O ALA A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 899 Processing helix chain 'A' and resid 900 through 901 No H-bonds generated for 'chain 'A' and resid 900 through 901' Processing helix chain 'A' and resid 902 through 907 removed outlier: 3.838A pdb=" N ARG A 906 " --> pdb=" O ARG A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 928 removed outlier: 3.719A pdb=" N VAL A 918 " --> pdb=" O LEU A 914 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N CYS A 920 " --> pdb=" O HIS A 916 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ARG A 926 " --> pdb=" O PHE A 922 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N THR A 927 " --> pdb=" O VAL A 923 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A 928 " --> pdb=" O ALA A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 950 removed outlier: 3.590A pdb=" N GLN A 939 " --> pdb=" O THR A 935 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N CYS A 944 " --> pdb=" O PHE A 940 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE A 945 " --> pdb=" O MET A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 979 No H-bonds generated for 'chain 'A' and resid 977 through 979' Processing helix chain 'A' and resid 999 through 1012 Processing helix chain 'A' and resid 1015 through 1024 removed outlier: 3.553A pdb=" N LEU A1019 " --> pdb=" O GLY A1015 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG A1022 " --> pdb=" O GLN A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1042 removed outlier: 3.822A pdb=" N ALA A1042 " --> pdb=" O VAL A1039 " (cutoff:3.500A) Processing helix chain 'A' and resid 1043 through 1052 removed outlier: 4.163A pdb=" N ILE A1049 " --> pdb=" O PHE A1045 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1068 Processing helix chain 'A' and resid 1083 through 1094 Processing helix chain 'A' and resid 1105 through 1117 removed outlier: 4.130A pdb=" N VAL A1111 " --> pdb=" O TYR A1107 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL A1114 " --> pdb=" O GLN A1110 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL A1115 " --> pdb=" O VAL A1111 " (cutoff:3.500A) Processing helix chain 'A' and resid 1117 through 1136 Processing helix chain 'A' and resid 1151 through 1173 removed outlier: 3.508A pdb=" N MET A1165 " --> pdb=" O PHE A1161 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS A1168 " --> pdb=" O GLU A1164 " (cutoff:3.500A) Processing helix chain 'A' and resid 1180 through 1204 removed outlier: 3.791A pdb=" N GLU A1201 " --> pdb=" O VAL A1197 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP A1203 " --> pdb=" O LEU A1199 " (cutoff:3.500A) Processing helix chain 'A' and resid 1232 through 1235 removed outlier: 3.661A pdb=" N PHE A1235 " --> pdb=" O SER A1232 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1232 through 1235' Processing helix chain 'A' and resid 1236 through 1241 removed outlier: 4.102A pdb=" N VAL A1240 " --> pdb=" O ARG A1236 " (cutoff:3.500A) Processing helix chain 'A' and resid 1242 through 1249 removed outlier: 3.642A pdb=" N SER A1248 " --> pdb=" O LYS A1245 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG A1249 " --> pdb=" O LEU A1246 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1266 removed outlier: 3.831A pdb=" N LEU A1256 " --> pdb=" O GLY A1252 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER A1263 " --> pdb=" O THR A1259 " (cutoff:3.500A) Processing helix chain 'A' and resid 1267 through 1289 removed outlier: 4.141A pdb=" N ALA A1271 " --> pdb=" O LEU A1267 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU A1273 " --> pdb=" O TYR A1269 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE A1274 " --> pdb=" O VAL A1270 " (cutoff:3.500A) Processing helix chain 'A' and resid 1308 through 1322 Processing helix chain 'A' and resid 1324 through 1332 removed outlier: 3.662A pdb=" N LEU A1330 " --> pdb=" O GLN A1326 " (cutoff:3.500A) Processing helix chain 'A' and resid 1356 through 1382 removed outlier: 3.621A pdb=" N ILE A1362 " --> pdb=" O TYR A1358 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET A1366 " --> pdb=" O ILE A1362 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A1373 " --> pdb=" O ALA A1369 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL A1379 " --> pdb=" O LEU A1375 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE A1380 " --> pdb=" O PHE A1376 " (cutoff:3.500A) Processing helix chain 'A' and resid 1383 through 1388 removed outlier: 3.790A pdb=" N THR A1388 " --> pdb=" O PHE A1384 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1410 removed outlier: 3.528A pdb=" N TYR A1409 " --> pdb=" O ILE A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1423 through 1429 removed outlier: 3.780A pdb=" N ILE A1429 " --> pdb=" O LEU A1426 " (cutoff:3.500A) Processing helix chain 'A' and resid 1430 through 1434 Processing helix chain 'E' and resid 6 through 27 removed outlier: 3.895A pdb=" N THR E 12 " --> pdb=" O LYS E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 127 removed outlier: 4.596A pdb=" N ILE E 123 " --> pdb=" O ILE E 119 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N CYS E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 164 removed outlier: 3.560A pdb=" N ALA E 140 " --> pdb=" O LEU E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 204 removed outlier: 3.627A pdb=" N VAL E 190 " --> pdb=" O CYS E 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 53 removed outlier: 3.579A pdb=" N ILE F 33 " --> pdb=" O SER F 29 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY F 53 " --> pdb=" O LYS F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 65 removed outlier: 4.029A pdb=" N TYR F 64 " --> pdb=" O ILE F 60 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N GLN F 65 " --> pdb=" O TYR F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 110 removed outlier: 3.527A pdb=" N ALA F 96 " --> pdb=" O ASN F 92 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU F 97 " --> pdb=" O ARG F 93 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG F 99 " --> pdb=" O LYS F 95 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU F 100 " --> pdb=" O ALA F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 188 Processing helix chain 'F' and resid 191 through 202 Processing helix chain 'F' and resid 243 through 250 Processing helix chain 'F' and resid 268 through 283 removed outlier: 3.985A pdb=" N LYS F 272 " --> pdb=" O GLY F 268 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 325 Processing helix chain 'F' and resid 334 through 346 Processing helix chain 'F' and resid 371 through 379 removed outlier: 3.681A pdb=" N PHE F 375 " --> pdb=" O ALA F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 406 Processing helix chain 'F' and resid 420 through 425 Processing helix chain 'F' and resid 426 through 430 removed outlier: 3.895A pdb=" N LEU F 429 " --> pdb=" O GLN F 426 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP F 430 " --> pdb=" O GLU F 427 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 426 through 430' Processing helix chain 'F' and resid 433 through 439 Processing helix chain 'F' and resid 440 through 444 removed outlier: 3.675A pdb=" N LYS F 444 " --> pdb=" O ASP F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 496 through 500 Processing helix chain 'F' and resid 542 through 546 removed outlier: 3.718A pdb=" N ARG F 546 " --> pdb=" O LEU F 543 " (cutoff:3.500A) Processing helix chain 'F' and resid 571 through 581 removed outlier: 3.659A pdb=" N GLU F 575 " --> pdb=" O ASP F 571 " (cutoff:3.500A) Processing helix chain 'F' and resid 640 through 650 removed outlier: 3.905A pdb=" N THR F 650 " --> pdb=" O ARG F 646 " (cutoff:3.500A) Processing helix chain 'F' and resid 652 through 654 No H-bonds generated for 'chain 'F' and resid 652 through 654' Processing helix chain 'F' and resid 655 through 660 Processing helix chain 'F' and resid 678 through 693 Processing helix chain 'F' and resid 701 through 722 Processing helix chain 'F' and resid 748 through 753 removed outlier: 3.600A pdb=" N GLU F 753 " --> pdb=" O LYS F 749 " (cutoff:3.500A) Processing helix chain 'F' and resid 760 through 763 Processing helix chain 'F' and resid 764 through 773 removed outlier: 3.570A pdb=" N ASP F 772 " --> pdb=" O LYS F 768 " (cutoff:3.500A) Processing helix chain 'F' and resid 820 through 830 Processing helix chain 'F' and resid 877 through 881 Processing helix chain 'F' and resid 882 through 892 Processing helix chain 'F' and resid 1045 through 1050 removed outlier: 3.553A pdb=" N MET F1049 " --> pdb=" O ASP F1045 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 225 through 228 Processing sheet with id=AA2, first strand: chain 'A' and resid 955 through 956 Processing sheet with id=AA3, first strand: chain 'A' and resid 971 through 975 Processing sheet with id=AA4, first strand: chain 'E' and resid 79 through 81 removed outlier: 3.600A pdb=" N ASN E 79 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA E 33 " --> pdb=" O PHE E 51 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 68 through 72 Processing sheet with id=AA6, first strand: chain 'F' and resid 124 through 125 removed outlier: 6.035A pdb=" N VAL F 124 " --> pdb=" O GLN F 145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'F' and resid 127 through 128 removed outlier: 6.822A pdb=" N TYR F 127 " --> pdb=" O VAL F 168 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL F 468 " --> pdb=" O LEU F 487 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N VAL F 489 " --> pdb=" O LEU F 466 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU F 466 " --> pdb=" O VAL F 489 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLY F 491 " --> pdb=" O GLY F 464 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLY F 464 " --> pdb=" O GLY F 491 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ASP F 493 " --> pdb=" O ILE F 462 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE F 462 " --> pdb=" O ASP F 493 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N SER F 495 " --> pdb=" O LEU F 460 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N LEU F 460 " --> pdb=" O SER F 495 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 127 through 128 removed outlier: 6.822A pdb=" N TYR F 127 " --> pdb=" O VAL F 168 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL F 468 " --> pdb=" O LEU F 487 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N VAL F 489 " --> pdb=" O LEU F 466 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU F 466 " --> pdb=" O VAL F 489 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLY F 491 " --> pdb=" O GLY F 464 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLY F 464 " --> pdb=" O GLY F 491 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ASP F 493 " --> pdb=" O ILE F 462 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE F 462 " --> pdb=" O ASP F 493 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N SER F 495 " --> pdb=" O LEU F 460 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N LEU F 460 " --> pdb=" O SER F 495 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 152 through 153 Processing sheet with id=AB1, first strand: chain 'F' and resid 300 through 302 removed outlier: 6.154A pdb=" N LYS F 254 " --> pdb=" O PHE F 290 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N ASN F 292 " --> pdb=" O LYS F 254 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N MET F 256 " --> pdb=" O ASN F 292 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ALA F 294 " --> pdb=" O MET F 256 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE F 258 " --> pdb=" O ALA F 294 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N PHE F 296 " --> pdb=" O ILE F 258 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N VAL F 260 " --> pdb=" O PHE F 296 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LYS F 358 " --> pdb=" O ARG F 385 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N PHE F 387 " --> pdb=" O LYS F 358 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ILE F 360 " --> pdb=" O PHE F 387 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N PHE F 389 " --> pdb=" O ILE F 360 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU F 362 " --> pdb=" O PHE F 389 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N VAL F 391 " --> pdb=" O LEU F 362 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR F 364 " --> pdb=" O VAL F 391 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 523 through 525 removed outlier: 6.183A pdb=" N ALA F 516 " --> pdb=" O LEU F 524 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 661 through 663 removed outlier: 3.741A pdb=" N PHE F 736 " --> pdb=" O GLY F 816 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LYS F 818 " --> pdb=" O LYS F 733 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 661 through 663 removed outlier: 3.741A pdb=" N PHE F 736 " --> pdb=" O GLY F 816 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N MET F 796 " --> pdb=" O THR F 779 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 803 through 804 Processing sheet with id=AB6, first strand: chain 'F' and resid 862 through 864 removed outlier: 6.651A pdb=" N ILE F 855 " --> pdb=" O LEU F 863 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LEU F1016 " --> pdb=" O LEU F1011 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ILE F1005 " --> pdb=" O GLU F1022 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 895 through 907 removed outlier: 4.270A pdb=" N GLN F 904 " --> pdb=" O CYS F 977 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N CYS F 977 " --> pdb=" O GLN F 904 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL F 906 " --> pdb=" O GLN F 975 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLN F 975 " --> pdb=" O VAL F 906 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ILE F 978 " --> pdb=" O SER F1041 " (cutoff:3.500A) 835 hydrogen bonds defined for protein. 2363 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: 3.87 Time building geometry restraints manager: 2.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2940 1.31 - 1.44: 5162 1.44 - 1.56: 10689 1.56 - 1.69: 20 1.69 - 1.82: 168 Bond restraints: 18979 Sorted by residual: bond pdb=" N09 C8U A1912 " pdb=" O10 C8U A1912 " ideal model delta sigma weight residual 1.220 1.402 -0.182 2.00e-02 2.50e+03 8.27e+01 bond pdb=" C05 C8U A1912 " pdb=" C06 C8U A1912 " ideal model delta sigma weight residual 1.364 1.537 -0.173 2.00e-02 2.50e+03 7.47e+01 bond pdb=" C02 C8U A1912 " pdb=" C03 C8U A1912 " ideal model delta sigma weight residual 1.351 1.518 -0.167 2.00e-02 2.50e+03 6.94e+01 bond pdb=" C21 3PE A1904 " pdb=" O21 3PE A1904 " ideal model delta sigma weight residual 1.316 1.455 -0.139 2.00e-02 2.50e+03 4.85e+01 bond pdb=" C21 3PE A1902 " pdb=" O21 3PE A1902 " ideal model delta sigma weight residual 1.316 1.454 -0.138 2.00e-02 2.50e+03 4.79e+01 ... (remaining 18974 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 24730 2.05 - 4.10: 755 4.10 - 6.15: 123 6.15 - 8.19: 20 8.19 - 10.24: 30 Bond angle restraints: 25658 Sorted by residual: angle pdb=" N VAL A 142 " pdb=" CA VAL A 142 " pdb=" C VAL A 142 " ideal model delta sigma weight residual 113.71 107.94 5.77 9.50e-01 1.11e+00 3.69e+01 angle pdb=" N ILE A1046 " pdb=" CA ILE A1046 " pdb=" C ILE A1046 " ideal model delta sigma weight residual 113.53 108.03 5.50 9.80e-01 1.04e+00 3.15e+01 angle pdb=" N LEU A 513 " pdb=" CA LEU A 513 " pdb=" C LEU A 513 " ideal model delta sigma weight residual 114.62 109.77 4.85 1.14e+00 7.69e-01 1.81e+01 angle pdb=" N VAL A 637 " pdb=" CA VAL A 637 " pdb=" C VAL A 637 " ideal model delta sigma weight residual 112.80 108.03 4.77 1.15e+00 7.56e-01 1.72e+01 angle pdb=" C LEU E 126 " pdb=" N MET E 127 " pdb=" CA MET E 127 " ideal model delta sigma weight residual 122.31 114.61 7.70 2.00e+00 2.50e-01 1.48e+01 ... (remaining 25653 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.99: 9960 21.99 - 43.99: 1092 43.99 - 65.98: 316 65.98 - 87.97: 57 87.97 - 109.96: 5 Dihedral angle restraints: 11430 sinusoidal: 4817 harmonic: 6613 Sorted by residual: dihedral pdb=" CB CYS F 406 " pdb=" SG CYS F 406 " pdb=" SG CYS F1074 " pdb=" CB CYS F1074 " ideal model delta sinusoidal sigma weight residual 93.00 32.96 60.04 1 1.00e+01 1.00e-02 4.81e+01 dihedral pdb=" CB CYS F1002 " pdb=" SG CYS F1002 " pdb=" SG CYS F1027 " pdb=" CB CYS F1027 " ideal model delta sinusoidal sigma weight residual 93.00 139.97 -46.97 1 1.00e+01 1.00e-02 3.05e+01 dihedral pdb=" CA THR F 628 " pdb=" C THR F 628 " pdb=" N TYR F 629 " pdb=" CA TYR F 629 " ideal model delta harmonic sigma weight residual 180.00 -152.93 -27.07 0 5.00e+00 4.00e-02 2.93e+01 ... (remaining 11427 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1723 0.041 - 0.082: 876 0.082 - 0.122: 208 0.122 - 0.163: 36 0.163 - 0.204: 4 Chirality restraints: 2847 Sorted by residual: chirality pdb=" CB ILE A 559 " pdb=" CA ILE A 559 " pdb=" CG1 ILE A 559 " pdb=" CG2 ILE A 559 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA TYR F 747 " pdb=" N TYR F 747 " pdb=" C TYR F 747 " pdb=" CB TYR F 747 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.64e-01 chirality pdb=" CB THR A1259 " pdb=" CA THR A1259 " pdb=" OG1 THR A1259 " pdb=" CG2 THR A1259 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.49e-01 ... (remaining 2844 not shown) Planarity restraints: 3201 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS F 526 " 0.037 5.00e-02 4.00e+02 5.57e-02 4.97e+00 pdb=" N PRO F 527 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO F 527 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO F 527 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN F 530 " 0.031 5.00e-02 4.00e+02 4.65e-02 3.47e+00 pdb=" N PRO F 531 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO F 531 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO F 531 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 243 " -0.029 5.00e-02 4.00e+02 4.45e-02 3.16e+00 pdb=" N PRO A 244 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 244 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 244 " -0.025 5.00e-02 4.00e+02 ... (remaining 3198 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 163 2.57 - 3.15: 15330 3.15 - 3.74: 26908 3.74 - 4.32: 39671 4.32 - 4.90: 66698 Nonbonded interactions: 148770 Sorted by model distance: nonbonded pdb=" CE1 PHE A 536 " pdb=" CE MET A 941 " model vdw 1.990 3.760 nonbonded pdb=" OD2 ASP F 711 " pdb=" OG1 THR F 739 " model vdw 2.040 3.040 nonbonded pdb=" O GLU F 184 " pdb=" OG1 THR F 188 " model vdw 2.079 3.040 nonbonded pdb=" O LEU A1420 " pdb=" N VAL A1423 " model vdw 2.117 3.120 nonbonded pdb=" O GLN F 644 " pdb=" OG SER F 648 " model vdw 2.126 3.040 ... (remaining 148765 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.050 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: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 19.030 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 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 : 0.011 0.755 18993 Z= 0.691 Angle : 0.903 10.242 25684 Z= 0.474 Chirality : 0.048 0.204 2847 Planarity : 0.005 0.056 3201 Dihedral : 19.603 109.963 7121 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.29 % Favored : 91.67 % Rotamer: Outliers : 10.50 % Allowed : 22.05 % Favored : 67.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.50 (0.14), residues: 2221 helix: -2.75 (0.12), residues: 1095 sheet: -2.17 (0.31), residues: 224 loop : -3.37 (0.17), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1038 TYR 0.021 0.002 TYR A1334 PHE 0.016 0.002 PHE E 146 TRP 0.020 0.002 TRP A1016 HIS 0.006 0.001 HIS A 270 Details of bonding type rmsd/Z covalent geometry : bond 0.00937 / 0.42 (18979) covalent geometry : angle 0.90217 / 0.47 (25658) SS BOND : bond 0.00353 / 0.19 ( 13) SS BOND : angle 1.66314 / 1.32 ( 26) hydrogen bonds : bond 0.18513 / 12.17 ( 813) hydrogen bonds : angle 7.31495 / 4.95 ( 2363) Misc. bond : bond 0.75492 / 39.73 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 209 poor density : 262 time to evaluate : 0.539 Fit side-chains revert: symmetry clash REVERT: A 58 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7703 (tt) REVERT: A 74 MET cc_start: 0.9000 (OUTLIER) cc_final: 0.8732 (mtm) REVERT: A 122 TRP cc_start: 0.7160 (m100) cc_final: 0.6828 (m100) REVERT: A 123 ASN cc_start: 0.8003 (OUTLIER) cc_final: 0.7699 (t0) REVERT: A 128 ILE cc_start: 0.8397 (mt) cc_final: 0.8092 (mt) REVERT: A 187 ASN cc_start: 0.8023 (t0) cc_final: 0.7723 (t0) REVERT: A 256 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8521 (mm) REVERT: A 342 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7091 (pt0) REVERT: A 479 MET cc_start: 0.7922 (tmm) cc_final: 0.7579 (ttp) REVERT: A 519 MET cc_start: 0.7690 (OUTLIER) cc_final: 0.7423 (mmm) REVERT: A 559 ILE cc_start: 0.6958 (mm) cc_final: 0.6673 (mt) REVERT: A 567 PHE cc_start: 0.7956 (t80) cc_final: 0.7641 (t80) REVERT: A 871 LEU cc_start: 0.7345 (OUTLIER) cc_final: 0.7070 (tt) REVERT: A 873 LEU cc_start: 0.6753 (OUTLIER) cc_final: 0.6503 (tt) REVERT: A 881 ILE cc_start: 0.6478 (OUTLIER) cc_final: 0.6220 (mt) REVERT: A 903 ARG cc_start: 0.5909 (OUTLIER) cc_final: 0.5692 (mtt180) REVERT: A 1086 ARG cc_start: 0.7226 (ttm170) cc_final: 0.5894 (tpt170) REVERT: A 1091 TYR cc_start: 0.8541 (t80) cc_final: 0.8311 (t80) REVERT: A 1101 TYR cc_start: 0.5992 (m-80) cc_final: 0.5748 (m-80) REVERT: A 1243 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8715 (mp) REVERT: A 1245 LYS cc_start: 0.8234 (ptpt) cc_final: 0.7950 (ptpt) REVERT: A 1249 ARG cc_start: 0.7840 (mtt90) cc_final: 0.6833 (mmm160) REVERT: A 1302 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.8168 (ptt-90) REVERT: A 1381 MET cc_start: 0.6474 (ptt) cc_final: 0.6183 (mmm) REVERT: E 14 PHE cc_start: 0.7629 (t80) cc_final: 0.7227 (t80) REVERT: E 50 HIS cc_start: 0.6049 (OUTLIER) cc_final: 0.4492 (m-70) REVERT: E 158 MET cc_start: 0.7070 (mmm) cc_final: 0.6781 (tmm) REVERT: E 159 ARG cc_start: 0.7046 (ttt180) cc_final: 0.6744 (mtp180) REVERT: E 162 VAL cc_start: 0.7592 (t) cc_final: 0.6858 (t) REVERT: E 209 GLN cc_start: 0.7842 (tm-30) cc_final: 0.7267 (tm-30) REVERT: F 34 LYS cc_start: 0.8323 (tttp) cc_final: 0.8085 (tptt) REVERT: F 39 LYS cc_start: 0.8217 (pptt) cc_final: 0.7991 (pptt) REVERT: F 66 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.7998 (p0) REVERT: F 158 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.6386 (mpp80) REVERT: F 234 LYS cc_start: 0.6154 (pmtt) cc_final: 0.5320 (ptmt) REVERT: F 299 ASN cc_start: 0.8236 (m-40) cc_final: 0.8009 (m-40) REVERT: F 355 ASN cc_start: 0.8866 (OUTLIER) cc_final: 0.8590 (m-40) REVERT: F 482 LYS cc_start: 0.1019 (OUTLIER) cc_final: 0.0703 (ptmt) REVERT: F 886 MET cc_start: 0.8746 (tpt) cc_final: 0.8413 (tpt) REVERT: F 1020 MET cc_start: 0.7949 (ttp) cc_final: 0.7304 (ttm) outliers start: 209 outliers final: 149 residues processed: 440 average time/residue: 0.1189 time to fit residues: 82.1926 Evaluate side-chains 383 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 218 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 252 ARG Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 529 CYS Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 812 SER Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain A residue 869 ASN Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 882 SER Chi-restraints excluded: chain A residue 903 ARG Chi-restraints excluded: chain A residue 908 ILE Chi-restraints excluded: chain A residue 910 ARG Chi-restraints excluded: chain A residue 927 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 939 GLN Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 999 ASN Chi-restraints excluded: chain A residue 1011 SER Chi-restraints excluded: chain A residue 1030 ASP Chi-restraints excluded: chain A residue 1108 GLN Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1117 SER Chi-restraints excluded: chain A residue 1154 ASN Chi-restraints excluded: chain A residue 1164 GLU Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1198 ILE Chi-restraints excluded: chain A residue 1202 ILE Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1247 LEU Chi-restraints excluded: chain A residue 1251 GLU Chi-restraints excluded: chain A residue 1263 SER Chi-restraints excluded: chain A residue 1265 GLN Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1287 GLN Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1296 ASP Chi-restraints excluded: chain A residue 1300 ILE Chi-restraints excluded: chain A residue 1302 ARG Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1344 TYR Chi-restraints excluded: chain A residue 1354 THR Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain A residue 1397 HIS Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain A residue 1425 LEU Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 51 PHE Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 161 SER Chi-restraints excluded: chain E residue 186 CYS Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 61 TYR Chi-restraints excluded: chain F residue 66 ASP Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 158 ARG Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 263 SER Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 348 ASN Chi-restraints excluded: chain F residue 355 ASN Chi-restraints excluded: chain F residue 381 ASP Chi-restraints excluded: chain F residue 417 SER Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 475 PHE Chi-restraints excluded: chain F residue 476 GLU Chi-restraints excluded: chain F residue 482 LYS Chi-restraints excluded: chain F residue 503 THR Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 517 ILE Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 592 THR Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 602 ILE Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 648 SER Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 671 SER Chi-restraints excluded: chain F residue 680 THR Chi-restraints excluded: chain F residue 710 LEU Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 774 ASP Chi-restraints excluded: chain F residue 775 ASN Chi-restraints excluded: chain F residue 793 SER Chi-restraints excluded: chain F residue 814 VAL Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 871 THR Chi-restraints excluded: chain F residue 881 ILE Chi-restraints excluded: chain F residue 906 VAL Chi-restraints excluded: chain F residue 976 SER Chi-restraints excluded: chain F residue 982 THR Chi-restraints excluded: chain F residue 997 LEU Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1014 THR Chi-restraints excluded: chain F residue 1033 LEU Chi-restraints excluded: chain F residue 1060 ASP Chi-restraints excluded: chain F residue 1068 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 0.0070 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 0.8980 chunk 212 optimal weight: 1.9990 overall best weight: 0.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 ASN A 445 ASN A 453 HIS A 797 ASN A 803 ASN A 939 GLN A 999 ASN A1058 ASN A1087 GLN A1110 GLN A1138 GLN A1148 HIS A1374 ASN A1398 HIS F 164 GLN F 169 HIS F 248 GLN ** F 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 408 ASN F 447 GLN F 450 ASN F 470 ASN F 483 ASN F 511 ASN F 655 ASN F 679 ASN F 697 ASN F 866 ASN F 872 ASN F 888 HIS ** F1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1013 ASN F1052 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.145468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.116765 restraints weight = 48964.222| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 4.58 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3281 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3281 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18993 Z= 0.126 Angle : 0.605 9.337 25684 Z= 0.313 Chirality : 0.042 0.161 2847 Planarity : 0.004 0.047 3201 Dihedral : 16.017 121.764 3132 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 6.23 % Allowed : 22.75 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.71 (0.16), residues: 2221 helix: -1.13 (0.15), residues: 1090 sheet: -1.54 (0.32), residues: 231 loop : -2.65 (0.19), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 93 TYR 0.022 0.001 TYR F 629 PHE 0.015 0.001 PHE A 502 TRP 0.014 0.001 TRP A 265 HIS 0.004 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (18979) covalent geometry : angle 0.60422 / 0.31 (25658) SS BOND : bond 0.00418 / 0.26 ( 13) SS BOND : angle 1.13206 / 0.78 ( 26) hydrogen bonds : bond 0.03986 / 2.60 ( 813) hydrogen bonds : angle 4.51171 / 3.09 ( 2363) Misc. bond : bond 0.00160 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 243 time to evaluate : 0.610 Fit side-chains revert: symmetry clash REVERT: A 122 TRP cc_start: 0.6994 (m100) cc_final: 0.6771 (m100) REVERT: A 123 ASN cc_start: 0.7423 (OUTLIER) cc_final: 0.7152 (m-40) REVERT: A 164 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7532 (pt) REVERT: A 174 ARG cc_start: 0.8339 (mtp85) cc_final: 0.8009 (mtp85) REVERT: A 342 GLU cc_start: 0.7355 (mm-30) cc_final: 0.7084 (pt0) REVERT: A 479 MET cc_start: 0.7936 (tmm) cc_final: 0.7600 (ttp) REVERT: A 519 MET cc_start: 0.7619 (OUTLIER) cc_final: 0.7345 (mmt) REVERT: A 871 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7436 (tt) REVERT: A 873 LEU cc_start: 0.6539 (OUTLIER) cc_final: 0.6285 (tt) REVERT: A 881 ILE cc_start: 0.6544 (OUTLIER) cc_final: 0.6275 (mt) REVERT: A 1056 MET cc_start: 0.8655 (tpp) cc_final: 0.8333 (tpp) REVERT: A 1086 ARG cc_start: 0.7092 (ttm170) cc_final: 0.6050 (tpt170) REVERT: A 1091 TYR cc_start: 0.8416 (t80) cc_final: 0.8143 (t80) REVERT: A 1125 PHE cc_start: 0.7034 (t80) cc_final: 0.6708 (t80) REVERT: A 1129 MET cc_start: 0.8396 (mmt) cc_final: 0.8090 (tpt) REVERT: A 1148 HIS cc_start: 0.6055 (OUTLIER) cc_final: 0.4916 (t-90) REVERT: A 1164 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.6327 (pp20) REVERT: A 1243 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8913 (mp) REVERT: A 1246 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8885 (pp) REVERT: A 1249 ARG cc_start: 0.7893 (mtt90) cc_final: 0.7022 (mmm160) REVERT: A 1374 ASN cc_start: 0.9078 (OUTLIER) cc_final: 0.8861 (t0) REVERT: E 50 HIS cc_start: 0.6004 (OUTLIER) cc_final: 0.4233 (m-70) REVERT: E 209 GLN cc_start: 0.7867 (tm-30) cc_final: 0.7405 (tm-30) REVERT: F 234 LYS cc_start: 0.6219 (pmtt) cc_final: 0.5486 (ptmt) REVERT: F 299 ASN cc_start: 0.8208 (m-40) cc_final: 0.7969 (m-40) REVERT: F 355 ASN cc_start: 0.8791 (OUTLIER) cc_final: 0.8374 (m-40) REVERT: F 618 ASP cc_start: 0.8902 (p0) cc_final: 0.8474 (p0) REVERT: F 983 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.7405 (mt0) REVERT: F 1020 MET cc_start: 0.7846 (ttp) cc_final: 0.7460 (ttm) outliers start: 124 outliers final: 66 residues processed: 343 average time/residue: 0.1177 time to fit residues: 63.4752 Evaluate side-chains 288 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 208 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 910 ARG Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 1030 ASP Chi-restraints excluded: chain A residue 1108 GLN Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain A residue 1134 CYS Chi-restraints excluded: chain A residue 1148 HIS Chi-restraints excluded: chain A residue 1154 ASN Chi-restraints excluded: chain A residue 1164 GLU Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1246 LEU Chi-restraints excluded: chain A residue 1247 LEU Chi-restraints excluded: chain A residue 1265 GLN Chi-restraints excluded: chain A residue 1287 GLN Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1344 TYR Chi-restraints excluded: chain A residue 1352 CYS Chi-restraints excluded: chain A residue 1374 ASN Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain F residue 61 TYR Chi-restraints excluded: chain F residue 263 SER Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 348 ASN Chi-restraints excluded: chain F residue 355 ASN Chi-restraints excluded: chain F residue 476 GLU Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 621 SER Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 710 LEU Chi-restraints excluded: chain F residue 729 ILE Chi-restraints excluded: chain F residue 732 VAL Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 765 SER Chi-restraints excluded: chain F residue 774 ASP Chi-restraints excluded: chain F residue 798 SER Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 867 HIS Chi-restraints excluded: chain F residue 874 ILE Chi-restraints excluded: chain F residue 983 GLN Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 997 LEU Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1014 THR Chi-restraints excluded: chain F residue 1068 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 39 optimal weight: 3.9990 chunk 212 optimal weight: 3.9990 chunk 135 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 115 optimal weight: 10.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1108 GLN A1148 HIS A1304 ASN ** F 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 483 ASN F 685 ASN F 720 GLN ** F1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1013 ASN ** F1015 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.142268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.109345 restraints weight = 39586.218| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 4.29 r_work: 0.2649 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2636 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2636 r_free = 0.2636 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2636 r_free = 0.2636 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2636 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 18993 Z= 0.229 Angle : 0.645 9.019 25684 Z= 0.334 Chirality : 0.045 0.247 2847 Planarity : 0.005 0.043 3201 Dihedral : 14.936 119.089 2953 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 6.43 % Allowed : 23.05 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.17), residues: 2221 helix: -0.65 (0.15), residues: 1087 sheet: -1.27 (0.32), residues: 248 loop : -2.45 (0.19), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 903 TYR 0.017 0.002 TYR F 629 PHE 0.015 0.002 PHE A1260 TRP 0.015 0.002 TRP A1016 HIS 0.007 0.001 HIS A1148 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.23 (18979) covalent geometry : angle 0.64428 / 0.33 (25658) SS BOND : bond 0.00350 / 0.22 ( 13) SS BOND : angle 1.25687 / 1.02 ( 26) hydrogen bonds : bond 0.04256 / 2.75 ( 813) hydrogen bonds : angle 4.46501 / 3.06 ( 2363) Misc. bond : bond 0.00077 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 211 time to evaluate : 0.548 Fit side-chains REVERT: A 122 TRP cc_start: 0.7088 (m100) cc_final: 0.6575 (m100) REVERT: A 128 ILE cc_start: 0.8254 (mt) cc_final: 0.7965 (mt) REVERT: A 164 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7918 (pt) REVERT: A 174 ARG cc_start: 0.8599 (mtp85) cc_final: 0.8334 (mtp85) REVERT: A 289 ILE cc_start: 0.9221 (OUTLIER) cc_final: 0.8901 (tt) REVERT: A 342 GLU cc_start: 0.7430 (mm-30) cc_final: 0.6948 (pt0) REVERT: A 479 MET cc_start: 0.8193 (tmm) cc_final: 0.7876 (ttp) REVERT: A 519 MET cc_start: 0.7531 (mpt) cc_final: 0.7289 (mmp) REVERT: A 837 ILE cc_start: 0.4224 (OUTLIER) cc_final: 0.3889 (pp) REVERT: A 871 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.7175 (tt) REVERT: A 1056 MET cc_start: 0.9007 (tpp) cc_final: 0.8697 (tpp) REVERT: A 1086 ARG cc_start: 0.7231 (ttm170) cc_final: 0.5788 (tpt170) REVERT: A 1091 TYR cc_start: 0.8555 (t80) cc_final: 0.8293 (t80) REVERT: A 1125 PHE cc_start: 0.7195 (t80) cc_final: 0.6729 (t80) REVERT: A 1243 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8844 (mp) REVERT: A 1249 ARG cc_start: 0.7962 (mtt90) cc_final: 0.6876 (mmm160) REVERT: A 1326 GLN cc_start: 0.9590 (OUTLIER) cc_final: 0.8517 (pm20) REVERT: E 1 MET cc_start: 0.5229 (ppp) cc_final: 0.4961 (tmm) REVERT: E 50 HIS cc_start: 0.6011 (OUTLIER) cc_final: 0.4443 (m-70) REVERT: E 51 PHE cc_start: 0.7086 (t80) cc_final: 0.6809 (t80) REVERT: E 209 GLN cc_start: 0.8187 (tm-30) cc_final: 0.7652 (tm-30) REVERT: F 234 LYS cc_start: 0.6179 (pmtt) cc_final: 0.5233 (ptmt) REVERT: F 348 ASN cc_start: 0.8947 (OUTLIER) cc_final: 0.8435 (m-40) REVERT: F 355 ASN cc_start: 0.9010 (OUTLIER) cc_final: 0.8624 (m-40) REVERT: F 618 ASP cc_start: 0.9109 (p0) cc_final: 0.8649 (p0) REVERT: F 846 ARG cc_start: 0.8029 (mmm160) cc_final: 0.7748 (tpt90) REVERT: F 1020 MET cc_start: 0.8433 (ttp) cc_final: 0.7702 (ttm) outliers start: 128 outliers final: 87 residues processed: 318 average time/residue: 0.1129 time to fit residues: 57.1271 Evaluate side-chains 297 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 201 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 908 ILE Chi-restraints excluded: chain A residue 910 ARG Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1030 ASP Chi-restraints excluded: chain A residue 1108 GLN Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1117 SER Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain A residue 1134 CYS Chi-restraints excluded: chain A residue 1154 ASN Chi-restraints excluded: chain A residue 1164 GLU Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1247 LEU Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1287 GLN Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1326 GLN Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1344 TYR Chi-restraints excluded: chain A residue 1352 CYS Chi-restraints excluded: chain A residue 1354 THR Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain F residue 61 TYR Chi-restraints excluded: chain F residue 91 SER Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 263 SER Chi-restraints excluded: chain F residue 286 SER Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 348 ASN Chi-restraints excluded: chain F residue 355 ASN Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 476 GLU Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 517 ILE Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 621 SER Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 710 LEU Chi-restraints excluded: chain F residue 732 VAL Chi-restraints excluded: chain F residue 765 SER Chi-restraints excluded: chain F residue 774 ASP Chi-restraints excluded: chain F residue 786 SER Chi-restraints excluded: chain F residue 798 SER Chi-restraints excluded: chain F residue 814 VAL Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 867 HIS Chi-restraints excluded: chain F residue 874 ILE Chi-restraints excluded: chain F residue 884 SER Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 997 LEU Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1014 THR Chi-restraints excluded: chain F residue 1068 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 162 optimal weight: 0.7980 chunk 40 optimal weight: 10.0000 chunk 161 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 204 optimal weight: 4.9990 chunk 145 optimal weight: 0.9980 chunk 114 optimal weight: 6.9990 chunk 11 optimal weight: 0.0770 chunk 16 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 187 ASN A1374 ASN ** F 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 ASN ** F 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1013 ASN ** F1015 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.144802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.116151 restraints weight = 49244.358| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 4.67 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3302 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3302 r_free = 0.3302 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3302 r_free = 0.3302 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3302 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18993 Z= 0.112 Angle : 0.566 8.974 25684 Z= 0.292 Chirality : 0.042 0.242 2847 Planarity : 0.004 0.046 3201 Dihedral : 13.859 115.734 2934 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 4.87 % Allowed : 25.11 % Favored : 70.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.17), residues: 2221 helix: -0.07 (0.16), residues: 1089 sheet: -1.03 (0.33), residues: 236 loop : -2.23 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 903 TYR 0.018 0.001 TYR F 629 PHE 0.014 0.001 PHE A 502 TRP 0.015 0.001 TRP F 187 HIS 0.003 0.001 HIS E 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (18979) covalent geometry : angle 0.56571 / 0.29 (25658) SS BOND : bond 0.00238 / 0.16 ( 13) SS BOND : angle 0.95830 / 0.79 ( 26) hydrogen bonds : bond 0.03392 / 2.22 ( 813) hydrogen bonds : angle 4.09891 / 2.79 ( 2363) Misc. bond : bond 0.00015 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 224 time to evaluate : 0.638 Fit side-chains REVERT: A 122 TRP cc_start: 0.6890 (m100) cc_final: 0.6523 (m100) REVERT: A 164 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7598 (pt) REVERT: A 174 ARG cc_start: 0.8259 (mtp85) cc_final: 0.7959 (mtp85) REVERT: A 289 ILE cc_start: 0.9064 (OUTLIER) cc_final: 0.8736 (tt) REVERT: A 479 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7641 (ttp) REVERT: A 1056 MET cc_start: 0.8762 (tpp) cc_final: 0.8466 (tpp) REVERT: A 1086 ARG cc_start: 0.7083 (ttm170) cc_final: 0.5995 (tpt170) REVERT: A 1091 TYR cc_start: 0.8472 (t80) cc_final: 0.8239 (t80) REVERT: A 1099 ARG cc_start: 0.7866 (mtm180) cc_final: 0.7575 (ttp-170) REVERT: A 1125 PHE cc_start: 0.7044 (t80) cc_final: 0.6834 (t80) REVERT: A 1164 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.6380 (pp20) REVERT: A 1243 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8964 (mp) REVERT: A 1249 ARG cc_start: 0.7830 (mtt90) cc_final: 0.6942 (mmm160) REVERT: A 1326 GLN cc_start: 0.9317 (OUTLIER) cc_final: 0.8169 (pm20) REVERT: E 209 GLN cc_start: 0.7870 (tm-30) cc_final: 0.7422 (tm-30) REVERT: F 234 LYS cc_start: 0.6229 (pmtt) cc_final: 0.5466 (ptmt) REVERT: F 618 ASP cc_start: 0.8892 (p0) cc_final: 0.8387 (p0) REVERT: F 983 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.7304 (mt0) REVERT: F 1020 MET cc_start: 0.7837 (ttp) cc_final: 0.7403 (ttm) outliers start: 97 outliers final: 61 residues processed: 303 average time/residue: 0.1129 time to fit residues: 54.1439 Evaluate side-chains 285 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 217 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 908 ILE Chi-restraints excluded: chain A residue 910 ARG Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1030 ASP Chi-restraints excluded: chain A residue 1108 GLN Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain A residue 1134 CYS Chi-restraints excluded: chain A residue 1154 ASN Chi-restraints excluded: chain A residue 1164 GLU Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1265 GLN Chi-restraints excluded: chain A residue 1287 GLN Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1326 GLN Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1344 TYR Chi-restraints excluded: chain A residue 1352 CYS Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain A residue 1397 HIS Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain F residue 36 TRP Chi-restraints excluded: chain F residue 61 TYR Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 348 ASN Chi-restraints excluded: chain F residue 476 GLU Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 621 SER Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 710 LEU Chi-restraints excluded: chain F residue 732 VAL Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 774 ASP Chi-restraints excluded: chain F residue 798 SER Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 867 HIS Chi-restraints excluded: chain F residue 874 ILE Chi-restraints excluded: chain F residue 983 GLN Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 997 LEU Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1068 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 65 optimal weight: 2.9990 chunk 5 optimal weight: 0.1980 chunk 89 optimal weight: 0.8980 chunk 202 optimal weight: 0.1980 chunk 52 optimal weight: 0.0370 chunk 146 optimal weight: 0.8980 chunk 114 optimal weight: 0.0000 chunk 12 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 211 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 overall best weight: 0.2662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1304 ASN F 145 GLN F 297 ASN ** F 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1013 ASN ** F1015 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.149068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.120641 restraints weight = 52536.191| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 4.78 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3339 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3339 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 18993 Z= 0.099 Angle : 0.534 9.547 25684 Z= 0.275 Chirality : 0.041 0.248 2847 Planarity : 0.004 0.045 3201 Dihedral : 12.782 111.781 2917 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 4.17 % Allowed : 25.77 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.18), residues: 2221 helix: 0.44 (0.16), residues: 1083 sheet: -0.80 (0.34), residues: 235 loop : -2.00 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 903 TYR 0.019 0.001 TYR F 629 PHE 0.022 0.001 PHE F 689 TRP 0.017 0.001 TRP F 187 HIS 0.002 0.000 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 (18979) covalent geometry : angle 0.53320 / 0.27 (25658) SS BOND : bond 0.00194 / 0.13 ( 13) SS BOND : angle 0.83971 / 0.71 ( 26) hydrogen bonds : bond 0.02980 / 1.95 ( 813) hydrogen bonds : angle 3.86739 / 2.63 ( 2363) Misc. bond : bond 0.00013 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 244 time to evaluate : 0.680 Fit side-chains REVERT: A 164 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7553 (pt) REVERT: A 174 ARG cc_start: 0.8201 (mtp85) cc_final: 0.7953 (mtp85) REVERT: A 289 ILE cc_start: 0.9131 (OUTLIER) cc_final: 0.8833 (tt) REVERT: A 479 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.7480 (ttp) REVERT: A 851 MET cc_start: 0.3749 (OUTLIER) cc_final: 0.3513 (mmp) REVERT: A 1086 ARG cc_start: 0.7047 (ttm170) cc_final: 0.6081 (tpt170) REVERT: A 1099 ARG cc_start: 0.7801 (mtm180) cc_final: 0.7508 (ttp-170) REVERT: A 1164 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.6215 (pp20) REVERT: A 1243 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8945 (mp) REVERT: A 1249 ARG cc_start: 0.7747 (mtt90) cc_final: 0.6949 (mmm160) REVERT: A 1323 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8369 (mm-30) REVERT: A 1326 GLN cc_start: 0.9174 (OUTLIER) cc_final: 0.7996 (pm20) REVERT: E 10 ARG cc_start: 0.6956 (mtp180) cc_final: 0.6659 (mmm-85) REVERT: E 158 MET cc_start: 0.7645 (mmm) cc_final: 0.7422 (tmm) REVERT: E 209 GLN cc_start: 0.7797 (tm-30) cc_final: 0.7458 (tm-30) REVERT: F 612 THR cc_start: 0.9040 (OUTLIER) cc_final: 0.8722 (p) REVERT: F 618 ASP cc_start: 0.8836 (p0) cc_final: 0.8436 (p0) REVERT: F 757 GLU cc_start: 0.8364 (mm-30) cc_final: 0.7757 (mm-30) REVERT: F 1020 MET cc_start: 0.7648 (ttp) cc_final: 0.7320 (ttm) outliers start: 83 outliers final: 49 residues processed: 311 average time/residue: 0.1068 time to fit residues: 52.7745 Evaluate side-chains 279 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 221 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 851 MET Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 910 ARG Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1108 GLN Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain A residue 1154 ASN Chi-restraints excluded: chain A residue 1164 GLU Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1200 SER Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1287 GLN Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1323 GLU Chi-restraints excluded: chain A residue 1326 GLN Chi-restraints excluded: chain A residue 1344 TYR Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain A residue 1397 HIS Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain A residue 1425 LEU Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain F residue 36 TRP Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 476 GLU Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 621 SER Chi-restraints excluded: chain F residue 676 SER Chi-restraints excluded: chain F residue 710 LEU Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 774 ASP Chi-restraints excluded: chain F residue 798 SER Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 867 HIS Chi-restraints excluded: chain F residue 874 ILE Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1068 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 95 optimal weight: 0.9990 chunk 194 optimal weight: 0.7980 chunk 186 optimal weight: 0.5980 chunk 200 optimal weight: 3.9990 chunk 101 optimal weight: 0.0050 chunk 147 optimal weight: 3.9990 chunk 192 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 116 optimal weight: 8.9990 chunk 132 optimal weight: 1.9990 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 297 ASN ** F 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 975 GLN ** F1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1013 ASN F1015 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.147035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.111527 restraints weight = 30224.921| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 3.23 r_work: 0.2826 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2807 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2807 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18993 Z= 0.117 Angle : 0.552 8.610 25684 Z= 0.284 Chirality : 0.042 0.192 2847 Planarity : 0.004 0.046 3201 Dihedral : 12.373 110.607 2902 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 4.62 % Allowed : 25.26 % Favored : 70.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.18), residues: 2221 helix: 0.61 (0.16), residues: 1089 sheet: -0.74 (0.33), residues: 245 loop : -1.82 (0.20), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 199 TYR 0.018 0.001 TYR A1091 PHE 0.025 0.001 PHE F 689 TRP 0.012 0.001 TRP F 187 HIS 0.003 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (18979) covalent geometry : angle 0.55170 / 0.28 (25658) SS BOND : bond 0.00198 / 0.13 ( 13) SS BOND : angle 0.94791 / 0.77 ( 26) hydrogen bonds : bond 0.03153 / 2.06 ( 813) hydrogen bonds : angle 3.84820 / 2.62 ( 2363) Misc. bond : bond 0.00022 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 221 time to evaluate : 0.646 Fit side-chains REVERT: A 164 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7824 (pt) REVERT: A 289 ILE cc_start: 0.9119 (OUTLIER) cc_final: 0.8805 (tt) REVERT: A 479 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7829 (ttp) REVERT: A 851 MET cc_start: 0.3874 (OUTLIER) cc_final: 0.3629 (mmp) REVERT: A 1086 ARG cc_start: 0.7145 (ttm170) cc_final: 0.5860 (tpt170) REVERT: A 1099 ARG cc_start: 0.7770 (mtm180) cc_final: 0.7476 (ttp-170) REVERT: A 1164 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.6700 (pp20) REVERT: A 1186 ASP cc_start: 0.8603 (OUTLIER) cc_final: 0.8314 (m-30) REVERT: A 1243 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8904 (mp) REVERT: A 1249 ARG cc_start: 0.7752 (mtt90) cc_final: 0.6798 (mmm160) REVERT: A 1323 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8683 (mm-30) REVERT: A 1326 GLN cc_start: 0.9488 (OUTLIER) cc_final: 0.8401 (pm20) REVERT: A 1381 MET cc_start: 0.8905 (mmp) cc_final: 0.8650 (mmp) REVERT: E 10 ARG cc_start: 0.6999 (mtp180) cc_final: 0.6730 (mmm-85) REVERT: E 158 MET cc_start: 0.8171 (mmm) cc_final: 0.7350 (tmm) REVERT: E 209 GLN cc_start: 0.8126 (tm-30) cc_final: 0.7698 (tm-30) REVERT: F 41 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8498 (tt0) REVERT: F 612 THR cc_start: 0.9319 (OUTLIER) cc_final: 0.8918 (p) REVERT: F 618 ASP cc_start: 0.8949 (p0) cc_final: 0.8608 (p0) REVERT: F 718 LEU cc_start: 0.9163 (tp) cc_final: 0.8914 (tt) REVERT: F 1020 MET cc_start: 0.8190 (ttp) cc_final: 0.7588 (ttm) outliers start: 92 outliers final: 66 residues processed: 292 average time/residue: 0.1099 time to fit residues: 51.1741 Evaluate side-chains 289 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 212 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 851 MET Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 910 ARG Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1030 ASP Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1108 GLN Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain A residue 1134 CYS Chi-restraints excluded: chain A residue 1154 ASN Chi-restraints excluded: chain A residue 1164 GLU Chi-restraints excluded: chain A residue 1186 ASP Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1287 GLN Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1323 GLU Chi-restraints excluded: chain A residue 1326 GLN Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1344 TYR Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain A residue 1397 HIS Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain A residue 1425 LEU Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain F residue 36 TRP Chi-restraints excluded: chain F residue 41 GLN Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 286 SER Chi-restraints excluded: chain F residue 297 ASN Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 476 GLU Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 621 SER Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 710 LEU Chi-restraints excluded: chain F residue 732 VAL Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 765 SER Chi-restraints excluded: chain F residue 774 ASP Chi-restraints excluded: chain F residue 798 SER Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 867 HIS Chi-restraints excluded: chain F residue 874 ILE Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1068 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 2 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 109 optimal weight: 20.0000 chunk 174 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 chunk 193 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 chunk 203 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 297 ASN F 299 ASN ** F1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1013 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.144109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.109192 restraints weight = 39106.253| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 4.88 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3171 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3171 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18993 Z= 0.185 Angle : 0.595 8.488 25684 Z= 0.308 Chirality : 0.044 0.160 2847 Planarity : 0.004 0.047 3201 Dihedral : 12.492 110.830 2902 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 5.47 % Allowed : 24.46 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.18), residues: 2221 helix: 0.51 (0.16), residues: 1092 sheet: -0.73 (0.32), residues: 245 loop : -1.81 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 846 TYR 0.018 0.001 TYR A1334 PHE 0.017 0.001 PHE F 689 TRP 0.018 0.001 TRP E 54 HIS 0.003 0.001 HIS F 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 (18979) covalent geometry : angle 0.59456 / 0.31 (25658) SS BOND : bond 0.00305 / 0.17 ( 13) SS BOND : angle 1.19800 / 0.97 ( 26) hydrogen bonds : bond 0.03711 / 2.40 ( 813) hydrogen bonds : angle 3.99528 / 2.73 ( 2363) Misc. bond : bond 0.00042 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 220 time to evaluate : 0.671 Fit side-chains REVERT: A 74 MET cc_start: 0.9090 (mmm) cc_final: 0.8816 (mtp) REVERT: A 164 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7732 (pt) REVERT: A 174 ARG cc_start: 0.8246 (mtp85) cc_final: 0.7906 (mtp85) REVERT: A 210 TYR cc_start: 0.9504 (m-80) cc_final: 0.9225 (m-80) REVERT: A 260 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7774 (pt0) REVERT: A 282 MET cc_start: 0.8654 (ttp) cc_final: 0.8445 (ttt) REVERT: A 289 ILE cc_start: 0.9186 (OUTLIER) cc_final: 0.8842 (tt) REVERT: A 479 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7739 (ttp) REVERT: A 1086 ARG cc_start: 0.7152 (ttm170) cc_final: 0.5853 (tpt170) REVERT: A 1099 ARG cc_start: 0.7914 (mtm180) cc_final: 0.7535 (ttp-170) REVERT: A 1164 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.6501 (pp20) REVERT: A 1186 ASP cc_start: 0.8439 (OUTLIER) cc_final: 0.8139 (m-30) REVERT: A 1243 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8766 (mp) REVERT: A 1249 ARG cc_start: 0.7800 (mtt90) cc_final: 0.6894 (mmm160) REVERT: A 1326 GLN cc_start: 0.9378 (OUTLIER) cc_final: 0.8411 (pm20) REVERT: E 158 MET cc_start: 0.7764 (mmm) cc_final: 0.7311 (tmm) REVERT: E 209 GLN cc_start: 0.7948 (tm-30) cc_final: 0.7571 (tm-30) REVERT: F 41 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.8372 (tt0) REVERT: F 618 ASP cc_start: 0.8916 (p0) cc_final: 0.8621 (p0) REVERT: F 757 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8057 (mm-30) REVERT: F 1020 MET cc_start: 0.7893 (ttp) cc_final: 0.7393 (ttm) outliers start: 109 outliers final: 78 residues processed: 305 average time/residue: 0.1163 time to fit residues: 56.2633 Evaluate side-chains 303 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 216 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 908 ILE Chi-restraints excluded: chain A residue 910 ARG Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1030 ASP Chi-restraints excluded: chain A residue 1108 GLN Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain A residue 1134 CYS Chi-restraints excluded: chain A residue 1154 ASN Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1164 GLU Chi-restraints excluded: chain A residue 1186 ASP Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1200 SER Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1287 GLN Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1326 GLN Chi-restraints excluded: chain A residue 1344 TYR Chi-restraints excluded: chain A residue 1354 THR Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain A residue 1397 HIS Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain A residue 1425 LEU Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain F residue 36 TRP Chi-restraints excluded: chain F residue 41 GLN Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 91 SER Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain F residue 286 SER Chi-restraints excluded: chain F residue 297 ASN Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 476 GLU Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 621 SER Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 710 LEU Chi-restraints excluded: chain F residue 732 VAL Chi-restraints excluded: chain F residue 765 SER Chi-restraints excluded: chain F residue 774 ASP Chi-restraints excluded: chain F residue 798 SER Chi-restraints excluded: chain F residue 814 VAL Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 867 HIS Chi-restraints excluded: chain F residue 874 ILE Chi-restraints excluded: chain F residue 884 SER Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1068 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 116 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 85 optimal weight: 7.9990 chunk 74 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 122 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 102 optimal weight: 0.0070 chunk 143 optimal weight: 0.9990 overall best weight: 0.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 ASN F 297 ASN F 299 ASN ** F 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1013 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.146835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.111737 restraints weight = 39646.054| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 4.86 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3204 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3204 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18993 Z= 0.112 Angle : 0.551 8.809 25684 Z= 0.283 Chirality : 0.041 0.167 2847 Planarity : 0.004 0.048 3201 Dihedral : 12.154 108.748 2901 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 4.32 % Allowed : 25.72 % Favored : 69.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.18), residues: 2221 helix: 0.73 (0.16), residues: 1089 sheet: -0.68 (0.33), residues: 245 loop : -1.72 (0.21), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 846 TYR 0.011 0.001 TYR A1360 PHE 0.020 0.001 PHE F 689 TRP 0.018 0.001 TRP A 122 HIS 0.002 0.001 HIS F 394 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (18979) covalent geometry : angle 0.55077 / 0.28 (25658) SS BOND : bond 0.00205 / 0.13 ( 13) SS BOND : angle 1.03167 / 0.83 ( 26) hydrogen bonds : bond 0.03197 / 2.08 ( 813) hydrogen bonds : angle 3.86660 / 2.64 ( 2363) Misc. bond : bond 0.00014 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 219 time to evaluate : 0.775 Fit side-chains revert: symmetry clash REVERT: A 74 MET cc_start: 0.9078 (mmm) cc_final: 0.8788 (mtp) REVERT: A 164 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7646 (pt) REVERT: A 174 ARG cc_start: 0.8250 (mtp85) cc_final: 0.7893 (mtp85) REVERT: A 282 MET cc_start: 0.8512 (ttp) cc_final: 0.8292 (ttt) REVERT: A 289 ILE cc_start: 0.9085 (OUTLIER) cc_final: 0.8761 (tt) REVERT: A 479 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.7626 (ttp) REVERT: A 837 ILE cc_start: 0.5030 (OUTLIER) cc_final: 0.4632 (pp) REVERT: A 1086 ARG cc_start: 0.7118 (ttm170) cc_final: 0.5906 (tpt170) REVERT: A 1099 ARG cc_start: 0.7845 (mtm180) cc_final: 0.7507 (ttp-170) REVERT: A 1164 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.6230 (pp20) REVERT: A 1249 ARG cc_start: 0.7835 (mtt90) cc_final: 0.6952 (mmm160) REVERT: A 1326 GLN cc_start: 0.9287 (OUTLIER) cc_final: 0.8319 (pm20) REVERT: A 1381 MET cc_start: 0.8566 (mmp) cc_final: 0.8328 (mmp) REVERT: E 158 MET cc_start: 0.7891 (mmm) cc_final: 0.7430 (tmm) REVERT: E 209 GLN cc_start: 0.7965 (tm-30) cc_final: 0.7597 (tm-30) REVERT: F 41 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.8390 (tt0) REVERT: F 311 GLN cc_start: 0.9054 (OUTLIER) cc_final: 0.8513 (tt0) REVERT: F 757 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8052 (mm-30) REVERT: F 1020 MET cc_start: 0.7852 (ttp) cc_final: 0.7544 (ttm) outliers start: 86 outliers final: 68 residues processed: 286 average time/residue: 0.1167 time to fit residues: 53.8402 Evaluate side-chains 288 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 212 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 910 ARG Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1030 ASP Chi-restraints excluded: chain A residue 1108 GLN Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain A residue 1134 CYS Chi-restraints excluded: chain A residue 1154 ASN Chi-restraints excluded: chain A residue 1164 GLU Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1200 SER Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1287 GLN Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1326 GLN Chi-restraints excluded: chain A residue 1344 TYR Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain A residue 1397 HIS Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain A residue 1425 LEU Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain F residue 36 TRP Chi-restraints excluded: chain F residue 41 GLN Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain F residue 286 SER Chi-restraints excluded: chain F residue 297 ASN Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 311 GLN Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 476 GLU Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 621 SER Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 710 LEU Chi-restraints excluded: chain F residue 732 VAL Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 765 SER Chi-restraints excluded: chain F residue 774 ASP Chi-restraints excluded: chain F residue 798 SER Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 867 HIS Chi-restraints excluded: chain F residue 874 ILE Chi-restraints excluded: chain F residue 884 SER Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1068 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 182 optimal weight: 1.9990 chunk 120 optimal weight: 10.0000 chunk 69 optimal weight: 0.7980 chunk 193 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 170 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 181 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 ASN F 292 ASN F 297 ASN F 299 ASN ** F 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 847 ASN ** F1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1013 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.144290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.109833 restraints weight = 42337.110| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 5.41 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3152 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3152 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 18993 Z= 0.183 Angle : 0.602 12.087 25684 Z= 0.309 Chirality : 0.044 0.172 2847 Planarity : 0.004 0.047 3201 Dihedral : 12.204 108.917 2899 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 4.57 % Allowed : 25.51 % Favored : 69.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.18), residues: 2221 helix: 0.59 (0.16), residues: 1094 sheet: -0.70 (0.32), residues: 245 loop : -1.75 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 846 TYR 0.016 0.001 TYR A1334 PHE 0.018 0.001 PHE F 689 TRP 0.021 0.001 TRP E 54 HIS 0.003 0.001 HIS F 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.18 (18979) covalent geometry : angle 0.60079 / 0.31 (25658) SS BOND : bond 0.00205 / 0.13 ( 13) SS BOND : angle 1.21473 / 0.95 ( 26) hydrogen bonds : bond 0.03649 / 2.36 ( 813) hydrogen bonds : angle 3.98822 / 2.73 ( 2363) Misc. bond : bond 0.00021 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 218 time to evaluate : 0.624 Fit side-chains revert: symmetry clash REVERT: A 74 MET cc_start: 0.9070 (mmm) cc_final: 0.8801 (mtp) REVERT: A 164 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7655 (pt) REVERT: A 174 ARG cc_start: 0.8277 (mtp85) cc_final: 0.7910 (mtp85) REVERT: A 210 TYR cc_start: 0.9509 (m-80) cc_final: 0.9220 (m-80) REVERT: A 282 MET cc_start: 0.8606 (ttp) cc_final: 0.8395 (ttt) REVERT: A 289 ILE cc_start: 0.9204 (OUTLIER) cc_final: 0.8865 (tt) REVERT: A 479 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.7760 (ttp) REVERT: A 837 ILE cc_start: 0.4732 (OUTLIER) cc_final: 0.4411 (pp) REVERT: A 1086 ARG cc_start: 0.7168 (ttm170) cc_final: 0.5835 (tpt170) REVERT: A 1099 ARG cc_start: 0.7881 (mtm180) cc_final: 0.7488 (ttp-170) REVERT: A 1164 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.6430 (pp20) REVERT: A 1249 ARG cc_start: 0.7848 (mtt90) cc_final: 0.6934 (mmm160) REVERT: A 1326 GLN cc_start: 0.9344 (OUTLIER) cc_final: 0.8405 (pm20) REVERT: E 158 MET cc_start: 0.7772 (mmm) cc_final: 0.7280 (tmm) REVERT: E 209 GLN cc_start: 0.7939 (tm-30) cc_final: 0.7559 (tm-30) REVERT: F 39 LYS cc_start: 0.8083 (pptt) cc_final: 0.7805 (pptt) REVERT: F 41 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8395 (tt0) REVERT: F 311 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.8471 (tt0) REVERT: F 757 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8011 (mm-30) REVERT: F 846 ARG cc_start: 0.7972 (mmp-170) cc_final: 0.7723 (tpm170) REVERT: F 1020 MET cc_start: 0.7922 (ttp) cc_final: 0.7516 (ttt) outliers start: 91 outliers final: 75 residues processed: 288 average time/residue: 0.1153 time to fit residues: 52.5434 Evaluate side-chains 294 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 211 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 910 ARG Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1030 ASP Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain A residue 1108 GLN Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain A residue 1134 CYS Chi-restraints excluded: chain A residue 1154 ASN Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1164 GLU Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1200 SER Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1287 GLN Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1326 GLN Chi-restraints excluded: chain A residue 1344 TYR Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain A residue 1397 HIS Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain A residue 1425 LEU Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain F residue 41 GLN Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 91 SER Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain F residue 286 SER Chi-restraints excluded: chain F residue 297 ASN Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 311 GLN Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 476 GLU Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 621 SER Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 710 LEU Chi-restraints excluded: chain F residue 732 VAL Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 765 SER Chi-restraints excluded: chain F residue 774 ASP Chi-restraints excluded: chain F residue 798 SER Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 867 HIS Chi-restraints excluded: chain F residue 874 ILE Chi-restraints excluded: chain F residue 884 SER Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1068 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 78 optimal weight: 6.9990 chunk 108 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 129 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 68 optimal weight: 0.6980 chunk 181 optimal weight: 0.9980 chunk 135 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 ASN ** F 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1013 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.146293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.113242 restraints weight = 35397.915| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 4.02 r_work: 0.2773 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2723 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2723 r_free = 0.2723 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2723 r_free = 0.2723 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2723 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18993 Z= 0.120 Angle : 0.563 11.023 25684 Z= 0.289 Chirality : 0.042 0.169 2847 Planarity : 0.004 0.047 3201 Dihedral : 11.939 107.351 2899 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 4.12 % Allowed : 26.17 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.18), residues: 2221 helix: 0.73 (0.16), residues: 1095 sheet: -0.66 (0.33), residues: 245 loop : -1.64 (0.21), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 846 TYR 0.011 0.001 TYR A1360 PHE 0.020 0.001 PHE F 689 TRP 0.021 0.001 TRP E 54 HIS 0.002 0.001 HIS E 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (18979) covalent geometry : angle 0.56179 / 0.29 (25658) SS BOND : bond 0.00185 / 0.12 ( 13) SS BOND : angle 1.09500 / 0.88 ( 26) hydrogen bonds : bond 0.03249 / 2.12 ( 813) hydrogen bonds : angle 3.89551 / 2.65 ( 2363) Misc. bond : bond 0.00016 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 214 time to evaluate : 0.598 Fit side-chains revert: symmetry clash REVERT: A 164 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7675 (pt) REVERT: A 174 ARG cc_start: 0.8551 (mtp85) cc_final: 0.8249 (mtp85) REVERT: A 289 ILE cc_start: 0.9200 (OUTLIER) cc_final: 0.8878 (tt) REVERT: A 479 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7717 (ttp) REVERT: A 837 ILE cc_start: 0.4272 (OUTLIER) cc_final: 0.3971 (pp) REVERT: A 1086 ARG cc_start: 0.7161 (ttm170) cc_final: 0.5711 (tpt170) REVERT: A 1099 ARG cc_start: 0.7838 (mtm180) cc_final: 0.7460 (ttp-170) REVERT: A 1164 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.6688 (pp20) REVERT: A 1243 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8730 (mp) REVERT: A 1249 ARG cc_start: 0.7826 (mtt90) cc_final: 0.6834 (mmm160) REVERT: A 1326 GLN cc_start: 0.9523 (OUTLIER) cc_final: 0.8556 (pm20) REVERT: A 1381 MET cc_start: 0.8950 (mmp) cc_final: 0.8674 (mmp) REVERT: E 127 MET cc_start: 0.8172 (ptp) cc_final: 0.7956 (ptp) REVERT: E 158 MET cc_start: 0.8176 (mmm) cc_final: 0.7328 (tmm) REVERT: E 209 GLN cc_start: 0.8177 (tm-30) cc_final: 0.7758 (tm-30) REVERT: F 39 LYS cc_start: 0.8407 (pptt) cc_final: 0.8149 (pptt) REVERT: F 41 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8538 (tt0) REVERT: F 311 GLN cc_start: 0.9320 (OUTLIER) cc_final: 0.8709 (tt0) REVERT: F 757 GLU cc_start: 0.8781 (mm-30) cc_final: 0.8208 (mm-30) REVERT: F 846 ARG cc_start: 0.7990 (mmp-170) cc_final: 0.7666 (tpm170) REVERT: F 1020 MET cc_start: 0.8301 (ttp) cc_final: 0.7867 (ttt) outliers start: 82 outliers final: 64 residues processed: 280 average time/residue: 0.1109 time to fit residues: 49.6277 Evaluate side-chains 282 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 209 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 910 ARG Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1030 ASP Chi-restraints excluded: chain A residue 1108 GLN Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain A residue 1134 CYS Chi-restraints excluded: chain A residue 1154 ASN Chi-restraints excluded: chain A residue 1164 GLU Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1287 GLN Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1326 GLN Chi-restraints excluded: chain A residue 1344 TYR Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain A residue 1397 HIS Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain A residue 1425 LEU Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain F residue 41 GLN Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 286 SER Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 311 GLN Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 476 GLU Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 710 LEU Chi-restraints excluded: chain F residue 732 VAL Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 765 SER Chi-restraints excluded: chain F residue 774 ASP Chi-restraints excluded: chain F residue 798 SER Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 867 HIS Chi-restraints excluded: chain F residue 874 ILE Chi-restraints excluded: chain F residue 884 SER Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1068 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 162 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 172 optimal weight: 0.0980 chunk 159 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 203 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 9 optimal weight: 0.5980 chunk 92 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 ASN F 292 ASN ** F 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1013 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.148157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.104880 restraints weight = 56412.258| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 3.21 r_work: 0.2866 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2843 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2843 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 18993 Z= 0.106 Angle : 0.540 10.515 25684 Z= 0.277 Chirality : 0.041 0.174 2847 Planarity : 0.004 0.048 3201 Dihedral : 11.437 104.259 2899 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 4.02 % Allowed : 25.92 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.18), residues: 2221 helix: 0.90 (0.16), residues: 1095 sheet: -0.63 (0.32), residues: 250 loop : -1.55 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 846 TYR 0.010 0.001 TYR A1360 PHE 0.026 0.001 PHE F 689 TRP 0.018 0.001 TRP E 54 HIS 0.002 0.000 HIS A 270 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (18979) covalent geometry : angle 0.53948 / 0.28 (25658) SS BOND : bond 0.00187 / 0.13 ( 13) SS BOND : angle 0.93244 / 0.74 ( 26) hydrogen bonds : bond 0.02989 / 1.95 ( 813) hydrogen bonds : angle 3.77306 / 2.57 ( 2363) Misc. bond : bond 0.00019 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3490.29 seconds wall clock time: 60 minutes 46.75 seconds (3646.75 seconds total)