Starting phenix.real_space_refine on Mon Aug 25 12:18:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yig_39318/08_2025/8yig_39318.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yig_39318/08_2025/8yig_39318.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8yig_39318/08_2025/8yig_39318.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yig_39318/08_2025/8yig_39318.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yig_39318/08_2025/8yig_39318.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yig_39318/08_2025/8yig_39318.map" } resolution = 3.15 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= 0.005 sd= 0.129 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 124 5.49 5 S 138 5.16 5 C 17532 2.51 5 N 4850 2.21 5 O 5510 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 100 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28154 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 11988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1478, 11988 Classifications: {'peptide': 1478} Link IDs: {'PTRANS': 61, 'TRANS': 1416} Chain breaks: 2 Chain: "B" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 759 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 84} Chain breaks: 1 Chain: "F" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 759 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 84} Chain breaks: 1 Chain: "D" Number of atoms: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1330 Classifications: {'DNA': 1, 'RNA': 62} Modifications used: {'5*END': 1, 'rna3p_pur': 34, 'rna3p_pyr': 28} Link IDs: {'rna3p': 62} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A%5*END:plan': 1, ' A%5*END:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 11988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1478, 11988 Classifications: {'peptide': 1478} Link IDs: {'PTRANS': 61, 'TRANS': 1416} Chain breaks: 2 Chain: "C" Number of atoms: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1330 Classifications: {'DNA': 1, 'RNA': 62} Modifications used: {'5*END': 1, 'rna3p_pur': 34, 'rna3p_pyr': 28} Link IDs: {'rna3p': 62} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A%5*END:plan': 1, ' A%5*END:plan2': 1} Unresolved non-hydrogen planarities: 13 Time building chain proxies: 6.65, per 1000 atoms: 0.24 Number of scatterers: 28154 At special positions: 0 Unit cell: (151.2, 218.16, 97.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 138 16.00 P 124 15.00 O 5510 8.00 N 4850 7.00 C 17532 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.46 Conformation dependent library (CDL) restraints added in 936.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5992 Finding SS restraints... Secondary structure from input PDB file: 141 helices and 21 sheets defined 54.3% alpha, 10.9% beta 50 base pairs and 85 stacking pairs defined. Time for finding SS restraints: 3.55 Creating SS restraints... Processing helix chain 'A' and resid 9 through 22 removed outlier: 3.737A pdb=" N LYS A 21 " --> pdb=" O ASP A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 45 removed outlier: 3.746A pdb=" N THR A 35 " --> pdb=" O GLY A 31 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA A 38 " --> pdb=" O LYS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 66 through 81 Processing helix chain 'A' and resid 89 through 97 removed outlier: 5.920A pdb=" N VAL A 94 " --> pdb=" O GLU A 91 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ASP A 95 " --> pdb=" O GLN A 92 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP A 96 " --> pdb=" O GLY A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 109 removed outlier: 3.519A pdb=" N GLU A 105 " --> pdb=" O MET A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 125 Processing helix chain 'A' and resid 129 through 131 No H-bonds generated for 'chain 'A' and resid 129 through 131' Processing helix chain 'A' and resid 140 through 144 Processing helix chain 'A' and resid 148 through 156 Processing helix chain 'A' and resid 157 through 159 No H-bonds generated for 'chain 'A' and resid 157 through 159' Processing helix chain 'A' and resid 183 through 195 removed outlier: 3.963A pdb=" N LYS A 187 " --> pdb=" O ASN A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 212 Processing helix chain 'A' and resid 232 through 251 removed outlier: 3.935A pdb=" N LEU A 251 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 292 removed outlier: 3.551A pdb=" N VAL A 277 " --> pdb=" O LYS A 273 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY A 292 " --> pdb=" O MET A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 314 removed outlier: 3.501A pdb=" N ILE A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 343 Processing helix chain 'A' and resid 344 through 348 removed outlier: 3.686A pdb=" N ASP A 348 " --> pdb=" O THR A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 362 removed outlier: 3.662A pdb=" N GLU A 356 " --> pdb=" O ASN A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 378 Processing helix chain 'A' and resid 382 through 386 removed outlier: 3.592A pdb=" N ILE A 386 " --> pdb=" O PRO A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 410 removed outlier: 3.638A pdb=" N CYS A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS A 399 " --> pdb=" O ARG A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 452 Processing helix chain 'A' and resid 484 through 495 removed outlier: 3.701A pdb=" N ALA A 495 " --> pdb=" O SER A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 535 Processing helix chain 'A' and resid 543 through 552 removed outlier: 3.584A pdb=" N PHE A 551 " --> pdb=" O ILE A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 569 No H-bonds generated for 'chain 'A' and resid 567 through 569' Processing helix chain 'A' and resid 570 through 582 removed outlier: 3.512A pdb=" N THR A 581 " --> pdb=" O ARG A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 607 Processing helix chain 'A' and resid 637 through 656 Processing helix chain 'A' and resid 667 through 680 removed outlier: 3.607A pdb=" N ILE A 675 " --> pdb=" O ARG A 671 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASP A 677 " --> pdb=" O ALA A 673 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N VAL A 678 " --> pdb=" O SER A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 687 removed outlier: 3.655A pdb=" N LYS A 685 " --> pdb=" O HIS A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 697 removed outlier: 3.683A pdb=" N ALA A 697 " --> pdb=" O VAL A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 748 Processing helix chain 'A' and resid 792 through 810 removed outlier: 3.731A pdb=" N PHE A 807 " --> pdb=" O HIS A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 852 Processing helix chain 'A' and resid 862 through 868 removed outlier: 4.318A pdb=" N GLN A 868 " --> pdb=" O GLN A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 930 removed outlier: 7.343A pdb=" N ASN A 927 " --> pdb=" O SER A 923 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ARG A 928 " --> pdb=" O LYS A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 967 removed outlier: 4.106A pdb=" N MET A 967 " --> pdb=" O SER A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 974 No H-bonds generated for 'chain 'A' and resid 972 through 974' Processing helix chain 'A' and resid 983 through 991 removed outlier: 3.993A pdb=" N PHE A 991 " --> pdb=" O LEU A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1016 removed outlier: 3.576A pdb=" N PHE A1001 " --> pdb=" O ASN A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1174 through 1182 Processing helix chain 'A' and resid 1183 through 1186 Processing helix chain 'A' and resid 1190 through 1199 Processing helix chain 'A' and resid 1209 through 1232 removed outlier: 3.728A pdb=" N LEU A1215 " --> pdb=" O ARG A1211 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1248 Processing helix chain 'A' and resid 1249 through 1259 Processing helix chain 'A' and resid 1260 through 1261 No H-bonds generated for 'chain 'A' and resid 1260 through 1261' Processing helix chain 'A' and resid 1262 through 1266 removed outlier: 3.586A pdb=" N LEU A1266 " --> pdb=" O PRO A1263 " (cutoff:3.500A) Processing helix chain 'A' and resid 1272 through 1277 removed outlier: 3.830A pdb=" N TRP A1277 " --> pdb=" O PRO A1273 " (cutoff:3.500A) Processing helix chain 'A' and resid 1285 through 1294 Processing helix chain 'A' and resid 1303 through 1308 Processing helix chain 'A' and resid 1313 through 1319 Processing helix chain 'A' and resid 1324 through 1338 Processing helix chain 'A' and resid 1348 through 1353 Processing helix chain 'A' and resid 1354 through 1356 No H-bonds generated for 'chain 'A' and resid 1354 through 1356' Processing helix chain 'A' and resid 1363 through 1393 removed outlier: 8.114A pdb=" N LEU A1383 " --> pdb=" O LYS A1379 " (cutoff:3.500A) removed outlier: 9.587A pdb=" N GLN A1384 " --> pdb=" O ASN A1380 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N HIS A1385 " --> pdb=" O TYR A1381 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LYS A1388 " --> pdb=" O GLN A1384 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N MET A1389 " --> pdb=" O HIS A1385 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU A1390 " --> pdb=" O ALA A1386 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU A1391 " --> pdb=" O PHE A1387 " (cutoff:3.500A) Processing helix chain 'A' and resid 1403 through 1410 removed outlier: 3.617A pdb=" N LEU A1407 " --> pdb=" O LEU A1404 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N LEU A1408 " --> pdb=" O THR A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1422 through 1430 removed outlier: 4.040A pdb=" N ILE A1426 " --> pdb=" O ASN A1422 " (cutoff:3.500A) Processing helix chain 'A' and resid 1432 through 1441 Processing helix chain 'A' and resid 1447 through 1455 Processing helix chain 'A' and resid 1468 through 1491 removed outlier: 3.763A pdb=" N ILE A1474 " --> pdb=" O GLU A1470 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA A1477 " --> pdb=" O PHE A1473 " (cutoff:3.500A) Processing helix chain 'A' and resid 1495 through 1507 Processing helix chain 'A' and resid 1508 through 1519 Processing helix chain 'A' and resid 1520 through 1525 removed outlier: 3.869A pdb=" N PHE A1523 " --> pdb=" O ARG A1520 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE A1524 " --> pdb=" O LEU A1521 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A1525 " --> pdb=" O HIS A1522 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1520 through 1525' Processing helix chain 'A' and resid 1529 through 1546 Processing helix chain 'A' and resid 1609 through 1628 removed outlier: 4.325A pdb=" N GLY A1613 " --> pdb=" O PRO A1609 " (cutoff:3.500A) Processing helix chain 'A' and resid 1629 through 1651 Proline residue: A1643 - end of helix removed outlier: 3.617A pdb=" N ARG A1650 " --> pdb=" O GLN A1646 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 262 Processing helix chain 'B' and resid 300 through 319 Processing helix chain 'F' and resid 250 through 262 removed outlier: 3.943A pdb=" N ARG F 262 " --> pdb=" O MET F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 281 removed outlier: 4.009A pdb=" N ARG F 281 " --> pdb=" O PRO F 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 319 Processing helix chain 'E' and resid 9 through 22 removed outlier: 3.658A pdb=" N LYS E 21 " --> pdb=" O ASP E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 45 removed outlier: 3.722A pdb=" N THR E 35 " --> pdb=" O GLY E 31 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA E 38 " --> pdb=" O LYS E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 56 Processing helix chain 'E' and resid 66 through 81 Processing helix chain 'E' and resid 89 through 97 removed outlier: 6.208A pdb=" N VAL E 94 " --> pdb=" O GLU E 91 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ASP E 95 " --> pdb=" O GLN E 92 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP E 96 " --> pdb=" O GLY E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 109 Processing helix chain 'E' and resid 116 through 125 Processing helix chain 'E' and resid 129 through 131 No H-bonds generated for 'chain 'E' and resid 129 through 131' Processing helix chain 'E' and resid 141 through 144 Processing helix chain 'E' and resid 148 through 156 Processing helix chain 'E' and resid 157 through 159 No H-bonds generated for 'chain 'E' and resid 157 through 159' Processing helix chain 'E' and resid 183 through 195 removed outlier: 3.872A pdb=" N LYS E 187 " --> pdb=" O ASN E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 213 Processing helix chain 'E' and resid 232 through 250 removed outlier: 3.542A pdb=" N ARG E 236 " --> pdb=" O LEU E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 292 removed outlier: 3.573A pdb=" N VAL E 277 " --> pdb=" O LYS E 273 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY E 292 " --> pdb=" O MET E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 314 removed outlier: 3.530A pdb=" N ILE E 301 " --> pdb=" O SER E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 343 Processing helix chain 'E' and resid 350 through 362 removed outlier: 3.836A pdb=" N GLU E 356 " --> pdb=" O ASN E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 378 Processing helix chain 'E' and resid 394 through 410 removed outlier: 3.596A pdb=" N CYS E 398 " --> pdb=" O ARG E 394 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS E 399 " --> pdb=" O ARG E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 445 through 452 Processing helix chain 'E' and resid 484 through 495 removed outlier: 3.736A pdb=" N ALA E 495 " --> pdb=" O SER E 491 " (cutoff:3.500A) Processing helix chain 'E' and resid 510 through 535 Processing helix chain 'E' and resid 543 through 552 removed outlier: 3.628A pdb=" N PHE E 551 " --> pdb=" O ILE E 547 " (cutoff:3.500A) Processing helix chain 'E' and resid 567 through 582 removed outlier: 4.466A pdb=" N LEU E 572 " --> pdb=" O PRO E 568 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ALA E 573 " --> pdb=" O ASN E 569 " (cutoff:3.500A) Processing helix chain 'E' and resid 598 through 607 Processing helix chain 'E' and resid 608 through 611 removed outlier: 4.330A pdb=" N LYS E 611 " --> pdb=" O VAL E 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 608 through 611' Processing helix chain 'E' and resid 637 through 656 Processing helix chain 'E' and resid 667 through 680 removed outlier: 3.604A pdb=" N ILE E 675 " --> pdb=" O ARG E 671 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ASP E 677 " --> pdb=" O ALA E 673 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N VAL E 678 " --> pdb=" O SER E 674 " (cutoff:3.500A) Processing helix chain 'E' and resid 681 through 687 removed outlier: 3.788A pdb=" N LYS E 685 " --> pdb=" O HIS E 682 " (cutoff:3.500A) Processing helix chain 'E' and resid 693 through 697 removed outlier: 3.708A pdb=" N ALA E 697 " --> pdb=" O VAL E 694 " (cutoff:3.500A) Processing helix chain 'E' and resid 741 through 748 Processing helix chain 'E' and resid 792 through 810 removed outlier: 3.692A pdb=" N PHE E 807 " --> pdb=" O HIS E 803 " (cutoff:3.500A) Processing helix chain 'E' and resid 845 through 852 removed outlier: 3.760A pdb=" N MET E 849 " --> pdb=" O ASP E 845 " (cutoff:3.500A) Processing helix chain 'E' and resid 862 through 868 removed outlier: 4.358A pdb=" N GLN E 868 " --> pdb=" O GLN E 864 " (cutoff:3.500A) Processing helix chain 'E' and resid 873 through 877 Processing helix chain 'E' and resid 916 through 930 removed outlier: 7.254A pdb=" N ASN E 927 " --> pdb=" O SER E 923 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ARG E 928 " --> pdb=" O LYS E 924 " (cutoff:3.500A) Processing helix chain 'E' and resid 960 through 967 removed outlier: 4.187A pdb=" N MET E 967 " --> pdb=" O SER E 963 " (cutoff:3.500A) Processing helix chain 'E' and resid 972 through 974 No H-bonds generated for 'chain 'E' and resid 972 through 974' Processing helix chain 'E' and resid 983 through 991 removed outlier: 4.000A pdb=" N PHE E 991 " --> pdb=" O LEU E 987 " (cutoff:3.500A) Processing helix chain 'E' and resid 991 through 1016 removed outlier: 3.580A pdb=" N PHE E1001 " --> pdb=" O ASN E 997 " (cutoff:3.500A) Processing helix chain 'E' and resid 1174 through 1182 Processing helix chain 'E' and resid 1183 through 1186 Processing helix chain 'E' and resid 1190 through 1199 Processing helix chain 'E' and resid 1209 through 1232 removed outlier: 3.676A pdb=" N LEU E1215 " --> pdb=" O ARG E1211 " (cutoff:3.500A) Processing helix chain 'E' and resid 1236 through 1248 Processing helix chain 'E' and resid 1249 through 1259 Processing helix chain 'E' and resid 1262 through 1266 removed outlier: 3.693A pdb=" N LEU E1266 " --> pdb=" O PRO E1263 " (cutoff:3.500A) Processing helix chain 'E' and resid 1272 through 1277 removed outlier: 3.887A pdb=" N TRP E1277 " --> pdb=" O PRO E1273 " (cutoff:3.500A) Processing helix chain 'E' and resid 1285 through 1294 Processing helix chain 'E' and resid 1297 through 1301 removed outlier: 3.849A pdb=" N LYS E1300 " --> pdb=" O GLU E1297 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE E1301 " --> pdb=" O PHE E1298 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1297 through 1301' Processing helix chain 'E' and resid 1303 through 1308 Processing helix chain 'E' and resid 1313 through 1319 Processing helix chain 'E' and resid 1324 through 1338 Processing helix chain 'E' and resid 1348 through 1357 removed outlier: 6.501A pdb=" N PHE E1354 " --> pdb=" O SER E1350 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N CYS E1355 " --> pdb=" O GLU E1351 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL E1356 " --> pdb=" O VAL E1352 " (cutoff:3.500A) Processing helix chain 'E' and resid 1363 through 1393 removed outlier: 8.051A pdb=" N LEU E1383 " --> pdb=" O LYS E1379 " (cutoff:3.500A) removed outlier: 9.515A pdb=" N GLN E1384 " --> pdb=" O ASN E1380 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N HIS E1385 " --> pdb=" O TYR E1381 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LYS E1388 " --> pdb=" O GLN E1384 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N MET E1389 " --> pdb=" O HIS E1385 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU E1390 " --> pdb=" O ALA E1386 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU E1391 " --> pdb=" O PHE E1387 " (cutoff:3.500A) Processing helix chain 'E' and resid 1403 through 1410 removed outlier: 3.629A pdb=" N LEU E1407 " --> pdb=" O LEU E1404 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N LEU E1408 " --> pdb=" O THR E1405 " (cutoff:3.500A) Processing helix chain 'E' and resid 1422 through 1430 removed outlier: 3.969A pdb=" N ILE E1426 " --> pdb=" O ASN E1422 " (cutoff:3.500A) Processing helix chain 'E' and resid 1432 through 1441 Processing helix chain 'E' and resid 1447 through 1455 Processing helix chain 'E' and resid 1468 through 1491 removed outlier: 3.789A pdb=" N ALA E1477 " --> pdb=" O PHE E1473 " (cutoff:3.500A) Processing helix chain 'E' and resid 1495 through 1507 Processing helix chain 'E' and resid 1508 through 1519 Processing helix chain 'E' and resid 1520 through 1525 removed outlier: 3.900A pdb=" N PHE E1523 " --> pdb=" O ARG E1520 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE E1525 " --> pdb=" O HIS E1522 " (cutoff:3.500A) Processing helix chain 'E' and resid 1529 through 1546 Processing helix chain 'E' and resid 1609 through 1628 removed outlier: 4.408A pdb=" N GLY E1613 " --> pdb=" O PRO E1609 " (cutoff:3.500A) Processing helix chain 'E' and resid 1629 through 1651 Proline residue: E1643 - end of helix removed outlier: 3.632A pdb=" N ARG E1650 " --> pdb=" O GLN E1646 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 88 removed outlier: 5.797A pdb=" N GLY A 86 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N THR A 115 " --> pdb=" O GLY A 86 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N TYR A 88 " --> pdb=" O THR A 115 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ARG A 59 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL A 136 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU A 61 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ILE A 138 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N MET A 63 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR A 172 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE A 25 " --> pdb=" O ILE A 200 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 421 through 424 removed outlier: 6.601A pdb=" N GLN A 422 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU A 389 " --> pdb=" O PHE A 477 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL A 476 " --> pdb=" O VAL A 503 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N PHE A 505 " --> pdb=" O VAL A 476 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ILE A 478 " --> pdb=" O PHE A 505 " (cutoff:3.500A) removed outlier: 8.911A pdb=" N ALA A 507 " --> pdb=" O ILE A 478 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR A 506 " --> pdb=" O VAL A 223 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 260 through 261 removed outlier: 4.631A pdb=" N ARG A 260 " --> pdb=" O ARG A 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 558 through 559 Processing sheet with id=AA5, first strand: chain 'A' and resid 593 through 596 Processing sheet with id=AA6, first strand: chain 'A' and resid 702 through 706 Processing sheet with id=AA7, first strand: chain 'A' and resid 768 through 772 Processing sheet with id=AA8, first strand: chain 'A' and resid 768 through 772 removed outlier: 4.583A pdb=" N TYR A 754 " --> pdb=" O ILE A 729 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 819 through 820 Processing sheet with id=AB1, first strand: chain 'A' and resid 969 through 971 removed outlier: 4.333A pdb=" N VAL A 969 " --> pdb=" O VAL A 942 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N MET A 939 " --> pdb=" O VAL A 898 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N VAL A 898 " --> pdb=" O MET A 939 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLU A 941 " --> pdb=" O THR A 896 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LYS A 880 " --> pdb=" O VAL A 895 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ILE A 881 " --> pdb=" O PHE A 979 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 268 through 275 removed outlier: 7.304A pdb=" N THR B 284 " --> pdb=" O GLU B 272 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N GLU B 274 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU B 282 " --> pdb=" O GLU B 274 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 268 through 275 removed outlier: 6.703A pdb=" N THR F 284 " --> pdb=" O GLU F 272 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLU F 274 " --> pdb=" O LEU F 282 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU F 282 " --> pdb=" O GLU F 274 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 357 through 358 removed outlier: 3.606A pdb=" N THR E 506 " --> pdb=" O VAL E 223 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL E 476 " --> pdb=" O VAL E 503 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N PHE E 505 " --> pdb=" O VAL E 476 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ILE E 478 " --> pdb=" O PHE E 505 " (cutoff:3.500A) removed outlier: 8.911A pdb=" N ALA E 507 " --> pdb=" O ILE E 478 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLN E 422 " --> pdb=" O ILE E 459 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 85 through 88 removed outlier: 3.584A pdb=" N THR E 115 " --> pdb=" O TYR E 88 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ARG E 59 " --> pdb=" O SER E 134 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N VAL E 136 " --> pdb=" O ARG E 59 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU E 61 " --> pdb=" O VAL E 136 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ILE E 138 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N MET E 63 " --> pdb=" O ILE E 138 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N SER E 134 " --> pdb=" O ARG E 167 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N VAL E 169 " --> pdb=" O SER E 134 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL E 136 " --> pdb=" O VAL E 169 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N LEU E 171 " --> pdb=" O VAL E 136 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE E 138 " --> pdb=" O LEU E 171 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ILE E 25 " --> pdb=" O ILE E 200 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 558 through 559 Processing sheet with id=AB7, first strand: chain 'E' and resid 593 through 596 Processing sheet with id=AB8, first strand: chain 'E' and resid 702 through 706 Processing sheet with id=AB9, first strand: chain 'E' and resid 768 through 772 Processing sheet with id=AC1, first strand: chain 'E' and resid 768 through 772 removed outlier: 4.632A pdb=" N TYR E 754 " --> pdb=" O ILE E 729 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 819 through 820 Processing sheet with id=AC3, first strand: chain 'E' and resid 969 through 971 removed outlier: 4.209A pdb=" N VAL E 969 " --> pdb=" O VAL E 942 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N MET E 939 " --> pdb=" O VAL E 898 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N VAL E 898 " --> pdb=" O MET E 939 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N GLU E 941 " --> pdb=" O THR E 896 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N LYS E 880 " --> pdb=" O VAL E 895 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ILE E 881 " --> pdb=" O PHE E 979 " (cutoff:3.500A) 1255 hydrogen bonds defined for protein. 3567 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 126 hydrogen bonds 236 hydrogen bond angles 0 basepair planarities 50 basepair parallelities 85 stacking parallelities Total time for adding SS restraints: 7.52 Time building geometry restraints manager: 3.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8663 1.34 - 1.46: 6061 1.46 - 1.58: 13834 1.58 - 1.70: 246 1.70 - 1.82: 218 Bond restraints: 29022 Sorted by residual: bond pdb=" CA PRO B 265 " pdb=" C PRO B 265 " ideal model delta sigma weight residual 1.514 1.524 -0.010 5.50e-03 3.31e+04 3.18e+00 bond pdb=" CB GLN E 266 " pdb=" CG GLN E 266 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.20e+00 bond pdb=" CG ARG F 263 " pdb=" CD ARG F 263 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.81e+00 bond pdb=" CA PRO B 266 " pdb=" C PRO B 266 " ideal model delta sigma weight residual 1.514 1.507 0.007 5.50e-03 3.31e+04 1.79e+00 bond pdb=" CB CYS A 624 " pdb=" SG CYS A 624 " ideal model delta sigma weight residual 1.808 1.770 0.038 3.30e-02 9.18e+02 1.33e+00 ... (remaining 29017 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.33: 39702 3.33 - 6.66: 144 6.66 - 10.00: 15 10.00 - 13.33: 3 13.33 - 16.66: 2 Bond angle restraints: 39866 Sorted by residual: angle pdb=" CA LEU E1619 " pdb=" CB LEU E1619 " pdb=" CG LEU E1619 " ideal model delta sigma weight residual 116.30 132.96 -16.66 3.50e+00 8.16e-02 2.27e+01 angle pdb=" CB MET A 487 " pdb=" CG MET A 487 " pdb=" SD MET A 487 " ideal model delta sigma weight residual 112.70 126.34 -13.64 3.00e+00 1.11e-01 2.07e+01 angle pdb=" CB MET F 260 " pdb=" CG MET F 260 " pdb=" SD MET F 260 " ideal model delta sigma weight residual 112.70 125.48 -12.78 3.00e+00 1.11e-01 1.81e+01 angle pdb=" CG ARG F 263 " pdb=" CD ARG F 263 " pdb=" NE ARG F 263 " ideal model delta sigma weight residual 112.00 121.26 -9.26 2.20e+00 2.07e-01 1.77e+01 angle pdb=" CB MET A 212 " pdb=" CG MET A 212 " pdb=" SD MET A 212 " ideal model delta sigma weight residual 112.70 123.69 -10.99 3.00e+00 1.11e-01 1.34e+01 ... (remaining 39861 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 15399 17.93 - 35.86: 1641 35.86 - 53.78: 417 53.78 - 71.71: 226 71.71 - 89.64: 67 Dihedral angle restraints: 17750 sinusoidal: 8508 harmonic: 9242 Sorted by residual: dihedral pdb=" CA MET F 260 " pdb=" C MET F 260 " pdb=" N GLN F 261 " pdb=" CA GLN F 261 " ideal model delta harmonic sigma weight residual 180.00 135.43 44.57 0 5.00e+00 4.00e-02 7.95e+01 dihedral pdb=" CA GLU A 435 " pdb=" C GLU A 435 " pdb=" N SER A 436 " pdb=" CA SER A 436 " ideal model delta harmonic sigma weight residual 180.00 154.60 25.40 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA MET A 101 " pdb=" C MET A 101 " pdb=" N TRP A 102 " pdb=" CA TRP A 102 " ideal model delta harmonic sigma weight residual 180.00 157.78 22.22 0 5.00e+00 4.00e-02 1.98e+01 ... (remaining 17747 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 3560 0.044 - 0.089: 773 0.089 - 0.133: 199 0.133 - 0.178: 12 0.178 - 0.222: 4 Chirality restraints: 4548 Sorted by residual: chirality pdb=" CB ILE A 137 " pdb=" CA ILE A 137 " pdb=" CG1 ILE A 137 " pdb=" CG2 ILE A 137 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA MET F 260 " pdb=" N MET F 260 " pdb=" C MET F 260 " pdb=" CB MET F 260 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.85e-01 chirality pdb=" CB ILE E 582 " pdb=" CA ILE E 582 " pdb=" CG1 ILE E 582 " pdb=" CG2 ILE E 582 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.13e-01 ... (remaining 4545 not shown) Planarity restraints: 4640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 903 " 0.032 5.00e-02 4.00e+02 4.84e-02 3.76e+00 pdb=" N PRO A 904 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 904 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 904 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 102 " 0.014 2.00e-02 2.50e+03 1.22e-02 3.73e+00 pdb=" CG TRP E 102 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP E 102 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP E 102 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 102 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP E 102 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP E 102 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 102 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 102 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP E 102 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 469 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.33e+00 pdb=" CG ASP A 469 " 0.032 2.00e-02 2.50e+03 pdb=" OD1 ASP A 469 " -0.012 2.00e-02 2.50e+03 pdb=" OD2 ASP A 469 " -0.011 2.00e-02 2.50e+03 ... (remaining 4637 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 562 2.66 - 3.22: 26827 3.22 - 3.78: 46959 3.78 - 4.34: 62602 4.34 - 4.90: 98931 Nonbonded interactions: 235881 Sorted by model distance: nonbonded pdb=" OG1 THR E 484 " pdb=" OD1 ASN E 486 " model vdw 2.101 3.040 nonbonded pdb=" OG1 THR E 896 " pdb=" OE1 GLU E 941 " model vdw 2.121 3.040 nonbonded pdb=" OG1 THR A 484 " pdb=" OD1 ASN A 486 " model vdw 2.127 3.040 nonbonded pdb=" OG1 THR A 896 " pdb=" OE1 GLU A 941 " model vdw 2.158 3.040 nonbonded pdb=" N GLN A 864 " pdb=" OE1 GLN A 864 " model vdw 2.172 3.120 ... (remaining 235876 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.320 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: 0.040 Extract box with map and model: 0.350 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 29.730 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 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 : 0.003 0.044 29022 Z= 0.140 Angle : 0.609 16.661 39866 Z= 0.320 Chirality : 0.039 0.222 4548 Planarity : 0.004 0.048 4640 Dihedral : 17.431 89.641 11758 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.25 % Allowed : 15.27 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 aren not related in a simple way. whole: 0.72 (0.15), residues: 3118 helix: 1.08 (0.13), residues: 1492 sheet: -0.11 (0.28), residues: 352 loop : 0.08 (0.18), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 281 TYR 0.019 0.001 TYR A 925 PHE 0.015 0.001 PHE B 283 TRP 0.031 0.002 TRP E 102 HIS 0.009 0.001 HIS B 310 Details of bonding type rmsd covalent geometry : bond 0.00304 (29022) covalent geometry : angle 0.60921 (39866) hydrogen bonds : bond 0.14809 ( 1361) hydrogen bonds : angle 5.58417 ( 3803) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 534 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LEU cc_start: 0.7006 (mt) cc_final: 0.6768 (mt) REVERT: A 75 MET cc_start: 0.7362 (tpp) cc_final: 0.6596 (mmm) REVERT: A 101 MET cc_start: 0.6802 (tmm) cc_final: 0.6372 (ptt) REVERT: A 107 LYS cc_start: 0.7820 (ttpp) cc_final: 0.7586 (tppt) REVERT: A 189 LYS cc_start: 0.7183 (tppt) cc_final: 0.6946 (tttt) REVERT: A 190 GLU cc_start: 0.7377 (tm-30) cc_final: 0.6896 (tt0) REVERT: A 193 ILE cc_start: 0.8045 (mt) cc_final: 0.7774 (mm) REVERT: A 236 ARG cc_start: 0.7124 (mmm-85) cc_final: 0.6838 (mtp180) REVERT: A 243 GLU cc_start: 0.7523 (mm-30) cc_final: 0.7246 (mm-30) REVERT: A 247 VAL cc_start: 0.7991 (t) cc_final: 0.7617 (m) REVERT: A 263 LYS cc_start: 0.7484 (tptm) cc_final: 0.6778 (mmtt) REVERT: A 384 LYS cc_start: 0.7939 (mtpt) cc_final: 0.7367 (ttpp) REVERT: A 513 LYS cc_start: 0.7744 (ptmm) cc_final: 0.7420 (ptpp) REVERT: A 562 ASN cc_start: 0.7760 (t0) cc_final: 0.7519 (t0) REVERT: A 616 ILE cc_start: 0.7280 (mm) cc_final: 0.6938 (mt) REVERT: A 620 MET cc_start: 0.6962 (tpt) cc_final: 0.6463 (mmm) REVERT: A 670 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7784 (mp0) REVERT: A 677 ASP cc_start: 0.8452 (t70) cc_final: 0.7911 (t0) REVERT: A 745 TYR cc_start: 0.7760 (t80) cc_final: 0.7445 (t80) REVERT: A 768 MET cc_start: 0.6489 (OUTLIER) cc_final: 0.6047 (ptp) REVERT: A 787 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7647 (pm20) REVERT: A 805 MET cc_start: 0.8315 (tmm) cc_final: 0.7689 (tmm) REVERT: A 854 ARG cc_start: 0.7564 (mtp-110) cc_final: 0.7101 (ttm110) REVERT: A 873 ARG cc_start: 0.6861 (mtm-85) cc_final: 0.6214 (ptp90) REVERT: A 918 TYR cc_start: 0.7896 (t80) cc_final: 0.7631 (t80) REVERT: A 943 ARG cc_start: 0.7315 (tpp80) cc_final: 0.6614 (ttm170) REVERT: A 1031 ARG cc_start: 0.8051 (mtp85) cc_final: 0.7842 (mtp-110) REVERT: A 1274 ARG cc_start: 0.8675 (ttm-80) cc_final: 0.8066 (mtp-110) REVERT: A 1320 LYS cc_start: 0.7663 (tptm) cc_final: 0.7376 (tptm) REVERT: A 1397 ARG cc_start: 0.7571 (ttm-80) cc_final: 0.7262 (ttm170) REVERT: A 1464 ILE cc_start: 0.8298 (pt) cc_final: 0.7964 (pt) REVERT: A 1470 GLU cc_start: 0.8100 (tt0) cc_final: 0.7811 (tt0) REVERT: A 1520 ARG cc_start: 0.6416 (mtp85) cc_final: 0.5864 (mtp85) REVERT: A 1528 GLU cc_start: 0.7560 (tt0) cc_final: 0.6793 (tt0) REVERT: F 258 MET cc_start: 0.3395 (mmm) cc_final: 0.1713 (ptm) REVERT: F 260 MET cc_start: -0.1183 (ppp) cc_final: -0.3594 (mpp) REVERT: F 295 MET cc_start: 0.4066 (tpp) cc_final: 0.1000 (mtp) REVERT: F 312 MET cc_start: 0.6882 (mmm) cc_final: 0.6624 (mmm) REVERT: E 22 SER cc_start: 0.7693 (t) cc_final: 0.7389 (p) REVERT: E 75 MET cc_start: 0.7208 (mmm) cc_final: 0.6325 (mtt) REVERT: E 94 VAL cc_start: 0.6060 (t) cc_final: 0.5840 (m) REVERT: E 101 MET cc_start: 0.5156 (tmm) cc_final: 0.4952 (ptt) REVERT: E 212 MET cc_start: 0.7255 (mmm) cc_final: 0.7026 (mmm) REVERT: E 260 ARG cc_start: 0.7047 (mmm160) cc_final: 0.6814 (mmm160) REVERT: E 263 LYS cc_start: 0.7943 (tppt) cc_final: 0.7478 (tttt) REVERT: E 312 ARG cc_start: 0.7427 (ttm-80) cc_final: 0.6937 (mtm110) REVERT: E 331 GLU cc_start: 0.7731 (tp30) cc_final: 0.7264 (mm-30) REVERT: E 523 LYS cc_start: 0.7529 (ptpp) cc_final: 0.7181 (ttpp) REVERT: E 590 VAL cc_start: 0.8293 (m) cc_final: 0.7949 (t) REVERT: E 639 LYS cc_start: 0.7614 (tppt) cc_final: 0.7270 (tttt) REVERT: E 670 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7406 (mt-10) REVERT: E 689 SER cc_start: 0.8253 (m) cc_final: 0.7721 (p) REVERT: E 768 MET cc_start: 0.7560 (ttm) cc_final: 0.7339 (ttp) REVERT: E 974 GLU cc_start: 0.7523 (mt-10) cc_final: 0.6481 (pm20) REVERT: E 1031 ARG cc_start: 0.7648 (mtp-110) cc_final: 0.7430 (mtp85) REVERT: E 1036 ASP cc_start: 0.7860 (t0) cc_final: 0.7573 (t0) REVERT: E 1172 LYS cc_start: 0.7857 (tptp) cc_final: 0.7273 (ttpt) REVERT: E 1185 HIS cc_start: 0.8483 (m90) cc_final: 0.7868 (m90) REVERT: E 1237 GLU cc_start: 0.7339 (tm-30) cc_final: 0.7085 (tm-30) REVERT: E 1295 ASN cc_start: 0.7701 (t0) cc_final: 0.6725 (m-40) REVERT: E 1300 LYS cc_start: 0.7952 (mtmt) cc_final: 0.7632 (mmpt) REVERT: E 1326 ILE cc_start: 0.8095 (pt) cc_final: 0.7750 (mp) REVERT: E 1360 THR cc_start: 0.8928 (t) cc_final: 0.8695 (m) REVERT: E 1470 GLU cc_start: 0.6778 (mt-10) cc_final: 0.6402 (mt-10) REVERT: E 1472 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7787 (tm-30) REVERT: E 1617 GLU cc_start: 0.7005 (mt-10) cc_final: 0.6714 (mt-10) REVERT: E 1626 ASP cc_start: 0.6123 (t0) cc_final: 0.5556 (t70) outliers start: 7 outliers final: 2 residues processed: 536 average time/residue: 0.1903 time to fit residues: 157.9005 Evaluate side-chains 382 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 379 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 768 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.0070 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 5.9990 overall best weight: 2.5604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 ASN A 228 GLN A 339 GLN A 580 GLN A 753 ASN A 815 HIS ** A 884 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 HIS A1433 HIS ** A1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 517 GLN E 595 HIS ** E 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 679 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 749 GLN E 773 ASN E 774 GLN E1433 HIS E1469 GLN E1491 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.178453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.131524 restraints weight = 36301.935| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.24 r_work: 0.3372 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 29022 Z= 0.202 Angle : 0.624 10.355 39866 Z= 0.322 Chirality : 0.043 0.159 4548 Planarity : 0.005 0.051 4640 Dihedral : 14.356 74.128 5386 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.30 % Allowed : 15.17 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 aren not related in a simple way. whole: 0.44 (0.15), residues: 3118 helix: 0.86 (0.13), residues: 1484 sheet: -0.32 (0.27), residues: 366 loop : -0.04 (0.17), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 281 TYR 0.027 0.002 TYR E1468 PHE 0.016 0.002 PHE E 938 TRP 0.031 0.002 TRP E 102 HIS 0.011 0.002 HIS E 595 Details of bonding type rmsd covalent geometry : bond 0.00481 (29022) covalent geometry : angle 0.62400 (39866) hydrogen bonds : bond 0.04570 ( 1361) hydrogen bonds : angle 4.52058 ( 3803) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 398 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 MET cc_start: 0.7030 (tmm) cc_final: 0.6642 (ttp) REVERT: A 189 LYS cc_start: 0.7971 (tppt) cc_final: 0.7681 (ttmt) REVERT: A 190 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7165 (tt0) REVERT: A 193 ILE cc_start: 0.8675 (mt) cc_final: 0.8452 (mm) REVERT: A 236 ARG cc_start: 0.7792 (mmm-85) cc_final: 0.7486 (mtp180) REVERT: A 243 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7697 (mm-30) REVERT: A 247 VAL cc_start: 0.8510 (t) cc_final: 0.8141 (m) REVERT: A 261 ARG cc_start: 0.7670 (mtm180) cc_final: 0.7380 (mtm180) REVERT: A 263 LYS cc_start: 0.7682 (tptm) cc_final: 0.7164 (mmtt) REVERT: A 465 GLU cc_start: 0.8690 (tt0) cc_final: 0.8397 (tt0) REVERT: A 513 LYS cc_start: 0.8010 (ptmm) cc_final: 0.7608 (ptpp) REVERT: A 620 MET cc_start: 0.8114 (tpt) cc_final: 0.7396 (mmm) REVERT: A 677 ASP cc_start: 0.8819 (t70) cc_final: 0.8399 (t0) REVERT: A 702 ASP cc_start: 0.8768 (p0) cc_final: 0.8389 (p0) REVERT: A 768 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7817 (ptp) REVERT: A 789 ILE cc_start: 0.8474 (mp) cc_final: 0.8218 (mp) REVERT: A 797 GLU cc_start: 0.8480 (tp30) cc_final: 0.7922 (tm-30) REVERT: A 873 ARG cc_start: 0.7398 (mtm-85) cc_final: 0.7086 (mtm-85) REVERT: A 876 ASP cc_start: 0.7690 (t0) cc_final: 0.7469 (p0) REVERT: A 918 TYR cc_start: 0.8237 (t80) cc_final: 0.7845 (t80) REVERT: A 922 MET cc_start: 0.7589 (mmm) cc_final: 0.7351 (mmm) REVERT: A 1288 VAL cc_start: 0.8745 (p) cc_final: 0.8498 (t) REVERT: A 1297 GLU cc_start: 0.7864 (pt0) cc_final: 0.7549 (mm-30) REVERT: A 1320 LYS cc_start: 0.7967 (tptm) cc_final: 0.7680 (tptm) REVERT: A 1397 ARG cc_start: 0.8055 (ttm-80) cc_final: 0.7634 (ttm170) REVERT: A 1464 ILE cc_start: 0.8734 (pt) cc_final: 0.8368 (pt) REVERT: A 1520 ARG cc_start: 0.7163 (mtp85) cc_final: 0.6928 (mtp85) REVERT: F 258 MET cc_start: 0.3927 (mmm) cc_final: 0.2162 (ptm) REVERT: F 295 MET cc_start: 0.3173 (tpp) cc_final: 0.0821 (mtp) REVERT: F 300 SER cc_start: 0.8765 (p) cc_final: 0.8543 (p) REVERT: F 314 MET cc_start: 0.3160 (ppp) cc_final: 0.2917 (tpp) REVERT: E 41 VAL cc_start: 0.8639 (m) cc_final: 0.8434 (p) REVERT: E 75 MET cc_start: 0.7989 (mmm) cc_final: 0.7451 (mtt) REVERT: E 94 VAL cc_start: 0.6404 (t) cc_final: 0.6156 (m) REVERT: E 107 LYS cc_start: 0.8449 (ptmt) cc_final: 0.7805 (mmtm) REVERT: E 120 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8193 (tt) REVERT: E 154 MET cc_start: 0.8909 (mmm) cc_final: 0.8700 (mmm) REVERT: E 213 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7538 (mp) REVERT: E 260 ARG cc_start: 0.7586 (mmm160) cc_final: 0.7296 (mmm160) REVERT: E 308 ASP cc_start: 0.8355 (t0) cc_final: 0.7927 (t0) REVERT: E 312 ARG cc_start: 0.7958 (ttm-80) cc_final: 0.7688 (mtm110) REVERT: E 341 LEU cc_start: 0.7542 (mm) cc_final: 0.7332 (mp) REVERT: E 344 MET cc_start: 0.5360 (OUTLIER) cc_final: 0.4023 (ttp) REVERT: E 410 GLN cc_start: 0.7581 (mm-40) cc_final: 0.7226 (mm-40) REVERT: E 433 ASP cc_start: 0.7461 (t0) cc_final: 0.7189 (t0) REVERT: E 458 MET cc_start: 0.9117 (tpt) cc_final: 0.8694 (tpt) REVERT: E 523 LYS cc_start: 0.7932 (ptpp) cc_final: 0.7624 (ttpp) REVERT: E 639 LYS cc_start: 0.8175 (tppt) cc_final: 0.7739 (tttp) REVERT: E 643 ILE cc_start: 0.7931 (mm) cc_final: 0.7573 (mt) REVERT: E 659 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7392 (mt) REVERT: E 791 GLN cc_start: 0.6895 (pm20) cc_final: 0.6345 (mm-40) REVERT: E 890 ASP cc_start: 0.6904 (p0) cc_final: 0.6553 (t0) REVERT: E 1014 THR cc_start: 0.8742 (m) cc_final: 0.8348 (p) REVERT: E 1031 ARG cc_start: 0.8049 (mtp-110) cc_final: 0.7353 (mtt180) REVERT: E 1172 LYS cc_start: 0.8145 (tptp) cc_final: 0.7617 (ttpt) REVERT: E 1185 HIS cc_start: 0.8613 (m90) cc_final: 0.8062 (m90) REVERT: E 1295 ASN cc_start: 0.8122 (t0) cc_final: 0.7438 (t0) REVERT: E 1300 LYS cc_start: 0.8708 (mtmt) cc_final: 0.8404 (mmtt) REVERT: E 1326 ILE cc_start: 0.8398 (pt) cc_final: 0.8144 (mp) REVERT: E 1520 ARG cc_start: 0.6595 (mtt180) cc_final: 0.6244 (mtm-85) REVERT: E 1551 THR cc_start: 0.6044 (OUTLIER) cc_final: 0.5827 (p) REVERT: E 1626 ASP cc_start: 0.7085 (t0) cc_final: 0.6852 (t0) outliers start: 65 outliers final: 33 residues processed: 441 average time/residue: 0.2089 time to fit residues: 143.2251 Evaluate side-chains 380 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 341 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1404 LEU Chi-restraints excluded: chain A residue 1417 MET Chi-restraints excluded: chain A residue 1551 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 84 LYS Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 344 MET Chi-restraints excluded: chain E residue 424 MET Chi-restraints excluded: chain E residue 565 VAL Chi-restraints excluded: chain E residue 590 VAL Chi-restraints excluded: chain E residue 659 LEU Chi-restraints excluded: chain E residue 756 ILE Chi-restraints excluded: chain E residue 788 VAL Chi-restraints excluded: chain E residue 933 VAL Chi-restraints excluded: chain E residue 1206 VAL Chi-restraints excluded: chain E residue 1356 VAL Chi-restraints excluded: chain E residue 1551 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 184 optimal weight: 8.9990 chunk 294 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 94 optimal weight: 8.9990 chunk 3 optimal weight: 0.6980 chunk 2 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 166 optimal weight: 10.0000 chunk 262 optimal weight: 7.9990 chunk 111 optimal weight: 0.6980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 595 HIS A 800 HIS A 884 GLN A1433 HIS ** A1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 GLN E 595 HIS ** E 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 679 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1433 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.179268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.132861 restraints weight = 36314.480| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.27 r_work: 0.3384 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29022 Z= 0.134 Angle : 0.531 11.393 39866 Z= 0.275 Chirality : 0.040 0.260 4548 Planarity : 0.004 0.050 4640 Dihedral : 14.316 73.765 5386 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.48 % Allowed : 16.05 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 aren not related in a simple way. whole: 0.51 (0.15), residues: 3118 helix: 0.98 (0.13), residues: 1502 sheet: -0.52 (0.26), residues: 378 loop : -0.01 (0.17), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 853 TYR 0.016 0.001 TYR A1000 PHE 0.026 0.001 PHE A 938 TRP 0.025 0.002 TRP E 885 HIS 0.008 0.001 HIS E 595 Details of bonding type rmsd covalent geometry : bond 0.00309 (29022) covalent geometry : angle 0.53143 (39866) hydrogen bonds : bond 0.04233 ( 1361) hydrogen bonds : angle 4.33620 ( 3803) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 369 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 MET cc_start: 0.7002 (tmm) cc_final: 0.6633 (ttp) REVERT: A 189 LYS cc_start: 0.8041 (tppt) cc_final: 0.7813 (ttmt) REVERT: A 190 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7302 (tt0) REVERT: A 204 ASP cc_start: 0.6743 (t0) cc_final: 0.6535 (m-30) REVERT: A 236 ARG cc_start: 0.7867 (mmm-85) cc_final: 0.7601 (mtp180) REVERT: A 243 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7712 (mm-30) REVERT: A 247 VAL cc_start: 0.8480 (t) cc_final: 0.8074 (m) REVERT: A 576 HIS cc_start: 0.7867 (t-90) cc_final: 0.6766 (m90) REVERT: A 616 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.7985 (mt) REVERT: A 620 MET cc_start: 0.8061 (tpt) cc_final: 0.7738 (mmm) REVERT: A 639 LYS cc_start: 0.7973 (tppt) cc_final: 0.7563 (tppt) REVERT: A 702 ASP cc_start: 0.8739 (OUTLIER) cc_final: 0.8333 (p0) REVERT: A 768 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.8133 (ptp) REVERT: A 789 ILE cc_start: 0.8525 (mp) cc_final: 0.8265 (mp) REVERT: A 797 GLU cc_start: 0.8487 (tp30) cc_final: 0.7991 (tm-30) REVERT: A 873 ARG cc_start: 0.7335 (mtm-85) cc_final: 0.6942 (mtm-85) REVERT: A 876 ASP cc_start: 0.7734 (t0) cc_final: 0.7447 (p0) REVERT: A 918 TYR cc_start: 0.8220 (t80) cc_final: 0.7754 (t80) REVERT: A 922 MET cc_start: 0.7614 (mmm) cc_final: 0.7144 (mmm) REVERT: A 970 ILE cc_start: 0.8273 (OUTLIER) cc_final: 0.7795 (mm) REVERT: A 1297 GLU cc_start: 0.7953 (pt0) cc_final: 0.7606 (mm-30) REVERT: A 1326 ILE cc_start: 0.8715 (OUTLIER) cc_final: 0.8418 (mp) REVERT: A 1430 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7080 (mm) REVERT: A 1464 ILE cc_start: 0.8685 (pt) cc_final: 0.8339 (pt) REVERT: A 1470 GLU cc_start: 0.8429 (tt0) cc_final: 0.8049 (pt0) REVERT: A 1501 ASP cc_start: 0.8632 (m-30) cc_final: 0.8408 (m-30) REVERT: A 1520 ARG cc_start: 0.7280 (mtp85) cc_final: 0.6883 (mtp85) REVERT: F 258 MET cc_start: 0.4271 (mmm) cc_final: 0.2627 (ptm) REVERT: F 295 MET cc_start: 0.2993 (tpp) cc_final: 0.0810 (mtp) REVERT: F 314 MET cc_start: 0.3424 (ppp) cc_final: 0.3132 (tpp) REVERT: E 75 MET cc_start: 0.8043 (mmm) cc_final: 0.7506 (mtt) REVERT: E 94 VAL cc_start: 0.6746 (t) cc_final: 0.6470 (m) REVERT: E 107 LYS cc_start: 0.8490 (ptmt) cc_final: 0.7870 (mmtm) REVERT: E 154 MET cc_start: 0.8856 (mmm) cc_final: 0.8586 (mmm) REVERT: E 207 GLU cc_start: 0.8364 (mt-10) cc_final: 0.7876 (mm-30) REVERT: E 260 ARG cc_start: 0.7720 (mmm160) cc_final: 0.7468 (mmm160) REVERT: E 312 ARG cc_start: 0.8008 (ttm-80) cc_final: 0.7662 (mtm110) REVERT: E 344 MET cc_start: 0.5655 (mmt) cc_final: 0.4271 (ttp) REVERT: E 433 ASP cc_start: 0.7451 (t0) cc_final: 0.7112 (t0) REVERT: E 523 LYS cc_start: 0.8005 (ptpp) cc_final: 0.7755 (ttpp) REVERT: E 543 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.7130 (pt0) REVERT: E 639 LYS cc_start: 0.8198 (tppt) cc_final: 0.7861 (tttp) REVERT: E 643 ILE cc_start: 0.8047 (mm) cc_final: 0.7715 (mt) REVERT: E 659 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.7235 (mt) REVERT: E 791 GLN cc_start: 0.6885 (pm20) cc_final: 0.6563 (mm-40) REVERT: E 890 ASP cc_start: 0.6822 (p0) cc_final: 0.6604 (t0) REVERT: E 920 PHE cc_start: 0.6736 (t80) cc_final: 0.6434 (t80) REVERT: E 967 MET cc_start: 0.6286 (mpp) cc_final: 0.5292 (ptt) REVERT: E 974 GLU cc_start: 0.7527 (mt-10) cc_final: 0.6621 (pm20) REVERT: E 1031 ARG cc_start: 0.8102 (mtp-110) cc_final: 0.7337 (mtt-85) REVERT: E 1172 LYS cc_start: 0.8169 (tptp) cc_final: 0.7623 (ttpt) REVERT: E 1185 HIS cc_start: 0.8593 (m90) cc_final: 0.8250 (m90) REVERT: E 1291 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8183 (tp) REVERT: E 1295 ASN cc_start: 0.8091 (t0) cc_final: 0.6985 (m-40) REVERT: E 1300 LYS cc_start: 0.8716 (mtmt) cc_final: 0.8377 (mmtt) REVERT: E 1326 ILE cc_start: 0.8461 (pt) cc_final: 0.8198 (mp) REVERT: E 1520 ARG cc_start: 0.6699 (mtt180) cc_final: 0.6412 (mtp85) REVERT: E 1626 ASP cc_start: 0.6995 (t0) cc_final: 0.6719 (t0) outliers start: 70 outliers final: 31 residues processed: 411 average time/residue: 0.1962 time to fit residues: 126.4274 Evaluate side-chains 375 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 335 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 702 ASP Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 970 ILE Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1326 ILE Chi-restraints excluded: chain A residue 1430 LEU Chi-restraints excluded: chain A residue 1551 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 424 MET Chi-restraints excluded: chain E residue 497 THR Chi-restraints excluded: chain E residue 543 GLU Chi-restraints excluded: chain E residue 565 VAL Chi-restraints excluded: chain E residue 582 ILE Chi-restraints excluded: chain E residue 659 LEU Chi-restraints excluded: chain E residue 675 ILE Chi-restraints excluded: chain E residue 702 ASP Chi-restraints excluded: chain E residue 788 VAL Chi-restraints excluded: chain E residue 895 VAL Chi-restraints excluded: chain E residue 970 ILE Chi-restraints excluded: chain E residue 1206 VAL Chi-restraints excluded: chain E residue 1291 LEU Chi-restraints excluded: chain E residue 1356 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 148 optimal weight: 8.9990 chunk 142 optimal weight: 9.9990 chunk 191 optimal weight: 5.9990 chunk 124 optimal weight: 0.5980 chunk 264 optimal weight: 1.9990 chunk 41 optimal weight: 0.0170 chunk 146 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 199 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 753 ASN A 884 GLN A1338 ASN A1433 HIS ** A1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 580 GLN E 595 HIS E1433 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.180820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.133924 restraints weight = 36158.966| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.35 r_work: 0.3401 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 29022 Z= 0.103 Angle : 0.501 12.902 39866 Z= 0.259 Chirality : 0.038 0.167 4548 Planarity : 0.004 0.051 4640 Dihedral : 14.258 73.841 5386 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.66 % Allowed : 16.19 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.15), residues: 3118 helix: 1.16 (0.13), residues: 1504 sheet: -0.48 (0.26), residues: 378 loop : 0.05 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 854 TYR 0.017 0.001 TYR A 925 PHE 0.019 0.001 PHE A 49 TRP 0.026 0.001 TRP E 102 HIS 0.008 0.001 HIS E1433 Details of bonding type rmsd covalent geometry : bond 0.00225 (29022) covalent geometry : angle 0.50100 (39866) hydrogen bonds : bond 0.03746 ( 1361) hydrogen bonds : angle 4.19542 ( 3803) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 393 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 MET cc_start: 0.6941 (tmm) cc_final: 0.6594 (ttp) REVERT: A 189 LYS cc_start: 0.7861 (tppt) cc_final: 0.7658 (ttmt) REVERT: A 190 GLU cc_start: 0.7637 (tm-30) cc_final: 0.7191 (tt0) REVERT: A 204 ASP cc_start: 0.6828 (t0) cc_final: 0.6562 (m-30) REVERT: A 243 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7702 (mm-30) REVERT: A 247 VAL cc_start: 0.8398 (t) cc_final: 0.7987 (m) REVERT: A 356 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6799 (mm-30) REVERT: A 357 GLU cc_start: 0.7514 (tt0) cc_final: 0.7306 (tt0) REVERT: A 364 THR cc_start: 0.8744 (p) cc_final: 0.8542 (p) REVERT: A 466 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7525 (mt-10) REVERT: A 576 HIS cc_start: 0.7769 (t-90) cc_final: 0.6800 (m90) REVERT: A 620 MET cc_start: 0.8065 (tpt) cc_final: 0.7766 (mmm) REVERT: A 636 ASP cc_start: 0.7830 (OUTLIER) cc_final: 0.7522 (p0) REVERT: A 639 LYS cc_start: 0.7928 (tppt) cc_final: 0.7599 (tppt) REVERT: A 702 ASP cc_start: 0.8687 (OUTLIER) cc_final: 0.8313 (p0) REVERT: A 768 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.8182 (ptp) REVERT: A 789 ILE cc_start: 0.8548 (mp) cc_final: 0.8248 (mp) REVERT: A 797 GLU cc_start: 0.8455 (tp30) cc_final: 0.7950 (tm-30) REVERT: A 876 ASP cc_start: 0.7800 (t0) cc_final: 0.7428 (p0) REVERT: A 918 TYR cc_start: 0.8251 (t80) cc_final: 0.7646 (t80) REVERT: A 922 MET cc_start: 0.7553 (mmm) cc_final: 0.7287 (mmm) REVERT: A 1297 GLU cc_start: 0.7994 (pt0) cc_final: 0.7588 (mm-30) REVERT: A 1320 LYS cc_start: 0.7964 (tptm) cc_final: 0.7679 (tptm) REVERT: A 1326 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8419 (mp) REVERT: A 1338 ASN cc_start: 0.8643 (OUTLIER) cc_final: 0.8109 (m-40) REVERT: A 1464 ILE cc_start: 0.8646 (pt) cc_final: 0.8323 (pt) REVERT: A 1501 ASP cc_start: 0.8574 (m-30) cc_final: 0.8367 (m-30) REVERT: F 258 MET cc_start: 0.4553 (mmm) cc_final: 0.2753 (ptm) REVERT: F 284 THR cc_start: 0.5262 (OUTLIER) cc_final: 0.4876 (m) REVERT: F 295 MET cc_start: 0.3096 (tpp) cc_final: 0.1011 (mtp) REVERT: E 63 MET cc_start: 0.8430 (ttp) cc_final: 0.8202 (ttp) REVERT: E 75 MET cc_start: 0.8021 (mmm) cc_final: 0.7463 (mtt) REVERT: E 94 VAL cc_start: 0.6757 (t) cc_final: 0.6482 (m) REVERT: E 107 LYS cc_start: 0.8538 (ptmt) cc_final: 0.7860 (mmtm) REVERT: E 154 MET cc_start: 0.8881 (mmm) cc_final: 0.8614 (mmm) REVERT: E 207 GLU cc_start: 0.8440 (mt-10) cc_final: 0.7846 (mm-30) REVERT: E 260 ARG cc_start: 0.7737 (mmm160) cc_final: 0.7468 (mmm160) REVERT: E 263 LYS cc_start: 0.8578 (tttt) cc_final: 0.8210 (tppt) REVERT: E 277 VAL cc_start: 0.8860 (t) cc_final: 0.8648 (m) REVERT: E 287 GLN cc_start: 0.7206 (mt0) cc_final: 0.6931 (mt0) REVERT: E 312 ARG cc_start: 0.8005 (ttm-80) cc_final: 0.7676 (mtm110) REVERT: E 344 MET cc_start: 0.5497 (OUTLIER) cc_final: 0.4094 (ttp) REVERT: E 410 GLN cc_start: 0.7419 (mm-40) cc_final: 0.7088 (mm-40) REVERT: E 414 GLU cc_start: 0.8552 (pm20) cc_final: 0.8202 (mt-10) REVERT: E 433 ASP cc_start: 0.7298 (t0) cc_final: 0.6923 (t0) REVERT: E 523 LYS cc_start: 0.8030 (ptpp) cc_final: 0.7619 (tppt) REVERT: E 552 GLN cc_start: 0.7052 (pp30) cc_final: 0.6689 (pt0) REVERT: E 570 ASN cc_start: 0.8489 (t0) cc_final: 0.8247 (t0) REVERT: E 639 LYS cc_start: 0.8166 (tppt) cc_final: 0.7759 (tttp) REVERT: E 643 ILE cc_start: 0.7957 (mm) cc_final: 0.7614 (mt) REVERT: E 659 LEU cc_start: 0.7322 (OUTLIER) cc_final: 0.7045 (mt) REVERT: E 890 ASP cc_start: 0.6956 (p0) cc_final: 0.6542 (t0) REVERT: E 967 MET cc_start: 0.6266 (mpp) cc_final: 0.5346 (ptt) REVERT: E 974 GLU cc_start: 0.7684 (mt-10) cc_final: 0.6784 (pm20) REVERT: E 1031 ARG cc_start: 0.8104 (mtp-110) cc_final: 0.7277 (mtt-85) REVERT: E 1034 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7700 (mm-30) REVERT: E 1172 LYS cc_start: 0.8138 (tptp) cc_final: 0.7600 (ttpt) REVERT: E 1185 HIS cc_start: 0.8596 (m90) cc_final: 0.8266 (m90) REVERT: E 1295 ASN cc_start: 0.8027 (t0) cc_final: 0.6908 (m-40) REVERT: E 1326 ILE cc_start: 0.8476 (pt) cc_final: 0.8194 (mp) REVERT: E 1520 ARG cc_start: 0.6622 (mtt180) cc_final: 0.6324 (mtp85) REVERT: E 1626 ASP cc_start: 0.6940 (t0) cc_final: 0.6613 (t0) outliers start: 75 outliers final: 40 residues processed: 435 average time/residue: 0.1800 time to fit residues: 125.5082 Evaluate side-chains 401 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 351 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 624 CYS Chi-restraints excluded: chain A residue 636 ASP Chi-restraints excluded: chain A residue 702 ASP Chi-restraints excluded: chain A residue 739 GLU Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1326 ILE Chi-restraints excluded: chain A residue 1338 ASN Chi-restraints excluded: chain A residue 1417 MET Chi-restraints excluded: chain A residue 1551 THR Chi-restraints excluded: chain F residue 261 GLN Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain F residue 357 ILE Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 208 MET Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 344 MET Chi-restraints excluded: chain E residue 424 MET Chi-restraints excluded: chain E residue 565 VAL Chi-restraints excluded: chain E residue 582 ILE Chi-restraints excluded: chain E residue 590 VAL Chi-restraints excluded: chain E residue 659 LEU Chi-restraints excluded: chain E residue 675 ILE Chi-restraints excluded: chain E residue 702 ASP Chi-restraints excluded: chain E residue 788 VAL Chi-restraints excluded: chain E residue 895 VAL Chi-restraints excluded: chain E residue 898 VAL Chi-restraints excluded: chain E residue 933 VAL Chi-restraints excluded: chain E residue 970 ILE Chi-restraints excluded: chain E residue 1206 VAL Chi-restraints excluded: chain E residue 1356 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 75 optimal weight: 5.9990 chunk 290 optimal weight: 4.9990 chunk 234 optimal weight: 0.5980 chunk 138 optimal weight: 0.9980 chunk 305 optimal weight: 6.9990 chunk 187 optimal weight: 0.8980 chunk 218 optimal weight: 0.3980 chunk 108 optimal weight: 2.9990 chunk 251 optimal weight: 0.9980 chunk 232 optimal weight: 9.9990 chunk 309 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 72 GLN A 734 GLN A1433 HIS ** A1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 250 ASN E 407 ASN E 580 GLN E 595 HIS E1433 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.180614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.132930 restraints weight = 36146.509| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.32 r_work: 0.3401 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 29022 Z= 0.105 Angle : 0.496 12.801 39866 Z= 0.256 Chirality : 0.038 0.156 4548 Planarity : 0.004 0.050 4640 Dihedral : 14.242 73.817 5386 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.73 % Allowed : 16.73 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.15), residues: 3118 helix: 1.22 (0.13), residues: 1506 sheet: -0.40 (0.26), residues: 380 loop : 0.08 (0.18), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 873 TYR 0.017 0.001 TYR A 925 PHE 0.027 0.001 PHE A1542 TRP 0.025 0.002 TRP E 102 HIS 0.008 0.001 HIS E 595 Details of bonding type rmsd covalent geometry : bond 0.00234 (29022) covalent geometry : angle 0.49646 (39866) hydrogen bonds : bond 0.03697 ( 1361) hydrogen bonds : angle 4.13444 ( 3803) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 375 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 MET cc_start: 0.6878 (tmm) cc_final: 0.6562 (ttp) REVERT: A 190 GLU cc_start: 0.7678 (tm-30) cc_final: 0.7219 (tt0) REVERT: A 204 ASP cc_start: 0.6867 (t0) cc_final: 0.6597 (m-30) REVERT: A 243 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7683 (mm-30) REVERT: A 247 VAL cc_start: 0.8402 (t) cc_final: 0.7983 (m) REVERT: A 384 LYS cc_start: 0.8539 (mtmm) cc_final: 0.7946 (ttpp) REVERT: A 576 HIS cc_start: 0.8132 (t-90) cc_final: 0.6835 (m90) REVERT: A 620 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7812 (mmm) REVERT: A 636 ASP cc_start: 0.7797 (OUTLIER) cc_final: 0.7551 (p0) REVERT: A 639 LYS cc_start: 0.7895 (tppt) cc_final: 0.7626 (tppt) REVERT: A 702 ASP cc_start: 0.8656 (OUTLIER) cc_final: 0.8291 (p0) REVERT: A 768 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.8207 (ptp) REVERT: A 789 ILE cc_start: 0.8549 (mp) cc_final: 0.8232 (mp) REVERT: A 797 GLU cc_start: 0.8496 (tp30) cc_final: 0.7968 (tm-30) REVERT: A 876 ASP cc_start: 0.7674 (t0) cc_final: 0.7369 (p0) REVERT: A 918 TYR cc_start: 0.8256 (t80) cc_final: 0.7535 (t80) REVERT: A 922 MET cc_start: 0.7590 (mmm) cc_final: 0.7100 (mmm) REVERT: A 941 GLU cc_start: 0.7686 (tm-30) cc_final: 0.6925 (tp30) REVERT: A 970 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7652 (mm) REVERT: A 1297 GLU cc_start: 0.8000 (pt0) cc_final: 0.7613 (mm-30) REVERT: A 1326 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8452 (mp) REVERT: A 1380 ASN cc_start: 0.8406 (m-40) cc_final: 0.7724 (m-40) REVERT: A 1430 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.6947 (mm) REVERT: A 1464 ILE cc_start: 0.8633 (pt) cc_final: 0.8317 (pt) REVERT: A 1501 ASP cc_start: 0.8579 (m-30) cc_final: 0.8374 (m-30) REVERT: B 258 MET cc_start: 0.2611 (tmm) cc_final: 0.2401 (ptp) REVERT: F 258 MET cc_start: 0.4510 (mmm) cc_final: 0.2862 (ptm) REVERT: F 284 THR cc_start: 0.5340 (OUTLIER) cc_final: 0.4981 (m) REVERT: F 295 MET cc_start: 0.3071 (tpp) cc_final: 0.1036 (mtp) REVERT: E 63 MET cc_start: 0.8442 (ttp) cc_final: 0.8235 (ttp) REVERT: E 75 MET cc_start: 0.8020 (mmm) cc_final: 0.7442 (mtt) REVERT: E 107 LYS cc_start: 0.8590 (ptmt) cc_final: 0.8047 (mmtp) REVERT: E 154 MET cc_start: 0.8857 (mmm) cc_final: 0.8535 (mmm) REVERT: E 207 GLU cc_start: 0.8452 (mt-10) cc_final: 0.7838 (mm-30) REVERT: E 263 LYS cc_start: 0.8578 (tttt) cc_final: 0.8227 (tppt) REVERT: E 277 VAL cc_start: 0.8855 (t) cc_final: 0.8655 (m) REVERT: E 287 GLN cc_start: 0.7117 (mt0) cc_final: 0.6856 (mt0) REVERT: E 312 ARG cc_start: 0.7938 (ttm-80) cc_final: 0.7631 (mtm110) REVERT: E 344 MET cc_start: 0.5384 (OUTLIER) cc_final: 0.4099 (ttp) REVERT: E 414 GLU cc_start: 0.8549 (pm20) cc_final: 0.8203 (mt-10) REVERT: E 523 LYS cc_start: 0.8060 (ptpp) cc_final: 0.7650 (tppt) REVERT: E 552 GLN cc_start: 0.7107 (pp30) cc_final: 0.6700 (pt0) REVERT: E 570 ASN cc_start: 0.8445 (t0) cc_final: 0.8201 (t0) REVERT: E 639 LYS cc_start: 0.8216 (tppt) cc_final: 0.7816 (tttp) REVERT: E 643 ILE cc_start: 0.7986 (mm) cc_final: 0.7648 (mt) REVERT: E 659 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.7007 (mt) REVERT: E 799 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8481 (tp) REVERT: E 890 ASP cc_start: 0.6967 (p0) cc_final: 0.6591 (t0) REVERT: E 967 MET cc_start: 0.6209 (mpp) cc_final: 0.5360 (ptt) REVERT: E 974 GLU cc_start: 0.7626 (mt-10) cc_final: 0.6822 (pm20) REVERT: E 1014 THR cc_start: 0.8599 (m) cc_final: 0.8277 (p) REVERT: E 1031 ARG cc_start: 0.8111 (mtp-110) cc_final: 0.7268 (mtt-85) REVERT: E 1034 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7717 (mm-30) REVERT: E 1172 LYS cc_start: 0.8147 (tptp) cc_final: 0.7605 (ttpt) REVERT: E 1185 HIS cc_start: 0.8508 (m90) cc_final: 0.8104 (m90) REVERT: E 1291 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8190 (tp) REVERT: E 1295 ASN cc_start: 0.8043 (t0) cc_final: 0.6896 (m-40) REVERT: E 1326 ILE cc_start: 0.8477 (pt) cc_final: 0.8207 (mp) REVERT: E 1472 GLU cc_start: 0.8641 (tm-30) cc_final: 0.8326 (tm-30) REVERT: E 1520 ARG cc_start: 0.6597 (mtt180) cc_final: 0.6311 (mtp85) REVERT: E 1626 ASP cc_start: 0.6989 (t0) cc_final: 0.6660 (t0) REVERT: E 1640 LEU cc_start: 0.8226 (mp) cc_final: 0.7950 (mp) outliers start: 77 outliers final: 45 residues processed: 420 average time/residue: 0.2032 time to fit residues: 136.5239 Evaluate side-chains 408 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 351 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 624 CYS Chi-restraints excluded: chain A residue 636 ASP Chi-restraints excluded: chain A residue 702 ASP Chi-restraints excluded: chain A residue 739 GLU Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 893 MET Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 970 ILE Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1326 ILE Chi-restraints excluded: chain A residue 1417 MET Chi-restraints excluded: chain A residue 1430 LEU Chi-restraints excluded: chain A residue 1551 THR Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain F residue 357 ILE Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 208 MET Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 344 MET Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 424 MET Chi-restraints excluded: chain E residue 497 THR Chi-restraints excluded: chain E residue 565 VAL Chi-restraints excluded: chain E residue 582 ILE Chi-restraints excluded: chain E residue 659 LEU Chi-restraints excluded: chain E residue 675 ILE Chi-restraints excluded: chain E residue 702 ASP Chi-restraints excluded: chain E residue 788 VAL Chi-restraints excluded: chain E residue 799 LEU Chi-restraints excluded: chain E residue 895 VAL Chi-restraints excluded: chain E residue 898 VAL Chi-restraints excluded: chain E residue 933 VAL Chi-restraints excluded: chain E residue 1206 VAL Chi-restraints excluded: chain E residue 1291 LEU Chi-restraints excluded: chain E residue 1356 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 42 optimal weight: 0.6980 chunk 283 optimal weight: 0.6980 chunk 299 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 chunk 187 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 211 optimal weight: 4.9990 chunk 304 optimal weight: 7.9990 chunk 213 optimal weight: 0.6980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 ASN A 517 GLN A1433 HIS ** A1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 250 ASN E 595 HIS E 679 HIS E1433 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.177122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.130208 restraints weight = 36152.111| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.20 r_work: 0.3348 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 29022 Z= 0.149 Angle : 0.537 13.563 39866 Z= 0.275 Chirality : 0.040 0.153 4548 Planarity : 0.004 0.049 4640 Dihedral : 14.217 73.851 5386 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.80 % Allowed : 17.26 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.15), residues: 3118 helix: 1.14 (0.13), residues: 1508 sheet: -0.56 (0.25), residues: 392 loop : 0.05 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 440 TYR 0.021 0.001 TYR E1468 PHE 0.027 0.001 PHE A1542 TRP 0.033 0.002 TRP E 102 HIS 0.008 0.001 HIS E 595 Details of bonding type rmsd covalent geometry : bond 0.00355 (29022) covalent geometry : angle 0.53692 (39866) hydrogen bonds : bond 0.04021 ( 1361) hydrogen bonds : angle 4.16685 ( 3803) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 361 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 GLU cc_start: 0.7753 (tm-30) cc_final: 0.7373 (tt0) REVERT: A 204 ASP cc_start: 0.6999 (t0) cc_final: 0.6727 (m-30) REVERT: A 243 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7749 (mm-30) REVERT: A 247 VAL cc_start: 0.8491 (t) cc_final: 0.8068 (m) REVERT: A 427 ARG cc_start: 0.7857 (mtp85) cc_final: 0.7636 (mtp85) REVERT: A 576 HIS cc_start: 0.8158 (t-90) cc_final: 0.6887 (m-70) REVERT: A 620 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.8112 (mmm) REVERT: A 639 LYS cc_start: 0.8084 (tppt) cc_final: 0.7729 (tppt) REVERT: A 702 ASP cc_start: 0.8732 (p0) cc_final: 0.8358 (p0) REVERT: A 789 ILE cc_start: 0.8669 (mp) cc_final: 0.8353 (mp) REVERT: A 797 GLU cc_start: 0.8636 (tp30) cc_final: 0.8006 (tm-30) REVERT: A 876 ASP cc_start: 0.7728 (t0) cc_final: 0.7460 (p0) REVERT: A 918 TYR cc_start: 0.8243 (t80) cc_final: 0.7476 (t80) REVERT: A 922 MET cc_start: 0.7683 (mmm) cc_final: 0.7159 (mmm) REVERT: A 941 GLU cc_start: 0.7642 (tm-30) cc_final: 0.6932 (tp30) REVERT: A 1297 GLU cc_start: 0.8025 (pt0) cc_final: 0.7721 (mm-30) REVERT: A 1320 LYS cc_start: 0.8115 (tptm) cc_final: 0.7841 (tptm) REVERT: A 1326 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8569 (mp) REVERT: A 1430 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.6915 (mm) REVERT: A 1464 ILE cc_start: 0.8679 (pt) cc_final: 0.8376 (pt) REVERT: A 1470 GLU cc_start: 0.8436 (tt0) cc_final: 0.8027 (pt0) REVERT: A 1501 ASP cc_start: 0.8661 (m-30) cc_final: 0.8427 (m-30) REVERT: B 258 MET cc_start: 0.2301 (tmm) cc_final: 0.2070 (ptp) REVERT: F 258 MET cc_start: 0.3988 (mmm) cc_final: 0.1985 (ttp) REVERT: F 284 THR cc_start: 0.5515 (OUTLIER) cc_final: 0.4445 (p) REVERT: F 295 MET cc_start: 0.3050 (tpp) cc_final: 0.0936 (mtp) REVERT: F 314 MET cc_start: 0.3112 (ppp) cc_final: 0.2531 (tpt) REVERT: E 75 MET cc_start: 0.8099 (mmm) cc_final: 0.7513 (mtt) REVERT: E 107 LYS cc_start: 0.8622 (ptmt) cc_final: 0.8107 (mmtp) REVERT: E 154 MET cc_start: 0.8991 (mmm) cc_final: 0.8751 (mmm) REVERT: E 207 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8018 (mm-30) REVERT: E 263 LYS cc_start: 0.8673 (tttt) cc_final: 0.8290 (tppt) REVERT: E 287 GLN cc_start: 0.7249 (mt0) cc_final: 0.6875 (mt0) REVERT: E 312 ARG cc_start: 0.7982 (ttm-80) cc_final: 0.7678 (mtm110) REVERT: E 344 MET cc_start: 0.5450 (OUTLIER) cc_final: 0.4128 (ttp) REVERT: E 523 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7904 (ttpp) REVERT: E 552 GLN cc_start: 0.7098 (pp30) cc_final: 0.6787 (pt0) REVERT: E 570 ASN cc_start: 0.8484 (t0) cc_final: 0.8222 (t0) REVERT: E 577 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.8176 (ttm-80) REVERT: E 639 LYS cc_start: 0.8313 (tppt) cc_final: 0.7933 (tttp) REVERT: E 643 ILE cc_start: 0.8118 (mm) cc_final: 0.7803 (mt) REVERT: E 799 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8538 (tp) REVERT: E 890 ASP cc_start: 0.7052 (p0) cc_final: 0.6653 (t0) REVERT: E 929 ILE cc_start: 0.7435 (pt) cc_final: 0.7195 (mt) REVERT: E 967 MET cc_start: 0.6267 (mpp) cc_final: 0.5494 (ptt) REVERT: E 1031 ARG cc_start: 0.8010 (mtp-110) cc_final: 0.7377 (mtt180) REVERT: E 1034 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7782 (mm-30) REVERT: E 1172 LYS cc_start: 0.8182 (tptp) cc_final: 0.7657 (ttpt) REVERT: E 1291 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8403 (tp) REVERT: E 1295 ASN cc_start: 0.8104 (t0) cc_final: 0.6957 (m-40) REVERT: E 1326 ILE cc_start: 0.8552 (pt) cc_final: 0.8335 (mp) REVERT: E 1472 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8283 (tm-30) REVERT: E 1626 ASP cc_start: 0.7173 (t0) cc_final: 0.6883 (t0) outliers start: 79 outliers final: 50 residues processed: 411 average time/residue: 0.1583 time to fit residues: 104.9648 Evaluate side-chains 399 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 340 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 624 CYS Chi-restraints excluded: chain A residue 739 GLU Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1207 PHE Chi-restraints excluded: chain A residue 1291 LEU Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1326 ILE Chi-restraints excluded: chain A residue 1417 MET Chi-restraints excluded: chain A residue 1430 LEU Chi-restraints excluded: chain A residue 1551 THR Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain F residue 357 ILE Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 84 LYS Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 208 MET Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 344 MET Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 400 CYS Chi-restraints excluded: chain E residue 424 MET Chi-restraints excluded: chain E residue 497 THR Chi-restraints excluded: chain E residue 523 LYS Chi-restraints excluded: chain E residue 565 VAL Chi-restraints excluded: chain E residue 577 ARG Chi-restraints excluded: chain E residue 582 ILE Chi-restraints excluded: chain E residue 590 VAL Chi-restraints excluded: chain E residue 675 ILE Chi-restraints excluded: chain E residue 788 VAL Chi-restraints excluded: chain E residue 799 LEU Chi-restraints excluded: chain E residue 898 VAL Chi-restraints excluded: chain E residue 933 VAL Chi-restraints excluded: chain E residue 953 VAL Chi-restraints excluded: chain E residue 1206 VAL Chi-restraints excluded: chain E residue 1291 LEU Chi-restraints excluded: chain E residue 1356 VAL Chi-restraints excluded: chain E residue 1461 THR Chi-restraints excluded: chain E residue 1482 LEU Chi-restraints excluded: chain E residue 1619 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 139 optimal weight: 3.9990 chunk 169 optimal weight: 10.0000 chunk 291 optimal weight: 0.8980 chunk 186 optimal weight: 3.9990 chunk 242 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 184 optimal weight: 7.9990 chunk 303 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 884 GLN A1340 GLN A1433 HIS A1491 ASN ** E 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 595 HIS E1433 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.176235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.127452 restraints weight = 36009.424| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.29 r_work: 0.3336 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 29022 Z= 0.152 Angle : 0.535 13.957 39866 Z= 0.274 Chirality : 0.040 0.150 4548 Planarity : 0.004 0.048 4640 Dihedral : 14.211 73.746 5381 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.62 % Allowed : 17.54 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.15), residues: 3118 helix: 1.11 (0.13), residues: 1514 sheet: -0.58 (0.25), residues: 392 loop : 0.06 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 873 TYR 0.019 0.001 TYR A 740 PHE 0.026 0.001 PHE A1542 TRP 0.034 0.002 TRP E 102 HIS 0.008 0.001 HIS E 595 Details of bonding type rmsd covalent geometry : bond 0.00363 (29022) covalent geometry : angle 0.53545 (39866) hydrogen bonds : bond 0.03965 ( 1361) hydrogen bonds : angle 4.17448 ( 3803) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 362 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 GLU cc_start: 0.7804 (tm-30) cc_final: 0.7501 (tt0) REVERT: A 204 ASP cc_start: 0.7063 (t0) cc_final: 0.6802 (m-30) REVERT: A 243 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7851 (mm-30) REVERT: A 576 HIS cc_start: 0.8086 (t-90) cc_final: 0.6924 (m-70) REVERT: A 620 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.7787 (mmm) REVERT: A 639 LYS cc_start: 0.8061 (tppt) cc_final: 0.7737 (tppt) REVERT: A 702 ASP cc_start: 0.8704 (p0) cc_final: 0.8369 (p0) REVERT: A 789 ILE cc_start: 0.8674 (mp) cc_final: 0.8363 (mp) REVERT: A 797 GLU cc_start: 0.8612 (tp30) cc_final: 0.8051 (tm-30) REVERT: A 876 ASP cc_start: 0.7716 (t0) cc_final: 0.7467 (p0) REVERT: A 894 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8567 (tp) REVERT: A 918 TYR cc_start: 0.8256 (t80) cc_final: 0.7897 (t80) REVERT: A 941 GLU cc_start: 0.7549 (tm-30) cc_final: 0.6682 (tp30) REVERT: A 970 ILE cc_start: 0.8304 (OUTLIER) cc_final: 0.7908 (mm) REVERT: A 1297 GLU cc_start: 0.8079 (pt0) cc_final: 0.7741 (mm-30) REVERT: A 1326 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8683 (mp) REVERT: A 1430 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7055 (mm) REVERT: A 1464 ILE cc_start: 0.8697 (pt) cc_final: 0.8394 (pt) REVERT: B 258 MET cc_start: 0.2343 (tmm) cc_final: 0.2027 (ptp) REVERT: B 260 MET cc_start: 0.0278 (mtm) cc_final: -0.0113 (tpt) REVERT: F 258 MET cc_start: 0.3470 (mmm) cc_final: 0.1450 (ttp) REVERT: F 284 THR cc_start: 0.5462 (OUTLIER) cc_final: 0.4439 (p) REVERT: F 295 MET cc_start: 0.3121 (tpp) cc_final: 0.1012 (mtp) REVERT: E 63 MET cc_start: 0.8565 (ttp) cc_final: 0.8314 (ttp) REVERT: E 75 MET cc_start: 0.8067 (mmm) cc_final: 0.7375 (mtp) REVERT: E 107 LYS cc_start: 0.8640 (ptmt) cc_final: 0.8129 (mmtp) REVERT: E 154 MET cc_start: 0.8971 (mmm) cc_final: 0.8736 (mmm) REVERT: E 207 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8049 (mm-30) REVERT: E 210 ASN cc_start: 0.8033 (t0) cc_final: 0.7696 (t0) REVERT: E 263 LYS cc_start: 0.8649 (tttt) cc_final: 0.8256 (tppt) REVERT: E 287 GLN cc_start: 0.7203 (mt0) cc_final: 0.6848 (mt0) REVERT: E 312 ARG cc_start: 0.8009 (ttm-80) cc_final: 0.7662 (mtm110) REVERT: E 344 MET cc_start: 0.5379 (OUTLIER) cc_final: 0.4226 (ttp) REVERT: E 410 GLN cc_start: 0.7570 (mm-40) cc_final: 0.7087 (tp-100) REVERT: E 513 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.8155 (ptpp) REVERT: E 523 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7927 (tmtt) REVERT: E 552 GLN cc_start: 0.7065 (pp30) cc_final: 0.6805 (pt0) REVERT: E 570 ASN cc_start: 0.8582 (t0) cc_final: 0.8257 (t0) REVERT: E 577 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.8227 (ttm-80) REVERT: E 639 LYS cc_start: 0.8317 (tppt) cc_final: 0.7933 (tttp) REVERT: E 643 ILE cc_start: 0.8094 (mm) cc_final: 0.7802 (mt) REVERT: E 662 ARG cc_start: 0.8370 (mtm-85) cc_final: 0.8060 (mtm180) REVERT: E 797 GLU cc_start: 0.8565 (tp30) cc_final: 0.8304 (tp30) REVERT: E 890 ASP cc_start: 0.7146 (p0) cc_final: 0.6740 (t0) REVERT: E 929 ILE cc_start: 0.7496 (pt) cc_final: 0.7183 (mt) REVERT: E 938 PHE cc_start: 0.8028 (p90) cc_final: 0.7720 (p90) REVERT: E 967 MET cc_start: 0.6195 (mpp) cc_final: 0.5470 (ptt) REVERT: E 974 GLU cc_start: 0.7517 (mt-10) cc_final: 0.6866 (pm20) REVERT: E 1031 ARG cc_start: 0.8021 (mtp-110) cc_final: 0.7315 (mtt180) REVERT: E 1034 GLU cc_start: 0.8410 (mt-10) cc_final: 0.7923 (mm-30) REVERT: E 1172 LYS cc_start: 0.8185 (tptp) cc_final: 0.7559 (ttpt) REVERT: E 1185 HIS cc_start: 0.8674 (m90) cc_final: 0.8206 (m90) REVERT: E 1291 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8320 (tp) REVERT: E 1295 ASN cc_start: 0.8071 (t0) cc_final: 0.6907 (m-40) REVERT: E 1417 MET cc_start: 0.3013 (ptm) cc_final: 0.2182 (ptm) REVERT: E 1472 GLU cc_start: 0.8610 (tm-30) cc_final: 0.8293 (tm-30) REVERT: E 1626 ASP cc_start: 0.7169 (t0) cc_final: 0.6863 (t0) outliers start: 74 outliers final: 49 residues processed: 409 average time/residue: 0.2049 time to fit residues: 133.7705 Evaluate side-chains 396 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 336 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 624 CYS Chi-restraints excluded: chain A residue 739 GLU Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 893 MET Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 970 ILE Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1326 ILE Chi-restraints excluded: chain A residue 1417 MET Chi-restraints excluded: chain A residue 1430 LEU Chi-restraints excluded: chain A residue 1551 THR Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain F residue 357 ILE Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 84 LYS Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 208 MET Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 344 MET Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 400 CYS Chi-restraints excluded: chain E residue 424 MET Chi-restraints excluded: chain E residue 497 THR Chi-restraints excluded: chain E residue 513 LYS Chi-restraints excluded: chain E residue 523 LYS Chi-restraints excluded: chain E residue 565 VAL Chi-restraints excluded: chain E residue 577 ARG Chi-restraints excluded: chain E residue 582 ILE Chi-restraints excluded: chain E residue 590 VAL Chi-restraints excluded: chain E residue 675 ILE Chi-restraints excluded: chain E residue 788 VAL Chi-restraints excluded: chain E residue 898 VAL Chi-restraints excluded: chain E residue 933 VAL Chi-restraints excluded: chain E residue 953 VAL Chi-restraints excluded: chain E residue 969 VAL Chi-restraints excluded: chain E residue 1206 VAL Chi-restraints excluded: chain E residue 1291 LEU Chi-restraints excluded: chain E residue 1319 VAL Chi-restraints excluded: chain E residue 1356 VAL Chi-restraints excluded: chain E residue 1461 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 13 optimal weight: 6.9990 chunk 257 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 chunk 215 optimal weight: 3.9990 chunk 311 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 303 optimal weight: 5.9990 chunk 308 optimal weight: 0.9980 chunk 201 optimal weight: 0.8980 chunk 172 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 753 ASN A 884 GLN A1433 HIS ** E 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 595 HIS E1433 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.175585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.126769 restraints weight = 36135.882| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.34 r_work: 0.3330 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 29022 Z= 0.156 Angle : 0.540 15.129 39866 Z= 0.277 Chirality : 0.040 0.156 4548 Planarity : 0.004 0.048 4640 Dihedral : 14.177 73.902 5381 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.62 % Allowed : 18.18 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.15), residues: 3118 helix: 1.09 (0.13), residues: 1516 sheet: -0.50 (0.26), residues: 382 loop : 0.02 (0.18), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E1520 TYR 0.019 0.001 TYR E1468 PHE 0.026 0.001 PHE A1542 TRP 0.034 0.002 TRP E 102 HIS 0.008 0.001 HIS E 595 Details of bonding type rmsd covalent geometry : bond 0.00371 (29022) covalent geometry : angle 0.53958 (39866) hydrogen bonds : bond 0.04005 ( 1361) hydrogen bonds : angle 4.17397 ( 3803) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 340 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 GLU cc_start: 0.6829 (pm20) cc_final: 0.6368 (tm-30) REVERT: A 190 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7558 (tt0) REVERT: A 204 ASP cc_start: 0.7096 (t0) cc_final: 0.6869 (m-30) REVERT: A 576 HIS cc_start: 0.8100 (t-90) cc_final: 0.6947 (m-70) REVERT: A 620 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.7904 (mmm) REVERT: A 639 LYS cc_start: 0.8076 (tppt) cc_final: 0.7750 (tppt) REVERT: A 702 ASP cc_start: 0.8748 (p0) cc_final: 0.8401 (p0) REVERT: A 746 LEU cc_start: 0.8303 (tp) cc_final: 0.8015 (tp) REVERT: A 789 ILE cc_start: 0.8735 (mp) cc_final: 0.8419 (mp) REVERT: A 797 GLU cc_start: 0.8565 (tp30) cc_final: 0.8046 (tm-30) REVERT: A 876 ASP cc_start: 0.7672 (t0) cc_final: 0.7457 (p0) REVERT: A 918 TYR cc_start: 0.8174 (t80) cc_final: 0.7747 (t80) REVERT: A 941 GLU cc_start: 0.7514 (tm-30) cc_final: 0.6650 (tp30) REVERT: A 970 ILE cc_start: 0.8237 (OUTLIER) cc_final: 0.8035 (mt) REVERT: A 1297 GLU cc_start: 0.8031 (pt0) cc_final: 0.7711 (mm-30) REVERT: A 1320 LYS cc_start: 0.8130 (tptm) cc_final: 0.7876 (tptm) REVERT: A 1326 ILE cc_start: 0.8987 (OUTLIER) cc_final: 0.8749 (mp) REVERT: A 1430 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7018 (mm) REVERT: A 1464 ILE cc_start: 0.8679 (pt) cc_final: 0.8389 (pt) REVERT: B 258 MET cc_start: 0.2747 (tmm) cc_final: 0.2367 (ptp) REVERT: B 260 MET cc_start: 0.0322 (mtm) cc_final: -0.0055 (tpt) REVERT: F 258 MET cc_start: 0.3414 (mmm) cc_final: 0.1463 (ttp) REVERT: F 284 THR cc_start: 0.5449 (OUTLIER) cc_final: 0.4447 (p) REVERT: F 295 MET cc_start: 0.3003 (tpp) cc_final: 0.0964 (mtp) REVERT: F 314 MET cc_start: 0.2917 (ppp) cc_final: 0.2317 (tpp) REVERT: E 75 MET cc_start: 0.8091 (mmm) cc_final: 0.7350 (mtp) REVERT: E 101 MET cc_start: 0.5710 (tmm) cc_final: 0.4919 (ptt) REVERT: E 107 LYS cc_start: 0.8677 (ptmt) cc_final: 0.8247 (mmtp) REVERT: E 140 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7612 (mt-10) REVERT: E 154 MET cc_start: 0.8975 (mmm) cc_final: 0.8744 (mmm) REVERT: E 207 GLU cc_start: 0.8641 (mt-10) cc_final: 0.7970 (mm-30) REVERT: E 210 ASN cc_start: 0.8010 (t0) cc_final: 0.7639 (t0) REVERT: E 212 MET cc_start: 0.7774 (mmm) cc_final: 0.7480 (mmm) REVERT: E 263 LYS cc_start: 0.8643 (tttt) cc_final: 0.8238 (tppt) REVERT: E 287 GLN cc_start: 0.7234 (mt0) cc_final: 0.6927 (mt0) REVERT: E 312 ARG cc_start: 0.7989 (ttm-80) cc_final: 0.7679 (mtm110) REVERT: E 344 MET cc_start: 0.5251 (OUTLIER) cc_final: 0.3962 (ttp) REVERT: E 384 LYS cc_start: 0.8476 (mtpt) cc_final: 0.8252 (ptpp) REVERT: E 410 GLN cc_start: 0.7576 (mm-40) cc_final: 0.7196 (tp-100) REVERT: E 466 GLU cc_start: 0.7998 (tt0) cc_final: 0.7471 (tt0) REVERT: E 513 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.8176 (ptpp) REVERT: E 523 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7996 (tmtt) REVERT: E 552 GLN cc_start: 0.7053 (pp30) cc_final: 0.6806 (pt0) REVERT: E 577 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.8228 (ttm-80) REVERT: E 639 LYS cc_start: 0.8302 (tppt) cc_final: 0.7954 (tttp) REVERT: E 643 ILE cc_start: 0.8150 (mm) cc_final: 0.7880 (mt) REVERT: E 662 ARG cc_start: 0.8337 (mtm-85) cc_final: 0.8012 (mtm180) REVERT: E 797 GLU cc_start: 0.8540 (tp30) cc_final: 0.8293 (tp30) REVERT: E 890 ASP cc_start: 0.7137 (p0) cc_final: 0.6732 (t0) REVERT: E 938 PHE cc_start: 0.8131 (p90) cc_final: 0.7877 (p90) REVERT: E 974 GLU cc_start: 0.7449 (mt-10) cc_final: 0.6832 (pm20) REVERT: E 1034 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8124 (mm-30) REVERT: E 1172 LYS cc_start: 0.8200 (tptp) cc_final: 0.7652 (ttpt) REVERT: E 1185 HIS cc_start: 0.8619 (m90) cc_final: 0.7987 (m90) REVERT: E 1291 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8334 (tp) REVERT: E 1295 ASN cc_start: 0.8044 (t0) cc_final: 0.6920 (m-40) REVERT: E 1417 MET cc_start: 0.2899 (ptm) cc_final: 0.2150 (ptm) REVERT: E 1472 GLU cc_start: 0.8651 (tm-30) cc_final: 0.8362 (tm-30) REVERT: E 1626 ASP cc_start: 0.7241 (t0) cc_final: 0.6933 (t0) outliers start: 74 outliers final: 55 residues processed: 387 average time/residue: 0.1953 time to fit residues: 121.0793 Evaluate side-chains 394 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 329 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 624 CYS Chi-restraints excluded: chain A residue 636 ASP Chi-restraints excluded: chain A residue 739 GLU Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 893 MET Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 970 ILE Chi-restraints excluded: chain A residue 1207 PHE Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1326 ILE Chi-restraints excluded: chain A residue 1417 MET Chi-restraints excluded: chain A residue 1430 LEU Chi-restraints excluded: chain A residue 1551 THR Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain F residue 357 ILE Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 84 LYS Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 208 MET Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 344 MET Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 400 CYS Chi-restraints excluded: chain E residue 424 MET Chi-restraints excluded: chain E residue 497 THR Chi-restraints excluded: chain E residue 513 LYS Chi-restraints excluded: chain E residue 523 LYS Chi-restraints excluded: chain E residue 565 VAL Chi-restraints excluded: chain E residue 577 ARG Chi-restraints excluded: chain E residue 582 ILE Chi-restraints excluded: chain E residue 590 VAL Chi-restraints excluded: chain E residue 675 ILE Chi-restraints excluded: chain E residue 788 VAL Chi-restraints excluded: chain E residue 898 VAL Chi-restraints excluded: chain E residue 933 VAL Chi-restraints excluded: chain E residue 953 VAL Chi-restraints excluded: chain E residue 969 VAL Chi-restraints excluded: chain E residue 1206 VAL Chi-restraints excluded: chain E residue 1239 THR Chi-restraints excluded: chain E residue 1291 LEU Chi-restraints excluded: chain E residue 1319 VAL Chi-restraints excluded: chain E residue 1356 VAL Chi-restraints excluded: chain E residue 1443 THR Chi-restraints excluded: chain E residue 1461 THR Chi-restraints excluded: chain E residue 1482 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 72 optimal weight: 5.9990 chunk 286 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 chunk 198 optimal weight: 0.4980 chunk 309 optimal weight: 4.9990 chunk 236 optimal weight: 0.8980 chunk 140 optimal weight: 4.9990 chunk 189 optimal weight: 0.2980 chunk 159 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 884 GLN A1385 HIS A1433 HIS E 143 HIS E 570 ASN ** E 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 623 ASN E1433 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.176919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.128673 restraints weight = 36062.498| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.31 r_work: 0.3356 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29022 Z= 0.117 Angle : 0.516 15.479 39866 Z= 0.265 Chirality : 0.039 0.153 4548 Planarity : 0.004 0.046 4640 Dihedral : 14.170 73.749 5381 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.23 % Allowed : 18.89 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.15), residues: 3118 helix: 1.19 (0.13), residues: 1514 sheet: -0.57 (0.26), residues: 392 loop : 0.01 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 873 TYR 0.018 0.001 TYR E1486 PHE 0.028 0.001 PHE A1542 TRP 0.033 0.002 TRP E 885 HIS 0.004 0.001 HIS E1433 Details of bonding type rmsd covalent geometry : bond 0.00273 (29022) covalent geometry : angle 0.51579 (39866) hydrogen bonds : bond 0.03746 ( 1361) hydrogen bonds : angle 4.11555 ( 3803) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 348 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 GLU cc_start: 0.6797 (pm20) cc_final: 0.6297 (tm-30) REVERT: A 384 LYS cc_start: 0.8536 (mtmm) cc_final: 0.8000 (ttpp) REVERT: A 552 GLN cc_start: 0.7594 (pp30) cc_final: 0.7386 (pp30) REVERT: A 576 HIS cc_start: 0.8162 (t-90) cc_final: 0.7075 (m90) REVERT: A 577 ARG cc_start: 0.8582 (ttp80) cc_final: 0.7986 (mtp180) REVERT: A 620 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.7815 (mmm) REVERT: A 639 LYS cc_start: 0.8079 (tppt) cc_final: 0.7775 (tppt) REVERT: A 702 ASP cc_start: 0.8728 (p0) cc_final: 0.8384 (p0) REVERT: A 746 LEU cc_start: 0.8266 (tp) cc_final: 0.7985 (tp) REVERT: A 789 ILE cc_start: 0.8717 (mp) cc_final: 0.8397 (mp) REVERT: A 797 GLU cc_start: 0.8546 (tp30) cc_final: 0.8045 (tm-30) REVERT: A 894 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8467 (tp) REVERT: A 918 TYR cc_start: 0.8192 (t80) cc_final: 0.7771 (t80) REVERT: A 938 PHE cc_start: 0.8397 (p90) cc_final: 0.7959 (p90) REVERT: A 941 GLU cc_start: 0.7524 (tm-30) cc_final: 0.6684 (tp30) REVERT: A 970 ILE cc_start: 0.8280 (OUTLIER) cc_final: 0.8046 (mt) REVERT: A 1297 GLU cc_start: 0.8070 (pt0) cc_final: 0.7731 (mm-30) REVERT: A 1326 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8746 (mp) REVERT: A 1430 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7097 (mm) REVERT: A 1464 ILE cc_start: 0.8682 (pt) cc_final: 0.8392 (pt) REVERT: B 258 MET cc_start: 0.2624 (tmm) cc_final: 0.2385 (ptp) REVERT: B 260 MET cc_start: 0.0244 (mtm) cc_final: -0.0080 (tpt) REVERT: F 258 MET cc_start: 0.3349 (mmm) cc_final: 0.1596 (ptm) REVERT: F 284 THR cc_start: 0.5542 (OUTLIER) cc_final: 0.4520 (p) REVERT: F 295 MET cc_start: 0.2995 (tpp) cc_final: 0.1013 (mtp) REVERT: E 75 MET cc_start: 0.8084 (mmm) cc_final: 0.7446 (mtt) REVERT: E 92 GLN cc_start: 0.6579 (mm-40) cc_final: 0.6149 (mt0) REVERT: E 101 MET cc_start: 0.5703 (tmm) cc_final: 0.4981 (ptt) REVERT: E 107 LYS cc_start: 0.8684 (ptmt) cc_final: 0.8250 (mmtp) REVERT: E 154 MET cc_start: 0.9040 (mmm) cc_final: 0.8812 (mmm) REVERT: E 207 GLU cc_start: 0.8656 (mt-10) cc_final: 0.7951 (mm-30) REVERT: E 210 ASN cc_start: 0.7973 (t0) cc_final: 0.7742 (t0) REVERT: E 212 MET cc_start: 0.7832 (mmm) cc_final: 0.7566 (mmm) REVERT: E 263 LYS cc_start: 0.8598 (tttt) cc_final: 0.8216 (tppt) REVERT: E 287 GLN cc_start: 0.7142 (mt0) cc_final: 0.6861 (mt0) REVERT: E 312 ARG cc_start: 0.7933 (ttm-80) cc_final: 0.7617 (mtm110) REVERT: E 344 MET cc_start: 0.5327 (OUTLIER) cc_final: 0.4116 (ttp) REVERT: E 410 GLN cc_start: 0.7615 (mm-40) cc_final: 0.7203 (tp-100) REVERT: E 466 GLU cc_start: 0.8095 (tt0) cc_final: 0.7698 (tt0) REVERT: E 523 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7986 (tmtt) REVERT: E 552 GLN cc_start: 0.7107 (pp30) cc_final: 0.6828 (pt0) REVERT: E 577 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.8213 (ttm-80) REVERT: E 639 LYS cc_start: 0.8321 (tppt) cc_final: 0.8006 (tttp) REVERT: E 643 ILE cc_start: 0.8142 (mm) cc_final: 0.7867 (mt) REVERT: E 662 ARG cc_start: 0.8370 (mtm-85) cc_final: 0.8132 (mtm180) REVERT: E 797 GLU cc_start: 0.8534 (tp30) cc_final: 0.8266 (tp30) REVERT: E 890 ASP cc_start: 0.7206 (p0) cc_final: 0.6745 (t0) REVERT: E 938 PHE cc_start: 0.8096 (p90) cc_final: 0.7893 (p90) REVERT: E 967 MET cc_start: 0.6401 (mpp) cc_final: 0.5486 (ptt) REVERT: E 974 GLU cc_start: 0.7492 (mt-10) cc_final: 0.6984 (pm20) REVERT: E 1034 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8112 (mm-30) REVERT: E 1172 LYS cc_start: 0.8201 (tptp) cc_final: 0.7573 (ttpt) REVERT: E 1185 HIS cc_start: 0.8580 (m90) cc_final: 0.8032 (m90) REVERT: E 1291 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8316 (tp) REVERT: E 1295 ASN cc_start: 0.8022 (t0) cc_final: 0.6930 (m-40) REVERT: E 1417 MET cc_start: 0.2908 (ptm) cc_final: 0.2134 (ptm) REVERT: E 1472 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8288 (tm-30) REVERT: E 1626 ASP cc_start: 0.7142 (t0) cc_final: 0.6808 (t0) REVERT: E 1640 LEU cc_start: 0.8302 (mp) cc_final: 0.8086 (mp) outliers start: 63 outliers final: 43 residues processed: 385 average time/residue: 0.2007 time to fit residues: 122.3654 Evaluate side-chains 385 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 332 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 624 CYS Chi-restraints excluded: chain A residue 636 ASP Chi-restraints excluded: chain A residue 739 GLU Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 893 MET Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 970 ILE Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1326 ILE Chi-restraints excluded: chain A residue 1430 LEU Chi-restraints excluded: chain A residue 1551 THR Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain F residue 357 ILE Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 344 MET Chi-restraints excluded: chain E residue 400 CYS Chi-restraints excluded: chain E residue 424 MET Chi-restraints excluded: chain E residue 497 THR Chi-restraints excluded: chain E residue 523 LYS Chi-restraints excluded: chain E residue 565 VAL Chi-restraints excluded: chain E residue 577 ARG Chi-restraints excluded: chain E residue 582 ILE Chi-restraints excluded: chain E residue 590 VAL Chi-restraints excluded: chain E residue 623 ASN Chi-restraints excluded: chain E residue 675 ILE Chi-restraints excluded: chain E residue 788 VAL Chi-restraints excluded: chain E residue 888 ASN Chi-restraints excluded: chain E residue 898 VAL Chi-restraints excluded: chain E residue 933 VAL Chi-restraints excluded: chain E residue 1206 VAL Chi-restraints excluded: chain E residue 1239 THR Chi-restraints excluded: chain E residue 1291 LEU Chi-restraints excluded: chain E residue 1356 VAL Chi-restraints excluded: chain E residue 1443 THR Chi-restraints excluded: chain E residue 1461 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 314 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 118 optimal weight: 4.9990 chunk 261 optimal weight: 8.9990 chunk 186 optimal weight: 4.9990 chunk 176 optimal weight: 4.9990 chunk 165 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 272 optimal weight: 3.9990 chunk 323 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 747 ASN A 884 GLN ** A1433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 623 ASN E 801 GLN E1433 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.173739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.124910 restraints weight = 36042.270| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.38 r_work: 0.3300 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 29022 Z= 0.201 Angle : 0.587 16.495 39866 Z= 0.299 Chirality : 0.041 0.147 4548 Planarity : 0.004 0.046 4640 Dihedral : 14.165 73.840 5381 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.16 % Allowed : 18.89 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.15), residues: 3118 helix: 1.03 (0.13), residues: 1512 sheet: -0.41 (0.26), residues: 370 loop : -0.12 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 873 TYR 0.024 0.002 TYR E1468 PHE 0.027 0.002 PHE A1542 TRP 0.042 0.002 TRP E 102 HIS 0.005 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00486 (29022) covalent geometry : angle 0.58659 (39866) hydrogen bonds : bond 0.04258 ( 1361) hydrogen bonds : angle 4.26096 ( 3803) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 329 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 GLU cc_start: 0.6849 (pm20) cc_final: 0.6362 (tm-30) REVERT: A 576 HIS cc_start: 0.8232 (t-90) cc_final: 0.7095 (m90) REVERT: A 577 ARG cc_start: 0.8597 (ttp80) cc_final: 0.8013 (mtp180) REVERT: A 614 HIS cc_start: 0.7674 (m170) cc_final: 0.7450 (m-70) REVERT: A 620 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.7976 (mmm) REVERT: A 639 LYS cc_start: 0.8100 (tppt) cc_final: 0.7758 (tppt) REVERT: A 702 ASP cc_start: 0.8784 (p0) cc_final: 0.8401 (p0) REVERT: A 746 LEU cc_start: 0.8344 (tp) cc_final: 0.8057 (tp) REVERT: A 789 ILE cc_start: 0.8725 (mp) cc_final: 0.8373 (mp) REVERT: A 797 GLU cc_start: 0.8615 (tp30) cc_final: 0.8163 (tm-30) REVERT: A 894 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8532 (tp) REVERT: A 918 TYR cc_start: 0.8161 (t80) cc_final: 0.7139 (t80) REVERT: A 922 MET cc_start: 0.7762 (mmm) cc_final: 0.7121 (mmm) REVERT: A 941 GLU cc_start: 0.7556 (tm-30) cc_final: 0.6698 (tp30) REVERT: A 1029 MET cc_start: 0.8505 (mpp) cc_final: 0.8134 (mpp) REVERT: A 1297 GLU cc_start: 0.8081 (pt0) cc_final: 0.7729 (mm-30) REVERT: A 1326 ILE cc_start: 0.9020 (OUTLIER) cc_final: 0.8805 (mp) REVERT: A 1430 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7060 (mm) REVERT: A 1464 ILE cc_start: 0.8681 (pt) cc_final: 0.8400 (pt) REVERT: B 258 MET cc_start: 0.2678 (tmm) cc_final: 0.2442 (ptp) REVERT: B 260 MET cc_start: 0.0279 (mtm) cc_final: -0.0057 (tpt) REVERT: F 258 MET cc_start: 0.3355 (mmm) cc_final: 0.1524 (ptm) REVERT: F 284 THR cc_start: 0.5852 (OUTLIER) cc_final: 0.4822 (p) REVERT: F 295 MET cc_start: 0.3071 (tpp) cc_final: 0.1055 (mtp) REVERT: E 75 MET cc_start: 0.8078 (mmm) cc_final: 0.7359 (mtp) REVERT: E 101 MET cc_start: 0.5822 (tmm) cc_final: 0.5167 (ptt) REVERT: E 107 LYS cc_start: 0.8684 (ptmt) cc_final: 0.8260 (mmtp) REVERT: E 154 MET cc_start: 0.9046 (mmm) cc_final: 0.8842 (mmm) REVERT: E 207 GLU cc_start: 0.8658 (mt-10) cc_final: 0.7996 (mm-30) REVERT: E 210 ASN cc_start: 0.7875 (t0) cc_final: 0.7651 (t0) REVERT: E 212 MET cc_start: 0.7899 (mmm) cc_final: 0.7638 (mmm) REVERT: E 263 LYS cc_start: 0.8607 (tttt) cc_final: 0.8208 (tppt) REVERT: E 287 GLN cc_start: 0.7318 (mt0) cc_final: 0.6933 (mt0) REVERT: E 312 ARG cc_start: 0.7983 (ttm-80) cc_final: 0.7617 (mtm110) REVERT: E 344 MET cc_start: 0.5146 (OUTLIER) cc_final: 0.3927 (ttp) REVERT: E 410 GLN cc_start: 0.7614 (mm-40) cc_final: 0.7270 (tp-100) REVERT: E 513 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8234 (ptpp) REVERT: E 523 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.8059 (tmtt) REVERT: E 552 GLN cc_start: 0.7141 (pp30) cc_final: 0.6853 (pt0) REVERT: E 577 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.8186 (ttm-80) REVERT: E 598 GLN cc_start: 0.7186 (mm-40) cc_final: 0.6900 (mp10) REVERT: E 639 LYS cc_start: 0.8319 (tppt) cc_final: 0.7986 (tttp) REVERT: E 643 ILE cc_start: 0.8184 (mm) cc_final: 0.7918 (mt) REVERT: E 662 ARG cc_start: 0.8379 (mtm-85) cc_final: 0.8127 (mtm180) REVERT: E 669 LYS cc_start: 0.8793 (mmmt) cc_final: 0.8317 (mmtt) REVERT: E 890 ASP cc_start: 0.7064 (p0) cc_final: 0.6551 (t0) REVERT: E 974 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7036 (pm20) REVERT: E 1034 GLU cc_start: 0.8529 (mt-10) cc_final: 0.8207 (mm-30) REVERT: E 1172 LYS cc_start: 0.8203 (tptp) cc_final: 0.7587 (ttpt) REVERT: E 1291 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8392 (tp) REVERT: E 1295 ASN cc_start: 0.8060 (t0) cc_final: 0.6960 (m-40) REVERT: E 1417 MET cc_start: 0.2932 (ptm) cc_final: 0.2300 (ptm) REVERT: E 1472 GLU cc_start: 0.8690 (tm-30) cc_final: 0.8346 (tm-30) REVERT: E 1626 ASP cc_start: 0.7365 (t0) cc_final: 0.7077 (t0) outliers start: 61 outliers final: 47 residues processed: 370 average time/residue: 0.1989 time to fit residues: 116.9816 Evaluate side-chains 374 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 317 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 624 CYS Chi-restraints excluded: chain A residue 636 ASP Chi-restraints excluded: chain A residue 739 GLU Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 893 MET Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1207 PHE Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1326 ILE Chi-restraints excluded: chain A residue 1430 LEU Chi-restraints excluded: chain A residue 1551 THR Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain F residue 357 ILE Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 84 LYS Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 344 MET Chi-restraints excluded: chain E residue 400 CYS Chi-restraints excluded: chain E residue 424 MET Chi-restraints excluded: chain E residue 497 THR Chi-restraints excluded: chain E residue 513 LYS Chi-restraints excluded: chain E residue 523 LYS Chi-restraints excluded: chain E residue 565 VAL Chi-restraints excluded: chain E residue 577 ARG Chi-restraints excluded: chain E residue 582 ILE Chi-restraints excluded: chain E residue 590 VAL Chi-restraints excluded: chain E residue 675 ILE Chi-restraints excluded: chain E residue 788 VAL Chi-restraints excluded: chain E residue 898 VAL Chi-restraints excluded: chain E residue 933 VAL Chi-restraints excluded: chain E residue 1206 VAL Chi-restraints excluded: chain E residue 1239 THR Chi-restraints excluded: chain E residue 1291 LEU Chi-restraints excluded: chain E residue 1319 VAL Chi-restraints excluded: chain E residue 1356 VAL Chi-restraints excluded: chain E residue 1443 THR Chi-restraints excluded: chain E residue 1461 THR Chi-restraints excluded: chain E residue 1482 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 235 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 307 optimal weight: 0.1980 chunk 68 optimal weight: 2.9990 chunk 319 optimal weight: 20.0000 chunk 32 optimal weight: 0.9990 chunk 201 optimal weight: 0.9990 chunk 171 optimal weight: 0.0570 chunk 137 optimal weight: 0.8980 chunk 149 optimal weight: 8.9990 chunk 150 optimal weight: 6.9990 overall best weight: 0.6302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 753 ASN A 884 GLN A 955 ASN A1433 HIS ** E 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1433 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.177362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.130242 restraints weight = 35911.732| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.17 r_work: 0.3383 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 29022 Z= 0.106 Angle : 0.524 16.570 39866 Z= 0.270 Chirality : 0.038 0.158 4548 Planarity : 0.004 0.045 4640 Dihedral : 14.187 73.696 5381 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.77 % Allowed : 19.49 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.15), residues: 3118 helix: 1.18 (0.13), residues: 1516 sheet: -0.58 (0.27), residues: 370 loop : -0.05 (0.18), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 873 TYR 0.020 0.001 TYR E 740 PHE 0.029 0.001 PHE A1542 TRP 0.033 0.002 TRP E 102 HIS 0.008 0.001 HIS E1433 Details of bonding type rmsd covalent geometry : bond 0.00235 (29022) covalent geometry : angle 0.52378 (39866) hydrogen bonds : bond 0.03647 ( 1361) hydrogen bonds : angle 4.14124 ( 3803) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8958.84 seconds wall clock time: 154 minutes 0.23 seconds (9240.23 seconds total)